Harvesting graphics power for MD simulations
van Meel, J.A.; Arnold, A.; Frenkel, D.; Portegies Zwart, S.F.; Belleman, R.G.
2008-01-01
We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a
Harvesting graphics power for MD simulations
Meel, J.A. van; Arnold, A.; Frenkel, D.; Portegies Zwart, S.F.; Belleman, R.G.
We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a
International Nuclear Information System (INIS)
Iglesias, Y.J.
2002-01-01
Classical Molecular dynamics (MD) and hybrid Quantum/Molecular Mechanics-Molecular Dynamics (QM/MM-MD) simulations have been performed to investigate structural properties of Mn(II), V(II), Cr(III) and Ti(III) cations in aqueous solution. The first hydration sphere in QM/MM-MD simulations is treated quantum mechanically, while the rest of the system is described by classical analytical two- and three-body potentials. The results obtained for the first hydration shell from this method are in agreement with experimental data, showing 100 % of 6 fold coordination around the ion in all cases. The results prove that non/additive contributions are mandatory for an accurate description of ion hydration. Within the QM/MM method, the inclusion of a perturbation field describing the remaining system was shown to be an accurate tool for evaluating the first shell structure, and thus to be a good alternative for systems, where the construction of a three-body correction function is difficult or too time-consuming. (author)
MD simulation of cluster formation during sputtering
International Nuclear Information System (INIS)
Muramoto, T.; Okai, M.; Yamashita, Y.; Yorizane, K.; Yamamura, Y.
2001-01-01
The cluster ejection due to cluster impact on a solid surface is studied through molecular dynamics (MD) simulations. Simulations are performed for Cu cluster impacts on the Cu(1 1 1) surface for cluster energy 100 eV/atom, and for clusters of 6, 13, 28 and 55 atoms. Interatomic interactions are described by the AMLJ-EAM potential. The vibration energy spectrum is independent of the incident cluster size and energy. This comes from the fact that sputtered clusters become stable through the successive fragmentation of nascent large sputtered clusters. The vibration energy spectra for large sputtered clusters have a peak, whose energy corresponds to the melting temperature of Cu. The exponent of the power-law fit of the abundance distribution and the total sputtering yield for the cluster impacts are higher than that for the monatomic ion impacts with the same total energy, where the exponent δ is given by Y n ∝n δ and Y n is the yield of sputtered n-atom cluster. The exponent δ follows a unified function of the total sputtering yield, which is a monotonic increase function, and it is nearly equal to δ ∼ -3 for larger yield
StandsSIM-MD: a Management Driven forest SIMulator
Energy Technology Data Exchange (ETDEWEB)
Barreiro, S.; Rua, J.; Tomé, M.
2016-07-01
Aim of the study. The existing stand level forest simulators available in Portugal were not developed with the aim of including up-to-date model versions and were limited in terms of accounting for forest management. The simulators’ platform, sIMfLOR was recently created to implement different growth models with a common philosophy. The objective was developing one easily-updatable, user-friendly, forest management and climate change sensitive simulator capable of projecting growth for the main tree species in Portugal. Area of the study: Portugal. Material and methods: The new simulator was programmed in a modular form consisting of several modules. The growth module integrates different forest growth and yield models (empirical and process-based) for the main wood production tree species in Portugal (eucalypt, umbrella and maritime pines); whereas the management module drives the growth projections along the planning horizon according to a range of forest management approaches and climate (at present only available for eucalypt). Main results: The main result is the StandsSIM-MD Management Driven simulator that overcomes the limitations of the existing stand level simulators. It is a step forward when compared to the models currently available in the sIMfLOR platform covering more tree species, stand structures and stand compositions. It is focused on end-users and it is based on similar concepts regarding the generation of required inputs and generated outputs. Research highlights: Forest Management Driven simulations approach. Multiple Prescriptions-Per-Stand functionality. StandsSIM-MD can be used to support landowners decisions on stand forest management. StandsSIM-MD simulations at regional level can be combined with optimization routines. (Author)
StandsSIM-MD: a Management Driven forest SIMulator
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Susana Barreiro
2016-07-01
Full Text Available Aim of the study: The existing stand level forest simulators available in Portugal were not developed with the aim of including up-to-date model versions and were limited in terms of accounting for forest management. The simulators’ platform, sIMfLOR was recently created to implement different growth models with a common philosophy. The objective was developing one easily-updatable, user-friendly, forest management and climate change sensitive simulator capable of projecting growth for the main tree species in Portugal. Area of the study: Portugal. Material and methods: The new simulator was programmed in a modular form consisting of several modules. The growth module integrates different forest growth and yield models (empirical and process-based for the main wood production tree species in Portugal (eucalypt, umbrella and maritime pines; whereas the management module drives the growth projections along the planning horizon according to a range of forest management approaches and climate (at present only available for eucalypt. Main results: The main result is the StandsSIM-MD Management Driven simulator that overcomes the limitations of the existing stand level simulators. It is a step forward when compared to the models currently available in the sIMfLOR platform covering more tree species, stand structures and stand compositions. It is focused on end-users and it is based on similar concepts regarding the generation of required inputs and generated outputs. Research highlights: - Forest Management Driven simulations approach - Multiple Prescriptions-Per-Stand functionality - StandsSIM-MD can be used to support landowners decisions on stand forest management - StandsSIM-MD simulations at regional level can be combined with optimization routines Keywords: Forest simulator, Forest Management Approaches; StandsSIM-MD; forest management.
2015-01-01
The reliability of free energy simulations (FES) is limited by two factors: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect
A molecular dynamics (MD simulation on tire-aggregate friction
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Fengyan Sun
2017-07-01
Full Text Available The friction between tire and road surface is fundamentally depending on the molecular forces. In this paper, the nanoscale 3D contact model is employed to investigate the tire-aggregate friction mechanism. The tire and aggregate micro-structure are both constructed to evaluate the microscopic performance of tire-aggregate friction influence. Simulation results show for a high velocity, the energy dissipation of sliding on crystal structure is small, which results in a small friction coefficient; temperature will have influences on the friction coefficient, and with the increasing of velocity, the effect will gradually reduce. Keywords: Tire, Aggregate, Friction coefficient, Microscopic mechanism, MD simulation
MD and BCA simulations of He and H bombardment of fuzz in bcc elements
Klaver, T. P. C.; Zhang, S.; Nordlund, K.
2017-08-01
We present results of MD simulations of low energy He ion bombardment of low density fuzz in bcc elements. He ions can penetrate several micrometers into sparse fuzz, which allows for a sufficient He flux through it to grow the fuzz further. He kinetic energy falls off exponentially with penetration depth. A BCA code was used to carry out the same ion bombardment on the same fuzz structures as in MD simulations, but with simpler, 10 million times faster calculations. Despite the poor theoretical basis of the BCA at low ion energies, and the use of somewhat different potentials in MD and BCA calculations, the ion penetration depths predicted by BCA are only ∼12% less than those predicted by MD. The MD-BCA differences are highly systematic and trends in the results of the two methods are very similar. We have carried out more than 200 BCA calculation runs of ion bombardment of fuzz, in which parameters in the ion bombardment process were varied. For most parameters, the results show that the ion bombardment process is quite generic. The ion species (He or H), ion mass, fuzz element (W, Ta, Mo, Fe) and fuzz element lattice parameter turned out to have a modest influence on ion penetration depths at most. An off-normal angle of incidence strongly reduces the ion penetration depth. Increasing the ion energy increases the ion penetration, but the rate by which ion energy drops off at high ion energies follows the same exponential pattern as at lower energies.
Novel 3D/VR interactive environment for MD simulations, visualization and analysis.
Doblack, Benjamin N; Allis, Tim; Dávila, Lilian P
2014-12-18
The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.
Analysis of MD5 authentication in various routing protocols using simulation tools
Dinakaran, M.; Darshan, K. N.; Patel, Harsh
2017-11-01
Authentication being an important paradigm of security and Computer Networks require secure paths to make the flow of the data even more secure through some security protocols. So MD-5(Message Digest 5) helps in providing data integrity to the data being sent through it and authentication to the network devices. This paper gives a brief introduction to the MD-5, simulation of the networks by including MD-5 authentication using various routing protocols like OSPF, EIGRP and RIPv2. GNS3 is being used to simulate the scenarios. Analysis of the MD-5 authentication is done in the later sections of the paper.
International Nuclear Information System (INIS)
Prinzio, M. Di; Aquaro, D.
2006-01-01
The erosion of the divertor and of the first wall determined on the base of the anticipated operating conditions, is a critical issue that could affect the performance and the operating schedule of the nuclear fusion reactor ITER. This paper deals with the analysis of beryllium thermal properties by means of MD simulations, in order to better predict thermal behaviour of beryllium armoured PFCs in fusion devices. The importance of this analysis is clearly connected to thermal response evaluation of PFCs to high heat flux exposure, during off-normal events and Edge Localized Modes. The ensuing strong over-heating, in fact, produces material ablation through vaporization of surface material layers and possible loss of melting material. The overall PFCs erosion has bearings on plasma contamination, due to eroded material transport, and components lifetime, due to armour thickness reduction. An important feature of beryllium is its high vapour pressure. During thermal transients the strong vaporization keeps surface temperature relatively low but eroded thickness results high as well. Small changes in beryllium vapour pressure produce not negligible differences in thermal analyses results. On the basis of available force fields, classical Molecular Dynamics simulations have been carried out in order to better understand surface vaporization in tokamak conditions and to evaluate the effect of beryllium oxides formation. This effect has been successfully modelled by MD simulation, carried out with Moldy code. Morse stretching and bending potential for Be-O bond simulation have been used, and partial charges method, accounting for molecular polarity, has been employed. Since during short thermal transients, such as ELMs, only a few microns of Be armour will be overheated and reach melting threshold, the effective thermal conductivity is very important in determining the temperature evolution of surface layers and the ensuing erosion. Thermal conductivity can be evaluated
Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.
Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes
2012-07-15
The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems. Copyright © 2012 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
Sandra Posch
2016-09-01
Full Text Available We here give information for a deeper understanding of single molecule force spectroscopy (SMFS data through the example of the blood protein von Willebrand factor (VWF. It is also shown, how fitting of rupture forces versus loading rate profiles in the molecular dynamics (MD loading-rate range can be used to demonstrate the qualitative agreement between SMFS and MD simulations. The recently developed model by Bullerjahn, Sturm, and Kroy (BSK was used for this demonstration. Further, Brownian dynamics (BD simulations, which can be utilized to estimate the lifetimes of intramolecular VWF interactions under physiological shear, are described. For interpretation and discussion of the methods and data presented here, we would like to directly point the reader to the related research paper, “Mutual A domain interactions in the force sensing protein von Willebrand Factor” (Posch et al., 2016 [1]. Keywords: Atomic force microscopy, Single molecule force spectroscopy, Molecular dynamics simulation, Brownian dynamics simulation, von Willebrand factor
PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs
International Nuclear Information System (INIS)
Kylasa, S.B.; Aktulga, H.M.; Grama, A.Y.
2014-01-01
We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors
PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs
Energy Technology Data Exchange (ETDEWEB)
Kylasa, S.B., E-mail: skylasa@purdue.edu [Department of Elec. and Comp. Eng., Purdue University, West Lafayette, IN 47907 (United States); Aktulga, H.M., E-mail: hmaktulga@lbl.gov [Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, MS 50F-1650, Berkeley, CA 94720 (United States); Grama, A.Y., E-mail: ayg@cs.purdue.edu [Department of Computer Science, Purdue University, West Lafayette, IN 47907 (United States)
2014-09-01
We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors.
Application of MD Simulations to Predict Membrane Properties of MOFs
Directory of Open Access Journals (Sweden)
Elda Adatoz
2015-01-01
Full Text Available Metal organic frameworks (MOFs are a new group of nanomaterials that have been widely examined for various chemical applications. Gas separation using MOF membranes has become an increasingly important research field in the last years. Several experimental studies have shown that thin-film MOF membranes can outperform well known polymer and zeolite membranes due to their higher gas permeances and selectivities. Given the very large number of available MOF materials, it is impractical to fabricate and test the performance of every single MOF membrane using purely experimental techniques. In this study, we used molecular simulations, Monte Carlo and Molecular Dynamics, to estimate both single-gas and mixture permeances of MOF membranes. Predictions of molecular simulations were compared with the experimental gas permeance data of MOF membranes in order to validate the accuracy of our computational approach. Results show that computational methodology that we described in this work can be used to accurately estimate membrane properties of MOFs prior to extensive experimental efforts.
Water at silica/liquid water interfaces investigated by DFT-MD simulations
Gaigeot, Marie-Pierre
This talk is dedicated to probing the microscopic structural organization of water at silica/liquid water interfaces including electrolytes by first principles DFT-based molecular dynamics simulations (DFT-MD). We will present our very recent DFT-MD simulations of electrolytic (KCl, NaCl, NaI) silica/liquid water interfaces in order to unravel the intertwined structural properties of water and electrolytes at the crystalline quartz/liquid water and amorphous silica/liquid water interfaces. DFT-MD simulations provide direct knowledge of the structural organization of water and the H-Bond network formed between the water molecules within the different water layers above the silica surface. One can furthermore extract vibrational signatures of the water molecules within the interfacial layers from the DFT-MD simulations, especially non-linear SFG (Sum Frequency generation) signatures that are active at solid/liquid interfaces. The strength of the simulated spectra is that a detailed analysis of the signatures in terms of the water/water H-Bond networks formed within the interfacial water layers and in terms of the water/silica or water/electrolytes H-Bond networks can be given. Comparisons of SFG spectra between quartz/water/electrolytes and amorphous silica/water/electrolytes interfaces allow us to definitely conclude on how the structural arrangements of liquid water at these electrolytic interfaces modulate the final spectroscopic signatures. Invited speaker.
Directory of Open Access Journals (Sweden)
Hui Yao
2017-01-01
Full Text Available This Molecular Dynamics (MD simulation paper presents a physical property comparison study between exfoliated graphite nanoplatelets (xGNP modified and control asphalt models, including density, glass transition temperature, viscosity and thermal conductivity. The three-component control asphalt model consists of asphaltenes, aromatics, and saturates based on previous references. The xGNP asphalt model was built by incorporating an xGNP and control asphalt model and controlling mass ratios to represent the laboratory prepared samples. The Amber Cornell Extension Force Field (ACEFF was used with assigned molecular electro-static potential (ESP charge from NWChem analysis. After optimization and ensemble relaxation, the properties of the control and xGNP modified asphalt models were computed and analyzed using the MD method. The MD simulated results have a similar trend as the test results. The property analysis showed that: (1 the density of the xGNP modified model is higher than that of the control model; (2 the glass transition temperature of the xGNP modified model is closer to the laboratory data of the Strategic Highway Research Program (SHRP asphalt binders than that of the control model; (3 the viscosities of the xGNP modified model at different temperatures are higher than those of the control model, and it coincides with the trend in the laboratory data; (4 the thermal conductivities of the xGNP modified asphalt model are higher than those of the control asphalt model at different temperatures, and it is consistent with the trend in the laboratory data.
Park, In-Hee; Venable, John D.; Steckler, Caitlin; Cellitti, Susan E.; Lesley, Scott A.; Spraggon, Glen; Brock, Ansgar
2015-01-01
Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure and dynamics. More recently, Hydrogen Exchange Mass Spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation of the wealth of data generated by HX-MS experiments as well as other HX methods would greatly benefit from the availability of exchange predictions derived from structures or models for comparison with experiment. Most reported computational HX modeling studies have employed solvent-accessible-surface-area based metrics in attempts to interpret HX data on the basis of structures or models. In this study, a computational HX-MS prediction method based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated. Analysis of the NH bonding configurations from Molecular Dynamics (MD) simulation snapshots is used to determine partitioning over bonded and non-bonded NH states and is directly mapped into a protection factor (PF) using a logistics growth function. Predicted PFs are then used for calculating deuteration values of peptides and compared with experimental data. Hydrogen exchange MS data for Fatty acid synthase thioesterase (FAS-TE) collected for a range of pHs and temperatures was used for detailed evaluation of the approach. High correlation between prediction and experiment for observable fragment peptides is observed in the FAS-TE and additional benchmarking systems that included various apo/holo proteins for which literature data were available. In addition, it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD. Successful rate class decompositions provide further evidence that the presented approach captures the underlying physical processes correctly at the single residue level. This assessment is further strengthened in a comparison of
International Nuclear Information System (INIS)
Ding Yinfeng; Zhang Zhibin; Ke Xuezhi; Zhu Zhiyuan; Zhu Dezhang; Wang Zhenxia; Xu Hongjie
2005-01-01
The single carbon atom transporting through the single-walled carbon nanotube has been studied by molecular-dynamics (MD) simulation. We got different trajectories of the carbon atom by changing the input parameters. The simulation results indicate that the single carbon atom with low energy can transport through the carbon nanotube under some input conditions and result in different trajectories being straight line or 'rosette' or circular. (authors)
Böddeker, B.; Teichler, H.
The MD simulation program TABB is motivated by the need of long time simulations for the investigation of slow processes near the glass transition of glass forming alloys. TABB is written in C++ with a high degree of flexibility: TABB allows the use of any short ranged pair potentials or EAM potentials, by generating and using a spline representation of all functions and their derivatives. TABB supports several numerical integration algorithms like the Runge-Kotta or the modified Gear-predictor-corrector algorithm of order five. The boundary conditions can be chosen to resemble the geometry of bulk materials or films. The simulation box length or the pressure can be fixed for each dimension separately. TABB may be used in isokinetic, isoenergeric or canonic (with random forces) mode. TABB contains a simple instruction interpreter to easily control the parameters and options during the simulation. The same source code can be compiled either for workstations or for parallel computers. The main optimization goal of TABB is to allow long time simulations of medium or small sized systems. To make this possible, much attention is spent on the optimized communication between the nodes. TABB uses a domain decomposition procedure. To use many nodes with a small system, the domain size has to be small compared to the range of particle interactions. In the limit of many nodes for only few atoms, the bottle neck of communication is the latency time. TABB minimizes the number of pairs of domains containing atoms that interact between these domains. This procedure minimizes the need of communication calls between pairs of nodes. TABB decides automatically, to how many, and to which directions the decomposition shall be applied. E.g., in the case of one dimensional domain decomposition, the simulation box is only split into "slabs" along a selected direction. The three dimensional domain decomposition is best with respect to the number of interacting domains only for simulations
PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.
Scheurer, Maximilian; Rodenkirch, Peter; Siggel, Marc; Bernardi, Rafael C; Schulten, Klaus; Tajkhorshid, Emad; Rudack, Till
2018-02-06
Molecular dynamics (MD) simulations have become ubiquitous in all areas of life sciences. The size and model complexity of MD simulations are rapidly growing along with increasing computing power and improved algorithms. This growth has led to the production of a large amount of simulation data that need to be filtered for relevant information to address specific biomedical and biochemical questions. One of the most relevant molecular properties that can be investigated by all-atom MD simulations is the time-dependent evolution of the complex noncovalent interaction networks governing such fundamental aspects as molecular recognition, binding strength, and mechanical and structural stability. Extracting, evaluating, and visualizing noncovalent interactions is a key task in the daily work of structural biologists. We have developed PyContact, an easy-to-use, highly flexible, and intuitive graphical user interface-based application, designed to provide a toolkit to investigate biomolecular interactions in MD trajectories. PyContact is designed to facilitate this task by enabling identification of relevant noncovalent interactions in a comprehensible manner. The implementation of PyContact as a standalone application enables rapid analysis and data visualization without any additional programming requirements, and also preserves full in-program customization and extension capabilities for advanced users. The statistical analysis representation is interactively combined with full mapping of the results on the molecular system through the synergistic connection between PyContact and VMD. We showcase the capabilities and scientific significance of PyContact by analyzing and visualizing in great detail the noncovalent interactions underlying the ion permeation pathway of the human P2X 3 receptor. As a second application, we examine the protein-protein interaction network of the mechanically ultrastable cohesin-dockering complex. Copyright © 2017 Biophysical Society
pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins.
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Priyanka Prakash
2015-10-01
Full Text Available Probe-based or mixed solvent molecular dynamics simulation is a useful approach for the identification and characterization of druggable sites in drug targets. However, thus far the method has been applied only to soluble proteins. A major reason for this is the potential effect of the probe molecules on membrane structure. We have developed a technique to overcome this limitation that entails modification of force field parameters to reduce a few pairwise non-bonded interactions between selected atoms of the probe molecules and bilayer lipids. We used the resulting technique, termed pMD-membrane, to identify allosteric ligand binding sites on the G12D and G13D oncogenic mutants of the K-Ras protein bound to a negatively charged lipid bilayer. In addition, we show that differences in probe occupancy can be used to quantify changes in the accessibility of druggable sites due to conformational changes induced by membrane binding or mutation.
Microsecond MD Simulations of Nano-patterned Polymer Brushes on Self-Assembled Monolayers
Buie, Creighton; Qiu, Liming; Cheng, Kwan; Park, Soyeun
2010-03-01
Nano-patterned polymer brushes end-grafted onto self-assembled monolayers have gained increasing research interests due to their unique thermodynamic properties and their chemical and biomedical applications in colloids, biosensing and tissue engineering. So far, the interactions between the polymer brushes with the surrounding environments such as the floor and solvent at the nanometer length scale and microsecond time scale are still difficult to obtained experimentally and computationally. Using a Coarse-Grained MD approach, polymer brushes of different monomeric lengths, grafting density and hydrophobicity of the monomers grafted on self-assembled monolayers and in explicit solvent were studied. Molecular level information, such as lateral diffusion, transverse height and volume contour of the brushes, were calculated from our microsecond-MD simulations. Our results demonstrated the significance of the hydration of the polymer in controlling the conformational arrangement of the polymer brushes.
Moon, Gi Jong; Yang, Yu Dong; Oh, Jung Min; Kang, In Seok
2017-11-01
Osmotic pressure plays an important role in the processes of charging and discharging of lithium batteries. In this work, osmotic pressure of the ionic liquids confined inside a nanoslit is calculated by using both MD simulation and continuum approach. In the case of MD simulation, an ionic liquid is modeled as singly charged spheres with a short-ranged repulsive Lennard-Jones potential. The radii of the spheres are 0.5nm, reflecting the symmetry of ion sizes for simplicity. The simulation box size is 11nm×11nm×7.5nm with 1050 ion pairs. The concentration of ionic liquid is about 1.922mol/L, and the total charge on an individual wall varies from +/-60e(7.944 μm/cm2) to +/-600e(79.44 μm/cm2) . In the case of continuum approach, we classify the problems according to the correlation length and steric factor, and considered the four separate cases: 1) zero correlation length and zero steric factor, 2) zero correlation length and non-zero steric factor, 3) non-zero correlation length and zero steric factor, and 4) non-zero correlation and non-zero steric factor. Better understanding of the osmotic pressure of ionic liquids confined inside a nanoslit can be achieved by comparing the results of MD simulation and continuum approach. This research was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (MSIP: Ministry of Science, ICT & Future Planning) (No. 2017R1D1A1B05035211).
Dhindsa, Gurpreet K.
Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, beta-Casein and Inorganic Pyrophosphatase (IPPase). RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and functionalizable high surface area, and thus actively considered for biomedical applications. In this thesis, we utilized two tools, quasielastic neutron scattering (QENS) and Molecular Dynamics Simulations to probe the effect of ND on RNA dynamics. Our work provides fundamental understanding of how hydrated RNA motions are affected in the RNA-ND nanocomposites. From the experimental and Molecular Dynamics Simulation (MD), we found that hydrated RNA motion is faster on ND surface than a freestanding one. MD Simulation results showed that the failure of Stokes Einstein relation results the presence of dynamic heterogeneities in the biomacromolecules. Radial pair distribution function from MD Simulation confirmed that the hydrophilic nature of ND attracts more water than RNA results the de-confinement of RNA on ND. Therefore, RNA exhibits faster motion in the presence of ND than freestanding RNA. In the second project, we studied the dynamics of a natively disordered protein beta-Casein which lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of beta-Casein are explored by Quasielastic Neutron Scattering (QENS). We investigated the mean square displacement (MSD) of
Directory of Open Access Journals (Sweden)
Yue Hou
2017-02-01
Full Text Available Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM experiments, Phase Dynamics Theory and Molecular Dynamics (MD Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.
Hou, Yue; Wang, Linbing; Wang, Dawei; Guo, Meng; Liu, Pengfei; Yu, Jianxin
2017-02-21
Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.
Directory of Open Access Journals (Sweden)
Asir Intisar Khan
2015-12-01
Full Text Available The thermal conductivity of graphene nanoribbons (GNRs has been investigated using equilibrium molecular dynamics (EMD simulation based on Green-Kubo (GK method to compare two interatomic potentials namely optimized Tersoff and 2nd generation Reactive Empirical Bond Order (REBO. Our comparative study includes the estimation of thermal conductivity as a function of temperature, length and width of GNR for both the potentials. The thermal conductivity of graphene nanoribbon decreases with the increase of temperature. Quantum correction has been introduced for thermal conductivity as a function of temperature to include quantum effect below Debye temperature. Our results show that for temperatures up to Debye temperature, thermal conductivity increases, attains its peak and then falls off monotonically. Thermal conductivity is found to decrease with the increasing length for optimized Tersoff potential. However, thermal conductivity has been reported to increase with length using 2nd generation REBO potential for the GNRs of same size. Thermal conductivity, for the specified range of width, demonstrates an increasing trend with the increase of width for both the concerned potentials. In comparison with 2nd generation REBO potential, optimized Tersoff potential demonstrates a better modeling of thermal conductivity as well as provides a more appropriate description of phonon thermal transport in graphene nanoribbon. Such comparative study would provide a good insight for the optimization of the thermal conductivity of graphene nanoribbons under diverse conditions.
Kuroki, Nahoko; Mori, Hirotoshi
2018-02-01
Effective fragment potential version 2 - molecular dynamics (EFP2-MD) simulations, where the EFP2 is a polarizable force field based on ab initio electronic structure calculations were applied to water-methanol binary mixture. Comparing EFP2s defined with (aug-)cc-pVXZ (X = D,T) basis sets, it was found that large sets are necessary to generate sufficiently accurate EFP2 for predicting mixture properties. It was shown that EFP2-MD could predict the excess molar volume. Since the computational cost of EFP2-MD are far less than ab initio MD, the results presented herein demonstrate that EFP2-MD is promising for predicting physicochemical properties of novel mixed solvents.
Shamim, Amen; Abbasi, Sumra Wajid; Azam, Syed Sikander
2015-07-01
β-Ketoacyl-ACP-synthase III (FabH or KAS III) has become an attractive target for the development of new antibacterial agents which can overcome the multidrug resistance. Unraveling the fatty acid biosynthesis (FAB) metabolic pathway and understanding structural coordinates of FabH will provide valuable insights to target Streptococcus gordonii for curing oral infection. In this study, we designed inhibitors against therapeutic target FabH, in order to block the FAB pathway. As compared to other targets, FabH has more interactions with other proteins, located on the leading strand with higher codon adaptation index value and associated with lipid metabolism category of COG. Current study aims to gain in silico insights into the structural and dynamical aspect of S. gordonii FabH via molecular docking and molecular dynamics (MD) simulations. The FabH protein is catalytically active in dimerization while it can lock in monomeric state. Current study highlights two residues Pro88 and Leu315 that are close to each other by dimerization. The active site of FabH is composed of the catalytic triad formed by residues Cys112, His249, and Asn279 in which Cys112 is involved in acetyl transfer, while His249 and Asn279 play an active role in decarboxylation. Docking analysis revealed that among the studied compounds, methyl-CoA disulfide has highest GOLD score (82.75), binding affinity (-11 kcal/mol) and exhibited consistently better interactions. During MD simulations, the FabH structure remained stable with the average RMSD value of 1.7 Å and 1.6 Å for undocked protein and docked complex, respectively. Further, crucial hydrogen bonding of the conserved catalytic triad for exhibiting high affinity between the FabH protein and ligand is observed by RDF analysis. The MD simulation results clearly demonstrated that binding of the inhibitor with S. gordonii FabH enhanced the structure and stabilized the dimeric FabH protein. Therefore, the inhibitor has the potential to become
Interaction and dynamics of homologous pairing protein 2 (HOP2) and DNA studied by MD simulation
Moktan, Hem; Pezza, Roberto; Zhou, Donghua
2015-03-01
The homologous pairing protein 2 (Hop2) plays an important role in meiosis and DNA repair. Together with protein Mnd1, Hop2 enhances the strand invasion activity of recombinase Dmc1 by over 30 times, facilitating proper synapsis of homologous chromosomes. We recently determined the NMR structure of the N-terminal domain of Hop2 and proposed a model of Protein-DNA complex based on NMR chemical shift perturbations and mutagenesis studies (Moktan, J Biol Chem 2014 10.1074/jbc.M114.548180). However structure and dynamics of the complex have not been studied at the atomic level yet. Here, we used classical MD simulations to study the interactions between the N-terminal HOP2 and DNA. The simulated results indicate that helix3 (H3) interacts with DNA in major groove and wing1 (W1) interacts mostly in minor groove mainly via direct hydrogen bonds. Also it is found that binding leads to reduced fluctuations in both protein and DNA. Several water bridge interactions have been identified. The residue-wise contributions to the interaction energy were evaluated. Also the functional motion of the protein is analyzed using principal component analysis. The results confirmed the importance of H3 and W1 for the stability of the complex, which is consistent with our previous experimental studies.
Montazeri, A.; Mobarghei, A.
2018-04-01
In this article, we report a series of MD-based nanoindentation tests aimed to examine the nanotribological characteristics of metal-based nanocomposites in the presence of graphene sheets. To evaluate the effects of graphene/matrix interactions on the results, nickel and copper are selected as metals having strong and weak interactions with graphene, respectively. Consequently, the influence of graphene layers sliding and their distance from the sample surface on the nanoindentation outputs is thoroughly examined. Additionally, the temperature dependence of the results is deeply investigated with emphasis on the underlying mechanisms. To verify the accuracy of nanoindentation outputs, results of this method are compared with the data obtained via the tensile test. It is concluded that the nanoindentation results are closer to the values obtained by means of experimental setups. Employing these numerical-based experiments enables us to perform parametric studies to find out the dominant factors affecting the nanotribological behavior of these nanocomposites at the atomic-scale.
Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.
2016-09-01
Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an
Alamethicin in lipid bilayers: combined use of X-ray scattering and MD simulations.
Pan, Jianjun; Tieleman, D Peter; Nagle, John F; Kucerka, Norbert; Tristram-Nagle, Stephanie
2009-06-01
We study fully hydrated bilayers of two di-monounsaturated phospholipids diC18:1PC (DOPC) and diC22:1PC with varying amounts of alamethicin (Alm). We combine the use of X-ray diffuse scattering and molecular dynamics simulations to determine the orientation of alamethicin in model lipids. Comparison of the experimental and simulated form factors shows that Alm helices are inserted transmembrane at high humidity and high concentrations, in agreement with earlier results. The X-ray scattering data and the MD simulations agree that membrane thickness changes very little up to 1/10 Alm/DOPC. In contrast, the X-ray data indicate that the thicker diC22:1PC membrane thins with added Alm, a total decrease in thickness of 4 A at 1/10 Alm/diC22:1PC. The different effect of Alm on the thickness changes of the two bilayers is consistent with Alm having a hydrophobic thickness close to the hydrophobic thickness of 27 A for DOPC; Alm is then mismatched with the 7 A thicker diC22:1PC bilayer. The X-ray data indicate that Alm decreases the bending modulus (K(C)) by a factor of approximately 2 in DOPC and a factor of approximately 10 in diC22:1PC membranes (P/L approximately 1/10). The van der Waals and fluctuational interactions between bilayers are also evaluated through determination of the anisotropic B compressibility modulus.
Hagita, Katsumi; Morita, Hiroshi; Takano, Hiroshi
We performed coarse grained molecular dynamics (MD) simulations based on Kremer-Grest model in order to investigate a fracture of polymer nanocomposites filled with spherical nanoparticles (NPs) under uniaxial elongation with a Poisson ratio of 0.4. In our model, the NP consists of 320 surface beads and one center bead. In order to make the NP spherical, a harmonic potential is applied to the surface particles from the center of the NP. Here, the initial volume fraction of the NPs is about 20%. The dependences of the fracture on the interactions between the NPs and polymers were examined. In order to observe the creation of nanovoids, the interaction among the polymers was set to be attractive. When the NP-polymer interaction is attractive, nanovoids appear in the bulk of polymers. On the other hand, for repulsive NP-polymer interaction, nanovoids are created at the surface between the polymers and NPs. At the same time, segregation of NPs is observed. We found that these behaviors depend on crosslink densities.
MD simulations of onset of tungsten fuzz formation under helium irradiation
International Nuclear Information System (INIS)
Lasa, A.; Henriksson, K.O.E.; Nordlund, K.
2013-01-01
When helium (He) escapes a fusion reactor plasma, a tungsten (W)-based divertor may, under some conditions, form a fuzz-like nano-morphology. This is a highly undesired phenomenon for the divertor, and is not well understood. We performed molecular dynamics simulations of high fluence He and also C-seeded He (He+C) irradiation on W, focusing on the effect of the high fluence, the temperature and the impurities on the onset of the structure formation. We concluded that MD reproduces the experimentally found square root of time dependence of the surface growth. The He atomic density decreases when increasing the number of He atoms in the cell. A higher temperature causes a larger bubble growth and desorption activity, specially for the pure He irradiation cases. It also it leads to W recrystallization for the He+C irradiation cases. Carbon acts as a local He trap for small clusters or single atoms and causes a larger loss of crystallinity of the W surface
International Nuclear Information System (INIS)
Pan, Wenxiao; Zhang, Dongju; Zhan, Jinhua
2011-01-01
Highlights: → We study the inclusion mechanism of TCDD with β-CD by theoretical methods. → Clearly, the formation of inclusion complex is an energetically driven process. → The inclusion complex can be detected by IR and Raman techniques. → The results imply that β-CD may be used as a host molecule to enrich TCDD molecules. - Abstract: The rapid enrichment and detection of trace polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) are currently challenging issues in the field of environmental science. In this paper, by performing quantum chemistry (QM) calculations and molecular dynamics (MD) simulations, we studied the inclusion complexation of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a representative PCDD molecule, with β-cyclodextrin (β-CD), one of the widely used compounds in supramolecular chemistry. The calculated results reveal that the stable inclusion complex can be formed in both the gas phase and solvent, which proposes that β-CD may serve as a potential substrate enriching TCDD. The calculated vibrational spectra indicate that the infrared (IR) and Raman spectroscopy may be suitable for the detection of β-CD-modified TCDD. The present theoretical results may be informative to environmental scientists who are devoting themselves to developing effective methods for detection and treatment of POPs.
ProtoMD: A prototyping toolkit for multiscale molecular dynamics
Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.
2016-05-01
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md.
A novel energy conversion based method for velocity correction in molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Jin, Hanhui [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Collaborative Innovation Center of Advanced Aero-Engine, Hangzhou 310027 (China); Liu, Ningning [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Ku, Xiaoke, E-mail: xiaokeku@zju.edu.cn [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Fan, Jianren [State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027 (China)
2017-05-01
Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.
A novel energy conversion based method for velocity correction in molecular dynamics simulations
International Nuclear Information System (INIS)
Jin, Hanhui; Liu, Ningning; Ku, Xiaoke; Fan, Jianren
2017-01-01
Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.
MD simulation of atomic displacement cascades near chromium-rich clusters in FeCr alloy
International Nuclear Information System (INIS)
Tikhonchev, M.; Svetukhin, V.; Gaganidze, E.
2013-01-01
The paper reports simulation of cascades in Fe–9 at.%Cr binary alloy containing chromium-rich clusters. The simulation is performed by the molecular dynamics method at the initial temperature of 300 K and primary knock-on atom energy of 15 and 20 keV. Spherical clusters containing 95 at.% of Cr with diameter of 1–5 nm have been considered. The properties of cascade evolution in the presence of chromium-rich cluster are studied. It is shown that these clusters tend to dissolve in collision cascades. However, clusters with diameter of ⩾3 nm exhibit only slight modifications and can be considered stable. Parameters of small (1–2 nm) clusters can change significantly and, in some cases, a 1 nm cluster can be totally dissolved
MD simulation of atomic displacement cascades near chromium-rich clusters in FeCr alloy
Energy Technology Data Exchange (ETDEWEB)
Tikhonchev, M., E-mail: tikhonchev@sv.ulsu.ru [Ulyanovsk State University, Research Institute of Technology, 42 Leo Tolstoy St., 432970 Ulyanovsk (Russian Federation); Svetukhin, V. [Ulyanovsk State University, Research Institute of Technology, 42 Leo Tolstoy St., 432970 Ulyanovsk (Russian Federation); Gaganidze, E. [Karlsruhe Institute of Technology, Institute for Applied Materials, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Karlsruhe (Germany)
2013-11-15
The paper reports simulation of cascades in Fe–9 at.%Cr binary alloy containing chromium-rich clusters. The simulation is performed by the molecular dynamics method at the initial temperature of 300 K and primary knock-on atom energy of 15 and 20 keV. Spherical clusters containing 95 at.% of Cr with diameter of 1–5 nm have been considered. The properties of cascade evolution in the presence of chromium-rich cluster are studied. It is shown that these clusters tend to dissolve in collision cascades. However, clusters with diameter of ⩾3 nm exhibit only slight modifications and can be considered stable. Parameters of small (1–2 nm) clusters can change significantly and, in some cases, a 1 nm cluster can be totally dissolved.
Indian Academy of Sciences (India)
Home; Journals; Pramana – Journal of Physics. Md Naimuddin. Articles written in Pramana – Journal of Physics. Volume 79 Issue 5 November 2012 pp 1255-1258 Poster Presentations. Model unspecific search for new physics in collision at s = 7 TeV · Shivali Malhotra Md Naimuddin Thomas Hebbeker Arnd Meyer ...
Accelerating all-atom MD simulations of lipids using a modified virtual-sites technique
DEFF Research Database (Denmark)
Loubet, Bastien; Kopec, Wojciech; Khandelia, Himanshu
2014-01-01
We present two new implementations of the virtual sites technique which completely suppresses the degrees of freedom of the hydrogen atoms in a lipid bilayer allowing for an increased time step of 5 fs in all-atom simulations of the CHARMM36 force field. One of our approaches uses the derivation...... of the virtual sites used in GROMACS while the other uses a new definition of the virtual sites of the CH2 groups. Our methods is tested on a DPPC (no unsaturated chain), a POPC (one unsaturated chain), and a DOPC (two unsaturated chains) lipid bilayers. We calculate various physical properties of the membrane...... of our simulations with and without virtual sites and explain the differences and similarity observed. The best agreements are obtained for the GROMACS original virtual sites on the DOPC bilayer where we get an area per lipid of 67.3 ± 0.3 A˚2 without virtual sites and 67.6 ± 0.3 A˚2 with virtual sites...
Dolenc, Jozica; Baron, Riccardo; Missimer, John H; Steinmetz, Michel O; van Gunsteren, Wilfred F
2008-07-21
The solvent structure and dynamics around ccbeta-p, a 17-residue peptide that forms a parallel three-stranded alpha-helical coiled coil in solution, was analysed through 10 ns explicit solvent molecular dynamics (MD) simulations at 278 and 330 K. Comparison with two corresponding simulations of the monomeric form of ccbeta-p was used to investigate the changes of hydration upon coiled-coil formation. Pronounced peaks in the solvent density distribution between residues Arg8 and Glu13 of neighbouring helices show the presence of water bridges between the helices of the ccbeta-p trimer; this is in agreement with the water sites observed in X-ray crystallography experiments. Interestingly, this water site is structurally conserved in many three-stranded coiled coils and, together with the Arg and Glu residues, forms part of a motif that determines three-stranded coiled-coil formation. Our findings show that little direct correlation exists between the solvent density distribution and the temporal ordering of water around the trimeric coiled coil. The MD-calculated effective residence times of up to 40 ps show rapid exchange of surface water molecules with the bulk phase, and indicate that the solvent distribution around biomolecules requires interpretation in terms of continuous density distributions rather than in terms of discrete molecules of water. Together, our study contributes to understanding the principles of three-stranded coiled-coil formation.
Simulation of multi-atomic interactions in H-O-W system with the MD code CADAC
International Nuclear Information System (INIS)
Landman, I.S.
2005-01-01
For future tokamak reactors, chemical erosion of tungsten armour surfaces under impact of hot deuterium-tritium plasma that contains impurities, for instance oxygen, is an important issue. Oxygen can form volatile molecular complexes O x W y at the surface, and the retained H-atoms form the volatile complexes H x O y , which mitigates the erosion (H states for hydrogen isotopes). The plasma impact can substantially destroy the complexes. To describe this H-O-W system, the molecular dynamics (MD) code CADAC was earlier developed using only pair-atomic interactions. Now CADAC is extended for multi-body forces to simulate molecular organization of atoms near the tungsten surface. The approach uses the Abell's model of empirical bond-order potentials in addition combined, for the first time, with a valence concept. CADAC simulates chemical features using atomic valences and the Morse potentials. The new model is introduced and model parameters are estimated
mdFoam+: Advanced molecular dynamics in OpenFOAM
Longshaw, S. M.; Borg, M. K.; Ramisetti, S. B.; Zhang, J.; Lockerby, D. A.; Emerson, D. R.; Reese, J. M.
2018-03-01
This paper introduces mdFoam+, which is an MPI parallelised molecular dynamics (MD) solver implemented entirely within the OpenFOAM software framework. It is open-source and released under the same GNU General Public License (GPL) as OpenFOAM. The source code is released as a publicly open software repository that includes detailed documentation and tutorial cases. Since mdFoam+ is designed entirely within the OpenFOAM C++ object-oriented framework, it inherits a number of key features. The code is designed for extensibility and flexibility, so it is aimed first and foremost as an MD research tool, in which new models and test cases can be developed and tested rapidly. Implementing mdFoam+ in OpenFOAM also enables easier development of hybrid methods that couple MD with continuum-based solvers. Setting up MD cases follows the standard OpenFOAM format, as mdFoam+ also relies upon the OpenFOAM dictionary-based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of an MD simulation is not typical of most OpenFOAM applications. Results show that mdFoam+ compares well to another well-known MD code (e.g. LAMMPS) in terms of benchmark problems, although it also has additional functionality that does not exist in other open-source MD codes.
International Nuclear Information System (INIS)
Miyashiro, S.; Fujita, S.; Okita, T.; Okuda, H.
2012-01-01
Highlights: ► Strain effects on defect formation were evaluated at various PKA energies by MD. ► Radiation-induced defects were increased numerically by external strain. ► Enhanced formation of larger clusters causes the numerical increase of defects. ► Strain influence on the number of defects was greatest at about 20 keV PKA. ► Cluster size, which is mostly affected by strain, was greater with higher PKA energy. - Abstract: Molecular Dynamics (MD) simulations were conducted to investigate the influence of applied tensile strain on defect production during cascade damages at various Primary Knock-on Atom (PKA) energies of 1–30 keV. When 1% strain was applied, the number of surviving defects increased at PKA energies higher than 5 keV, although they did not increase at 1 keV. The rate of increase by strain application was higher with higher PKA energy, and attained the maximum at 20 keV PKA energy with a subsequent gradual decrease at 30 keV PKA energy The cluster size, mostly affected by strain, was larger with higher PKA energy, although clusters with fewer than seven interstitials did not increase in number at any PKA energy.
GEM simulation methods development
International Nuclear Information System (INIS)
Tikhonov, V.; Veenhof, R.
2002-01-01
A review of methods used in the simulation of processes in gas electron multipliers (GEMs) and in the accurate calculation of detector characteristics is presented. Such detector characteristics as effective gas gain, transparency, charge collection and losses have been calculated and optimized for a number of GEM geometries and compared with experiment. A method and a new special program for calculations of detector macro-characteristics such as signal response in a real detector readout structure, and spatial and time resolution of detectors have been developed and used for detector optimization. A detailed development of signal induction on readout electrodes and electronics characteristics are included in the new program. A method for the simulation of charging-up effects in GEM detectors is described. All methods show good agreement with experiment
Ahamad, Shahzaib; Hassan, Md Imtaiyaz; Dwivedi, Neeraja
2018-05-01
Tuberculosis (Tb) is an airborne infectious disease caused by Mycobacterium tuberculosis. Beta-carbonic anhydrase 1 ( β-CA1 ) has emerged as one of the potential targets for new antitubercular drug development. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking, and molecular dynamics (MD) simulation approaches were performed on a series of natural and synthetic phenol-based β-CA1 inhibitors. The developed 3D-QSAR model ( r 2 = 0.94, q 2 = 0.86, and pred_r 2 = 0.74) indicated that the steric and electrostatic factors are important parameters to modulate the bioactivity of phenolic compounds. Based on this indication, we designed 72 new phenolic inhibitors, out of which two compounds (D25 and D50) effectively stabilized β-CA1 receptor and, thus, are potential candidates for new generation antitubercular drug discovery program.
Solid state NMR investigations and MD simulations of triblock copolymers in lipid bilayers
Czech Academy of Sciences Publication Activity Database
Baerenwald, R.; Ferreira, T. M.; Ollila, Samuli; Saalwaechter, K.
2017-01-01
Roč. 46, Suppl 1 (2017), S117 ISSN 0175-7571. [IUPAB congress /19./ and EBSA congress /11./. 16.07.2017-20.07.2017, Edinburgh] Institutional support: RVO:61388963 Keywords : solid state NMR * molecular dynamic simulations Subject RIV: BO - Biophysics
DEFF Research Database (Denmark)
Boscia, Alexander L.; Treece, Bradley W.; Mohammadyani, Dariush
2014-01-01
TMCL. Coarse grain molecular dynamics simulations confirm the experimental thickening of 2 Å for 20 mol% TMCL and locate the TMCL headgroups near the glycerol-carbonyl region of DMPC; i.e., they are sequestered below the DMPC phosphocholine headgroup. Our results suggest that TMCL plays a role similar...... to cholesterol in that it thickens and stiffens DMPC membranes, orders chains, and is positioned under the umbrella of the PC headgroup. CL may be necessary for hydrophobic matching to inner mitochondrial membrane proteins. Differential scanning calorimetry, S Xray and CGMD simulations all suggest that TMCL does......Cardiolipins (CLs) are important biologically for their unique role in biomembranes that couple phosphorylation and electron transport like bacterial plasma membranes, chromatophores, chloroplasts and mitochondria. CLs are often tightly coupled to proteins involved in oxidative phosphorylation...
Low-energy oxygen bombardment of silicon by MD simulations making use of a reactive force field
International Nuclear Information System (INIS)
Philipp, P.; Briquet, L.; Wirtz, T.; Kieffer, J.
2011-01-01
In the field of Secondary Ion Mass Spectrometry (SIMS), ion-matter interactions have been largely investigated by numerical simulations. For MD simulations related to inorganic samples, mostly classical force fields assuming stable bonding structure have been used. In materials science, level-three force fields capable of simulating the breaking and formation of chemical bonds have recently been conceived. One such force field has been developed by John Kieffer . This potential includes directional covalent bonds, Coulomb and dipolar interaction terms, dispersion terms, etc. Important features of this force field for simulating systems that undergo significant structural reorganization are (i) the ability to account for the redistribution of electron density upon ionization, formation, or breaking of bonds, through a charge transfer term, and (ii) the fact that the angular constraints dynamically adjust when a change in the coordination number of an atom occurs. In this paper, the modification of the force field to allow for an exact description of the sputtering process, the influence of this modification on previous results obtained for phase transitions in glasses as well as properties of particles sputtered at 250-1000 eV from a mono-crystalline silicon sample will be presented. The simulation results agree qualitatively with predictions from experiments or models. Most atoms are sputtered from the first monolayer: for an impact energy of 250 eV up to 86% of the atoms are sputtered from the first monolayer and for 750 eV, this percentage drops to 61%, with 89% of the atoms being sputtered from the first two monolayers. For sputtering yields, 250 and 500 eV results agree with experimental data, but for 750 eV sub-channelling in the pristine sample becomes more important than in experiments where samples turn amorphous under ion bombardment.
Evaluation of GEOS-5 sulfur dioxide simulations during the Frostburg, MD 2010 field campaign
Directory of Open Access Journals (Sweden)
V. Buchard
2014-02-01
Full Text Available Sulfur dioxide (SO2 is a major atmospheric pollutant with a strong anthropogenic component mostly produced by the combustion of fossil fuel and other industrial activities. As a precursor of sulfate aerosols that affect climate, air quality, and human health, this gas needs to be monitored on a global scale. Global climate and chemistry models including aerosol processes along with their radiative effects are important tools for climate and air quality research. Validation of these models against in-situ and satellite measurements is essential to ascertain the credibility of these models and to guide model improvements. In this study, the Goddard Chemistry, Aerosol, Radiation, and Transport (GOCART module running on-line inside the Goddard Earth Observing System version 5 (GEOS-5 model is used to simulate aerosol and SO2 concentrations. Data taken in November 2010 over Frostburg, Maryland during an SO2 field campaign involving ground instrumentation and aircraft are used to evaluate GEOS-5 simulated SO2 concentrations. Preliminary data analysis indicated the model overestimated surface SO2 concentration, which motivated the examination of the specification of SO2 anthropogenic emission rates. As a result of this analysis, a revision of anthropogenic emission inventories in GEOS-5 was implemented, and the vertical placement of SO2 sources was updated. Results show that these revisions improve the model agreement with observations locally and in regions outside the area of this field campaign. In particular, we use the ground-based measurements collected by the United States Environmental Protection Agency (US EPA for the year 2010 to evaluate the revised model simulations over North America.
Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant.
Directory of Open Access Journals (Sweden)
Md Zahid Kamal
Full Text Available Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.
Electroreduction Property and MD Simulation of Nitrobenzene in Ionic Liquid [BMim][Tf2N]/[BMim][BF4
International Nuclear Information System (INIS)
Zeng, Jianping; Zhang, Yinxu; Sun, Ruyao; Chen, Song
2014-01-01
Highlights: • The two different common accessible ionic liquids are mixed in a simple and economic way. • In some compound ratios, the dynamic performance of nitrobenzene is superior to either of ionic liquids. • Modification and functionalization of ionic liquids in electrochemical field is feasible. • The mass transfer of diffusion of nitrobenzene in ionic liquids can be simulated with molecular dynamics. • Molecular dynamics explains the improvement of nitrobenzene in composite ionic liquids. - Abstract: The two different common accessible ionic liquids [BMim][BF 4 ] and [BMim][Tf 2 N] were mixed each other in a simple and economic way. In some compound ratios, the dynamic performance of nitrobenzene in electric reduction was superior to that of any single kind of ionic liquid has been appeared. The interaction and mass transfer of diffusion of nitrobenzene in composite ionic liquids with different volume ratios were studied with molecular dynamics (MD) simulation. The improvement of the electroreduction performance of nitrobenzene in composite ionic liquids was verified and was tried to explain. This provides a new idea for the modification and functionalization of ionic liquids in electrochemical field. The experimental results showed that kinematic viscosity and electroconductibility of different ionic liquid systems display a regular change. And the change law has been basically unchanged after adding water. The two different functional ionic liquids were complemented each other in a simple and economic way, which has compensated for the disadvantage of mono-component ionic liquids. At 25 °C, electroreduction property of V [BMim][BF4] :V [BMim][Tf2N] = 1:1 is the best in cyclic voltammetry experiments of nitrobenzene in different composite ionic liquids. Its electrochemical behavior is significantly affected by scan rate, temperature, concentration of nitrobenzene and concentration of water. The MD simulation results showed most of interaction
Simulation of multi-atomic interactions in H-O-W system with the MD code CADAC
Energy Technology Data Exchange (ETDEWEB)
Landman, I.S. [Forschungszentrum Karlsruhe, Institute for Pulsed Power and Microwave Technology, P.O. Box 3640, 76021 Karlsruhe (Germany)]. E-mail: igor.landman@ihm.fzk.de
2005-11-15
For future tokamak reactors, chemical erosion of tungsten armour surfaces under impact of hot deuterium-tritium plasma that contains impurities, for instance oxygen, is an important issue. Oxygen can form volatile molecular complexes O {sub x}W {sub y} at the surface, and the retained H-atoms form the volatile complexes H {sub x}O {sub y}, which mitigates the erosion (H states for hydrogen isotopes). The plasma impact can substantially destroy the complexes. To describe this H-O-W system, the molecular dynamics (MD) code CADAC was earlier developed using only pair-atomic interactions. Now CADAC is extended for multi-body forces to simulate molecular organization of atoms near the tungsten surface. The approach uses the Abell's model of empirical bond-order potentials in addition combined, for the first time, with a valence concept. CADAC simulates chemical features using atomic valences and the Morse potentials. The new model is introduced and model parameters are estimated.
Energy Technology Data Exchange (ETDEWEB)
Kamiyama, H. (Aomori Public College, 153-4 Yamazaki, Goushi-zawa, Aomori 030-01 (Japan)); Rafii-Tabar, H. (Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980 (Japan)); Kawazoe, Y. (Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980 (Japan)); Matsui, H. (Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980 (Japan))
1994-09-01
According to our model on the mechanism of dislocation bias reduction based on the interaction of dumbbell self-interstitial atoms (SIAs) with dislocation, the bias is significantly different depending on the dumbbell configuration in the dislocation strain field. A large-scale molecular dynamics (MD) simulation is performed to reveal the stability and the mechanism of diffusion of dumbbell SIAs near the edge dislocation core in bcc iron. Most SIAs take the crowdion configuration parallel to the Burgers vector in the expansion side of the dislocation. Such crowdions are stable in the temperature range of this simulation, i.e. between 373 and 473 K, making one-dimensional random to-and-fro motion parallel to the dislocation Burgers vector staying at several atomic layers below'' the dislocation core. This means that the SIA does not approach the dislocation core. These results suggest that the stable configuration of SIAs is seriously affected by the dislocation resulting in a reduction of bias factor. ((orig.))
International Nuclear Information System (INIS)
Kamiyama, H.; Rafii-Tabar, H.; Kawazoe, Y.; Matsui, H.
1994-01-01
According to our model on the mechanism of dislocation bias reduction based on the interaction of dumbbell self-interstitial atoms (SIAs) with dislocation, the bias is significantly different depending on the dumbbell configuration in the dislocation strain field. A large-scale molecular dynamics (MD) simulation is performed to reveal the stability and the mechanism of diffusion of dumbbell SIAs near the edge dislocation core in bcc iron. Most SIAs take the crowdion configuration parallel to the Burgers vector in the expansion side of the dislocation. Such crowdions are stable in the temperature range of this simulation, i.e. between 373 and 473 K, making one-dimensional random to-and-fro motion parallel to the dislocation Burgers vector staying at several atomic layers ''below'' the dislocation core. This means that the SIA does not approach the dislocation core. These results suggest that the stable configuration of SIAs is seriously affected by the dislocation resulting in a reduction of bias factor. ((orig.))
MD simulation of plastic deformation nucleation in stressed crystallites under irradiation
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Korchuganov, A. V., E-mail: avkor@ispms.tsc.ru; Zolnikov, K. P., E-mail: kost@ispms.tsc.ru; Kryzhevich, D. S., E-mail: kryzhev@ispms.tsc.ru [Russian Academy of Sciences, Institute of Strength Physics and Materials Science, Siberian Branch (Russian Federation); Chernov, V. M., E-mail: VMChernov@bochvar.ru [National Research Tomsk State University (Russian Federation); Psakhie, S. G., E-mail: sp@ispms.tsc.ru [Russian Academy of Sciences, Institute of Strength Physics and Materials Science, Siberian Branch (Russian Federation)
2016-12-15
The investigation of plastic deformation nucleation in metals and alloys under irradiation and mechanical loading is one of the topical issues of materials science. Specific features of nucleation and evolution of the defect system in stressed and irradiated iron, vanadium, and copper crystallites were studied by molecular dynamics simulation. Mechanical loading was performed in such a way that the modeled crystallite volume remained unchanged. The energy of the primary knock-on atom initiating a cascade of atomic displacements in a stressed crystallite was varied from 0.05 to 50 keV. It was found that atomic displacement cascades might cause global structural transformations in a region far larger than the radiation-damaged area. These changes are similar to the ones occurring in the process of mechanical loading of samples. They are implemented by twinning (in iron and vanadium) or through the formation of partial dislocation loops (in copper).
DEFF Research Database (Denmark)
Vestergaard, Mikkel; Kraft, Johan Frederik; Vosegaard, Thomas
2015-01-01
present molecular dynamics simulations to elucidate structural and dynamic properties of small bicelles and compare them to a large alignable bicelle, a small nanodisc, and a lipid bilayer. Properties such as lipid packing and properties related to embedding both an α-helical peptide and a transmembrane...... protein are investigated. The small bicelles are found to be very dynamic and mainly assume a prolate shape substantiating that small bicelles cannot be regarded as well-defined disclike structures. However, addition of a peptide results in an increased tendency to form disc-shaped bicelles. The small......The increased interest in studying membrane proteins has led to the development of new membrane mimics such as bicelles and nanodiscs. However, only limited knowledge is available of how these membrane mimics are affected by embedded proteins and how well they mimic a lipid bilayer. Herein, we...
MD simulation of atomic displacement cascades in Fe-10 at.%Cr binary alloy
International Nuclear Information System (INIS)
Tikhonchev, M.; Svetukhin, V.; Kadochkin, A.; Gaganidze, E.
2009-01-01
Molecular dynamics simulation of atomic displacement cascades up to 20 keV has been performed in Fe-10 at.%Cr binary alloy at a temperature of 600 K. The N-body interatomic potentials of Finnis-Sinclair type were used. According to the obtained results the dependence of 'surviving' defects amount is well approximated by power function that coincides with other researchers' results. Obtained cascade efficiency for damage energy in the range from 10 to 20 keV is ∼0.2 NRT that is slightly higher than for pure α-Fe. In post-cascade area Cr fraction in interstitials is in range 2-5% that is essentially lower than Cr content in the base alloy. The results on size and amount of vacancy and interstitial clusters generated in displacement cascades are obtained. For energies of 2 keV and higher the defect cluster average size increases and it is well approximated by a linear dependence on cascade energy both for interstitials and vacancies.
MD simulation of atomic displacement cascades in Fe-10 at.%Cr binary alloy
Energy Technology Data Exchange (ETDEWEB)
Tikhonchev, M., E-mail: tikhonchev@sv.ulsu.r [Ulyanovsk State University, Leo Tolstoy Str., 42, Ulyanovsk 432970 (Russian Federation); Joint Stock Company, ' State Scientific Center Research Institute of Atomic Reactors' , 433510 Dimitrovgrad-10 (Russian Federation); Svetukhin, V.; Kadochkin, A. [Ulyanovsk State University, Leo Tolstoy Str., 42, Ulyanovsk 432970 (Russian Federation); Gaganidze, E. [Forschungszentrum Karlsruhe, IMF II, 3640, D-76021 Karlsruhe (Germany)
2009-12-15
Molecular dynamics simulation of atomic displacement cascades up to 20 keV has been performed in Fe-10 at.%Cr binary alloy at a temperature of 600 K. The N-body interatomic potentials of Finnis-Sinclair type were used. According to the obtained results the dependence of 'surviving' defects amount is well approximated by power function that coincides with other researchers' results. Obtained cascade efficiency for damage energy in the range from 10 to 20 keV is approx0.2 NRT that is slightly higher than for pure alpha-Fe. In post-cascade area Cr fraction in interstitials is in range 2-5% that is essentially lower than Cr content in the base alloy. The results on size and amount of vacancy and interstitial clusters generated in displacement cascades are obtained. For energies of 2 keV and higher the defect cluster average size increases and it is well approximated by a linear dependence on cascade energy both for interstitials and vacancies.
Idrees, Danish; Prakash, Amresh; Haque, Md Anzarul; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz
2016-09-01
Carbonic anhydrase VA (CAVA) is primarily expressed in the mitochondria and involved in numerous physiological processes including lipogenesis, insulin secretion from pancreatic cells, ureagenesis, gluconeogenesis and neuronal transmission. To understand the biophysical properties of CAVA, we carried out a reversible urea-induced isothermal denaturation at pH 7.0 and 25°C. Spectroscopic probes, [θ]222 (mean residue ellipticity at 222 nm), F344 (Trp-fluorescence emission intensity at 344 nm) and Δε280 (difference absorption at 280 nm) were used to monitor the effect of urea on the structure and stability of CAVA. The urea-induced reversible denaturation curves were used to estimate [Formula: see text], Gibbs free energy in the absence of urea; Cm, the mid-point of the denaturation curve, i.e. molar urea concentration ([urea]) at which ΔGD = 0; and m, the slope (=∂ΔGD/∂[urea]). Coincidence of normalized transition curves of all optical properties suggests that unfolding/refolding of CAVA is a two-state process. We further performed 40 ns molecular dynamics simulation of CAVA to see the dynamics at different urea concentrations. An excellent agreement was observed between in silico and in vitro studies.
Roy, Sourav; Basu, Sankar; Dasgupta, Dipak; Bhattacharyya, Dhananjay; Banerjee, Rahul
2015-01-01
Currently, considerable interest exists with regard to the dissociation of close packed aminoacids within proteins, in the course of unfolding, which could result in either wet or dry moltenglobules. The progressive disjuncture of residues constituting the hydrophobic core ofcyclophilin from L. donovani (LdCyp) has been studied during the thermal unfolding of the molecule, by molecular dynamics simulations. LdCyp has been represented as a surface contactnetwork (SCN) based on the surface complementarity (Sm) of interacting residues within themolecular interior. The application of Sm to side chain packing within proteins make it a very sensitive indicator of subtle perturbations in packing, in the thermal unfolding of the protein. Network based metrics have been defined to track the sequential changes in the disintegration ofthe SCN spanning the hydrophobic core of LdCyp and these metrics prove to be highly sensitive compared to traditional metrics in indicating the increased conformational (and dynamical) flexibility in the network. These metrics have been applied to suggest criteria distinguishing DMG, WMG and transition state ensembles and to identify key residues involved in crucial conformational/topological events during the unfolding process. PMID:26545107
International Nuclear Information System (INIS)
Gupta, Bhupender S.; Taha, Mohamed; Lee, Ming-Jer
2017-01-01
Highlights: • A green conceptual design for separating propanols from their aqueous solutions is proposed. • TRIS is biocompatible and non-volatile and can be used as an auxiliary agent for the separation. • Isobaric VLE data for 1-propanol/2-propanol + water + TRIS were measured at 101.3 kPa. • The azeotropic compositions are significantly shifted in the presence of TRIS. • Intermolecular interactions were studied with fluorescence, COSMO-RS, and MD simulation. - Abstract: In the present study, we have found that a common and relatively inexpensive biological buffer tris(hydroxymethyl)aminomethane (TRIS) is potentially applicable to shift the azeotrope compositions of aqueous solutions of 1-propanol and 2-propanol. By taking the advantage of our findings, we are proposing a green process for the recovery of these organics from their respective aqueous solutions. In order to confirm the effect of TRIS buffer on vapor–liquid equilibrium behavior of the aqueous propanol systems, we measured the isobaric vapor–liquid equilibrium (VLE) data at 101.3 kPa for the 1-proponol + water + TRIS and 2-propanol + water + TRIS systems over the azeotropic range with various concentrations of TRIS (0.02, 0.04, 0.08, and 0.12 in mole fraction). The binary interaction parameters were obtained for TRIS with water, TRIS with 1-propanol, and TRIS with 2-propanol by correlating the new VLE data with the NRTL model. The isobaric VLE properties for the investigated propanol + water mixtures in the presence of various concentrations of TRIS were also predicted with the conductor-like screening model COSMO-RS. Based on the predicted excess molar enthalpies (H E m ) from the COSMO-RS, the interactions between all constituent pairs of molecules were estimated. To explore the mechanism of TRIS-based separation of 1-propanol/2-propanol from their aqueous solutions, the interactions between different pairs of molecules were also investigated by using fluorescence analysis and
Efficient approach to obtain free energy gradient using QM/MM MD simulation
International Nuclear Information System (INIS)
Asada, Toshio; Koseki, Shiro; Ando, Kanta
2015-01-01
The efficient computational approach denoted as charge and atom dipole response kernel (CDRK) model to consider polarization effects of the quantum mechanical (QM) region is described using the charge response and the atom dipole response kernels for free energy gradient (FEG) calculations in the quantum mechanical/molecular mechanical (QM/MM) method. CDRK model can reasonably reproduce energies and also energy gradients of QM and MM atoms obtained by expensive QM/MM calculations in a drastically reduced computational time. This model is applied on the acylation reaction in hydrated trypsin-BPTI complex to optimize the reaction path on the free energy surface by means of FEG and the nudged elastic band (NEB) method
International Nuclear Information System (INIS)
Kornich, G.V.; Betz, G.; Bazhin, A.I.
1999-01-01
MD simulations of 100 eV Ar ion bombardment of (1 0 0) Ni and Al as well as Al/Ni bilayer crystals at 300 K have been performed and compared to previous calculations at 0 K. The Al/Ni bilayer crystal consisted of one Al layer on a (1 0 0) Ni substrate. Sputtering yields for Ni and Al/Ni show no temperature dependence, while for Al a pronounced increase with temperature was observed. The contributions of different mechanisms to the production of surface and bulk defects are discussed. The mean square displacement (MSD) of atoms is in all cases larger at 300 K as compared to 0 K. The larger MSD at 300 K is mainly due to an increase in lateral (perpendicular to the ion beam) motion of displaced atoms. Similar the number of atomic jumps, in which an atom leaves its original Wigner-Seitz cell, increases in all cases with temperature. For the pure elements the production of bulk vacancies and interstitials decreases with temperature, but the number of surface vacancies and ad-atoms increases with temperature. For the bilayer system practically no temperature dependence for defects was observed
International Nuclear Information System (INIS)
Swiatla-Wojcik, D.; Mozumder, A.
2014-01-01
We present a novel, molecular dynamics (MD) simulation based, strategy to analyze how the degree of hydrogen bonding may influence the ionization and dissociation of water upon heating from ambient to supercritical temperatures. Calculations show a negligible change in the ionization energy up to 200 °C. At higher temperatures the ionization energy increases due to the decreasing degree of hydrogen bonding. The influence of density (pressure) is pronounced in the supercritical region. The ionization is more energy consuming in the less dense fluid. We also show that high temperature and low density may promote dissociation of the electronically excited water molecules. Implications on the initial radiation chemical yields of the hydrated electron, hydrogen atom and hydroxyl radical are discussed. - Highlights: • Up to 200 °C changes in the vertical and adiabatic ionization potentials are negligible. • At higher temperatures ionization is more energy consuming. • Ionization potential increases with decreasing density of supercritical water. • High temperature and low density promote dissociation of the excited molecules
Directory of Open Access Journals (Sweden)
Fei Xiao
Full Text Available The gap junction protein connexin43 (Cx43 binds to the second PDZ domain of Zonula occludens-1 (ZO-1 through its C-terminal tail, mediating the regulation of gap junction plaque size and dynamics. Biochemical study demonstrated that the very C-terminal 12 residues of Cx43 are necessary and sufficient for ZO-1 PDZ2 binding and phosphorylation at residues Ser (-9 and Ser (-10 of the peptide can disrupt the association. However, only a crystal structure of ZO-1 PDZ2 in complex with a shorter 9 aa peptide of connexin43 was solved experimentally. Here, the interactions between ZO-1 PDZ2 and the short, long and phosphorylated Cx43 peptides were studied using molecular dynamics (MD simulations and free energy calculation. The short peptide bound to PDZ2 exhibits large structural variations, while the extension of three upstream residues stabilizes the peptide conformation and enhanced the interaction. Phosphorylation at Ser(-9 significantly weakens the binding and results in conformational flexibility of the peptide. Glu210 of ZO-1 PDZ2 was found to be a key regulatory point in Cx43 binding and phosphorylation induced dissociation.
Methods of channeling simulation
International Nuclear Information System (INIS)
Barrett, J.H.
1989-06-01
Many computer simulation programs have been used to interpret experiments almost since the first channeling measurements were made. Certain aspects of these programs are important in how accurately they simulate ions in crystals; among these are the manner in which the structure of the crystal is incorporated, how any quantity of interest is computed, what ion-atom potential is used, how deflections are computed from the potential, incorporation of thermal vibrations of the lattice atoms, correlations of thermal vibrations, and form of stopping power. Other aspects of the programs are included to improve the speed; among these are table lookup, importance sampling, and the multiparameter method. It is desirable for programs to facilitate incorporation of special features of interest in special situations; examples are relaxations and enhanced vibrations of surface atoms, easy substitution of an alternate potential for comparison, change of row directions from layer to layer in strained-layer lattices, and different vibration amplitudes for substitutional solute or impurity atoms. Ways of implementing all of these aspects and features and the consequences of them will be discussed. 30 refs., 3 figs
Xiao, Minyu; Wei, Shuai; Li, Yaoxin; Jasensky, Joshua; Chen, Junjie; Brooks, Charles L.
2017-01-01
Two-dimensional (2D) materials such as graphene, molybdenum disulfide (MoS2), tungsten diselenide (WSe2), and black phosphorous are being developed for sensing applications with excellent selectivity and high sensitivity. In such applications, 2D materials extensively interact with various analytes including biological molecules. Understanding the interfacial molecular interactions of 2D materials with various targets becomes increasingly important for the progression of better-performing 2D-material based sensors. In this research, molecular interactions between several de novo designed alpha-helical peptides and monolayer MoS2 have been studied. Molecular dynamics simulations were used to validate experimental data. The results suggest that, in contrast to peptide–graphene interactions, peptide aromatic residues do not interact strongly with the MoS2 surface. It is also found that charged amino acids are important for ensuring a standing-up pose for peptides interacting with MoS2. By performing site-specific mutations on the peptide, we could mediate the peptide–MoS2 interactions to control the peptide orientation on MoS2. PMID:29675220
Moustafa, Ibrahim M; Gohara, David W; Uchida, Akira; Yennawar, Neela; Cameron, Craig E
2015-11-23
The genomes of RNA viruses are relatively small. To overcome the small-size limitation, RNA viruses assign distinct functions to the processed viral proteins and their precursors. This is exemplified by poliovirus 3CD protein. 3C protein is a protease and RNA-binding protein. 3D protein is an RNA-dependent RNA polymerase (RdRp). 3CD exhibits unique protease and RNA-binding activities relative to 3C and is devoid of RdRp activity. The origin of these differences is unclear, since crystal structure of 3CD revealed "beads-on-a-string" structure with no significant structural differences compared to the fully processed proteins. We performed molecular dynamics (MD) simulations on 3CD to investigate its conformational dynamics. A compact conformation of 3CD was observed that was substantially different from that shown crystallographically. This new conformation explained the unique properties of 3CD relative to the individual proteins. Interestingly, simulations of mutant 3CD showed altered interface. Additionally, accelerated MD simulations uncovered a conformational ensemble of 3CD. When we elucidated the 3CD conformations in solution using small-angle X-ray scattering (SAXS) experiments a range of conformations from extended to compact was revealed, validating the MD simulations. The existence of conformational ensemble of 3CD could be viewed as a way to expand the poliovirus proteome, an observation that may extend to other viruses.
Murthy, P. Krishna; Smitha, M.; Sheena Mary, Y.; Armaković, Stevan; Armaković, Sanja J.; Rao, R. Sreenivasa; Suchetan, P. A.; Giri, L.; Pavithran, Rani; Van Alsenoy, C.
2017-12-01
Crystal and molecular structure of newly synthesized compound 5-bromo-7-methoxy-1-methyl-1H-benzoimidazole (BMMBI) has been authenticated by single crystal X-ray diffraction, FT-IR, FT-Raman, 1H NMR, 13C NMR and UV-Visible spectroscopic techniques; compile both experimental and theoretical results which are performed by DFT/B3LYP/6-311++G(d,p) method at ground state in gas phase. Visualize nature and type of intermolecular interactions and crucial role of these interactions in supra-molecular architecture has been investigated by use of a set of graphical tools 3D-Hirshfeld surfaces and 2D-fingerprint plots analysis. The title compound stabilized by strong intermolecular hydrogen bonds N⋯Hsbnd O and O⋯Hsbnd O, which are envisaged by dark red spots on dnorm mapped surfaces and weak Br⋯Br contacts envisaged by red spot on dnorm mapped surface. The detailed fundamental vibrational assignments of wavenumbers were aid by with help of Potential Energy distribution (PED) analysis by using GAR2PED program and shows good agreement with experimental values. Besides frontier orbitals analysis, global reactivity descriptors, natural bond orbitals and Mullikan charges analysis were performed by same basic set at ground state in gas phase. Potential reactive sites of the title compound have been identified by ALIE, Fukui functions and MEP, which are mapped to the electron density surfaces. Stability of BMMBI have been investigated from autoxidation process and pronounced interaction with water (hydrolysis) by using bond dissociation energies (BDE) and radial distribution functions (RDF), respectively after MD simulations. In order to identify molecule's most important reactive spots we have used a combination of DFT calculations and MD simulations. Reactivity study encompassed calculations of a set of quantities such as: HOMO-LUMO gap, MEP and ALIE surfaces, Fukui functions, bond dissociation energies and radial distribution functions. To confirm the potential
Directory of Open Access Journals (Sweden)
Yesylevskyy S. O.
2010-04-01
Full Text Available Aim. Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD simulations. The goal of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed
Directory of Open Access Journals (Sweden)
Kaori Asamitsu
Full Text Available In this study, we applied molecular dynamics (MD simulation to analyze the dynamic behavior of the Tat/CycT1/CDK9 tri-molecular complex and revealed the structural changes of P-TEFb upon Tat binding. We found that Tat could deliberately change the local flexibility of CycT1. Although the structural coordinates of the H1 and H2 helices did not substantially change, H1', H2', and H3' exhibited significant changes en masse. Consequently, the CycT1 residues involved in Tat binding, namely Tat-recognition residues (TRRs, lost their flexibility with the addition of Tat to P-TEFb. In addition, we clarified the structural variation of CDK9 in complex with CycT1 in the presence or absence of Tat. Interestingly, Tat addition significantly reduced the structural variability of the T-loop, thus consolidating the structural integrity of P-TEFb. Finally, we deciphered the formation of the hidden catalytic cavity of CDK9 upon Tat binding. MD simulation revealed that the PITALRE signature sequence of CDK9 flips the inactive kinase cavity of CDK9 into the active form by connecting with Thr186, which is crucial for its activity, thus presumably recruiting the substrate peptide such as the C-terminal domain of RNA pol II. These findings provide vital information for the development of effective novel anti-HIV drugs with CDK9 catalytic activity as the target.
Kametani, Shunsuke; Tasei, Yugo; Nishimura, Akio; Asakura, Tetsuo
2017-08-09
Polyalanine (polyA) sequences are well known as the simplest sequence that naturally forms anti-parallel β-sheets and constitute a key element in the structure of spider and wild silkworm silk fibers. We have carried out a systematic analysis of the packing of anti-parallel β-sheets for (Ala) n , n = 5, 6, 7 and 12, using primarily 13 C solid-state NMR and MD simulation. HFIP and TFA are frequently used as the dope solvents for recombinant silks, and polyA was solidified from both HFIP and TFA solutions by drying. An analysis of Ala Cβ peaks in the 13 C CP/MAS NMR spectra indicated that polyA from HFIP was mainly rectangular but polyA from TFA was mainly staggered. The transition from the rectangular to the staggered arrangement in (Ala) 6 was observed for the first time from the change in the Ala Cβ peak through heat treatment at 200 °C for 4 h. The removal of the bound water was confirmed by thermal analysis. This transition could be reproduced by MD simulation of (Ala) 6 molecules at 200 °C after removal of the bound water molecules. In this way, the origin of the stability of the different packing arrangements of polyA was clarified.
New methods in plasma simulation
International Nuclear Information System (INIS)
Mason, R.J.
1990-01-01
The development of implicit methods of particle-in-cell (PIC) computer simulation in recent years, and their merger with older hybrid methods have created a new arsenal of simulation techniques for the treatment of complex practical problems in plasma physics. The new implicit hybrid codes are aimed at transitional problems that lie somewhere between the long time scale, high density regime associated with MHD modeling, and the short time scale, low density regime appropriate to PIC particle-in-cell techniques. This transitional regime arises in ICF coronal plasmas, in pulsed power plasma switches, in Z-pinches, and in foil implosions. Here, we outline how such a merger of implicit and hybrid methods has been carried out, specifically in the ANTHEM computer code, and demonstrate the utility of implicit hybrid simulation in applications. 25 refs., 5 figs
Simulation of the 2-dimensional Drude’s model using molecular dynamics method
Energy Technology Data Exchange (ETDEWEB)
Naa, Christian Fredy; Amin, Aisyah; Ramli,; Suprijadi,; Djamal, Mitra [Theoretical High Energy Physics and Instrumentation Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132 (Indonesia); Wahyoedi, Seramika Ari; Viridi, Sparisoma, E-mail: viridi@cphys.fi.itb.ac.id [Nuclear and Biophysics Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132 (Indonesia)
2015-04-16
In this paper, we reported the results of the simulation of the electronic conduction in solids. The simulation is based on the Drude’s models by applying molecular dynamics (MD) method, which uses the fifth-order predictor-corrector algorithm. A formula of the electrical conductivity as a function of lattice length and ion diameter τ(L, d) cand be obtained empirically based on the simulation results.
MD Simulation on Collision Behavior Between Nano-Scale TiO₂ Particles During Vacuum Cold Spraying.
Yao, Hai-Long; Yang, Guan-Jun; Li, Chang-Jiu
2018-04-01
Particle collision behavior influences significantly inter-nano particle bonding formation during the nano-ceramic coating deposition by vacuum cold spraying (or aerosol deposition method). In order to illuminate the collision behavior between nano-scale ceramic particles, molecular dynamic simulation was applied to explore impact process between nano-scale TiO2 particles through controlling impact velocities. Results show that the recoil efficiency of the nano-scale TiO2 particle is decreased with the increase of the impact velocity. Nano-scale TiO2 particle exhibits localized plastic deformation during collision at low velocities, while it is intensively deformed by collision at high velocities. This intensive deformation promotes the nano-particle adhesion rather than rebounding off. A relationship between the adhesion energy and the rebound energy is established for the bonding formation of the nano-scale TiO2 particle. The adhesion energy required to the bonding formation between nano-scale ceramic particles can be produced by high velocity collision.
Directory of Open Access Journals (Sweden)
Claire Jantz
2014-09-01
Full Text Available We build upon much of the accumulated knowledge of the widely used SLEUTH urban land change model and offer advances. First, we use SLEUTH’s exclusion/attraction layer to identify and test different urban land cover change drivers; second, we leverage SLEUTH’s self-modification capability to incorporate a demographic model; and third, we develop a validation procedure to quantify the influence of land cover change drivers and assess uncertainty. We found that, contrary to our a priori expectations, new development is not attracted to areas serviced by existing or planned water and sewer infrastructure. However, information about where population and employment growth is likely to occur did improve model performance. These findings point to the dominant role of centrifugal forces in post-industrial cities like Baltimore, MD. We successfully developed a demographic model that allowed us to constrain the SLEUTH model forecasts and address uncertainty related to the dynamic relationship between changes in population and employment and urban land use. Finally, we emphasize the importance of model validation. In this work the validation procedure played a key role in rigorously assessing the impacts of different exclusion/attraction layers and in assessing uncertainty related to population and employment forecasts.
Directory of Open Access Journals (Sweden)
Xuelu Huan
Full Text Available The 16 EphA and EphB receptors represent the largest family of receptor tyrosine kinases, and their interactions with 9 ephrin-A and ephrin-B ligands initiate bidirectional signals controlling many physiological and pathological processes. Most interactions occur between receptor and ephrins of the same class, and only EphA4 can bind all A and B ephrins. To understand the structural and dynamic principles that enable Eph receptors to utilize the same jellyroll β-sandwich fold to bind ephrins, the VAPB-MSP domain, peptides and small molecules, we have used crystallography, NMR and molecular dynamics (MD simulations to determine the first structure and dynamics of the EphA5 ligand-binding domain (LBD, which only binds ephrin-A ligands. Unexpectedly, despite being unbound, the high affinity ephrin-binding pocket of EphA5 resembles that of other Eph receptors bound to ephrins, with a helical conformation over the J-K loop and an open pocket. The openness of the pocket is further supported by NMR hydrogen/deuterium exchange data and MD simulations. Additionally, the EphA5 LBD undergoes significant picosecond-nanosecond conformational exchanges over the loops, as revealed by NMR and MD simulations, but lacks global conformational exchanges on the microsecond-millisecond time scale. This is markedly different from the EphA4 LBD, which shares 74% sequence identity and 87% homology. Consequently, the unbound EphA5 LBD appears to comprise an ensemble of open conformations that have only small variations over the loops and appear ready to bind ephrin-A ligands. These findings show how two proteins with high sequence homology and structural similarity are still able to achieve distinctive binding specificities through different dynamics, which may represent a general mechanism whereby the same protein fold can serve for different functions. Our findings also suggest that a promising strategy to design agonists/antagonists with high affinity and selectivity
Page, Alister J.; Chandrakumar, K. R. S.; Irle, Stephan; Morokuma, Keiji
2011-05-01
Quantum chemical molecular dynamics (QM/MD) simulations of pristine and carbon-doped SiO 2 nanoparticles have been performed between 1000 and 3000 K. At temperatures above 1600 K, pristine nanoparticle SiO 2 decomposes rapidly, primarily forming SiO. Similarly, carbon-doped nanoparticle SiO 2 decomposes at temperatures above 2000 K, primarily forming SiO and CO. Analysis of the physical states of these pristine and carbon-doped SiO 2 nanoparticles indicate that they remain in the solid phase throughout decomposition. This process is therefore one of sublimation, as the liquid phase is never entered. Ramifications of these observations with respect to presently debated mechanisms of carbon nanotube growth on SiO 2 nanoparticles will be discussed.
International Nuclear Information System (INIS)
Blanco, Jose L. Jimenez; Rooijen, Johannes J.M. van; Erbel, Paul J.A.; Leeflang, Bas R.; Kamerling, Johannis P.; Vliegenthart, Johannes F.G.
2000-01-01
The conformational behaviour of the spacer-linked synthetic Sd a tetrasaccharide β-d-GalpNAc-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O) (CH 2 ) 5 NH 2 (1) and the two mimics β-d-Galp-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O)(CH 2 ) 5 NH 2 (2) and β-d-GlcpNAc-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O) (CH 2 ) 5 NH 2 (3) were investigated by 1 H NMR spectroscopy in combination with molecular dynamics (MD) simulations in water. Experimental 2D 1 H ROESY cross-peak intensities (ROEs) of the tetrasaccharides were compared with calculated ROEs derived from MD trajectories using the CROSREL program. Analysis of these data indicated that the oligosaccharidic skeletons of the compounds 1-3 are rather rigid, especially the β-d-Hex(NAc)-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp fragments. The α- Neu5-Ac-(2 → 3)-β-d-Galp linkage occurred in two different energy minima in the three-dimensional structure of the compounds 1-3 in aqueous solution. Experimental data and dynamics simulations supported the finding that the higher energy rotamer (CHEAT forcefield) was abundant in compounds 1 and 3 due to the existence of a hydrogen bond between the carboxyl group of the sialic acid and the acetamido group of the terminal monosaccharide (GalNAc or GlcNAc) unit. The conformational similarity between 1 and 3 leads to the suggestion that also their activities will be alike.
Kandadai, Venk; Yang, Haodong; Jiang, Ling; Yang, Christopher C; Fleisher, Linda; Winston, Flaura Koplin
2016-05-05
Little is known about the ability of individual stakeholder groups to achieve health information dissemination goals through Twitter. This study aimed to develop and apply methods for the systematic evaluation and optimization of health information dissemination by stakeholders through Twitter. Tweet content from 1790 followers of @SafetyMD (July-November 2012) was examined. User emphasis, a new indicator of Twitter information dissemination, was defined and applied to retweets across two levels of retweeters originating from @SafetyMD. User interest clusters were identified based on principal component analysis (PCA) and hierarchical cluster analysis (HCA) of a random sample of 170 followers. User emphasis of keywords remained across levels but decreased by 9.5 percentage points. PCA and HCA identified 12 statistically unique clusters of followers within the @SafetyMD Twitter network. This study is one of the first to develop methods for use by stakeholders to evaluate and optimize their use of Twitter to disseminate health information. Our new methods provide preliminary evidence that individual stakeholders can evaluate the effectiveness of health information dissemination and create content-specific clusters for more specific targeted messaging.
DEFF Research Database (Denmark)
Knudsen, Lars Ramkilde; Mathiassen, John Erik; Muller, Frédéric
2010-01-01
This paper considers the hash function MD2 which was developed by Ron Rivest in 1989. Despite its age, MD2 has withstood cryptanalytic attacks until recently. This paper contains the state-of-the-art cryptanalytic results on MD2, in particular collision and preimage attacks on the full hash...
Energy Technology Data Exchange (ETDEWEB)
Demmel, F. [ISIS Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX (United Kingdom); Mukhopadhyay, S. [ISIS Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX (United Kingdom); Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ (United Kingdom)
2016-01-07
The ionic stochastic motions in the molten alkali halide NaF are investigated by quasielastic neutron scattering and first principles molecular dynamics simulation. Quasielastic neutron scattering was employed to extract the diffusion behavior of the sodium ions in the melt. An extensive first principles based simulation on a box of up to 512 particles has been performed to complement the experimental data. From that large box, a smaller 64-particle box has then been simulated over a runtime of 60 ps. A good agreement between calculated and neutron data on the level of spectral shape has been obtained. The obtained sodium diffusion coefficients agree very well. The simulation predicts a fluorine diffusion coefficient similar to the sodium one. Applying the Nernst-Einstein equation, a remarkable large cross correlation between both ions can be deduced. The velocity cross correlations demonstrate a positive correlation between the ions over a period of 0.1 ps. That strong correlation is evidence that the unlike ions do not move completely statistically independent and have a strong association over a short period of time.
Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design.
Ludwiczak, Jan; Jarmula, Adam; Dunin-Horkawicz, Stanislaw
2018-07-01
Computational protein design is a set of procedures for computing amino acid sequences that will fold into a specified structure. Rosetta Design, a commonly used software for protein design, allows for the effective identification of sequences compatible with a given backbone structure, while molecular dynamics (MD) simulations can thoroughly sample near-native conformations. We benchmarked a procedure in which Rosetta design is started on MD-derived structural ensembles and showed that such a combined approach generates 20-30% more diverse sequences than currently available methods with only a slight increase in computation time. Importantly, the increase in diversity is achieved without a loss in the quality of the designed sequences assessed by their resemblance to natural sequences. We demonstrate that the MD-based procedure is also applicable to de novo design tasks started from backbone structures without any sequence information. In addition, we implemented a protocol that can be used to assess the stability of designed models and to select the best candidates for experimental validation. In sum our results demonstrate that the MD ensemble-based flexible backbone design can be a viable method for protein design, especially for tasks that require a large pool of diverse sequences. Copyright © 2018 Elsevier Inc. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Kritz, A.; Keyes, D.
2007-05-18
The mission of the Fusion Simulation Project is to develop a predictive capability for the integrated modeling of magnetically confined plasmas. This FSP report adds to the previous activities that defined an approach to integrated modeling in magnetic fusion. These previous activities included a Fusion Energy Sciences Advisory Committee panel that was charged to study integrated simulation in 2002. The report of that panel [Journal of Fusion Energy 20, 135 (2001)] recommended the prompt initiation of a Fusion Simulation Project. In 2003, the Office of Fusion Energy Sciences formed a steering committee that developed a project vision, roadmap, and governance concepts [Journal of Fusion Energy 23, 1 (2004)]. The current FSP planning effort involved forty-six physicists, applied mathematicians and computer scientists, from twenty-one institutions, formed into four panels and a coordinating committee. These panels were constituted to consider: Status of Physics Components, Required Computational and Applied Mathematics Tools, Integration and Management of Code Components, and Project Structure and Management. The ideas, reported here, are the products of these panels, working together over several months and culminating in a three-day workshop in May 2007.
Energy Technology Data Exchange (ETDEWEB)
None
2007-05-16
The mission of the Fusion Simulation Project is to develop a predictive capability for the integrated modeling of magnetically confined plasmas. This FSP report adds to the previous activities that defined an approach to integrated modeling in magnetic fusion. These previous activities included a Fusion Energy Sciences Advisory Committee panel that was charged to study integrated simulation in 2002. The report of that panel [Journal of Fusion Energy 20, 135 (2001)] recommended the prompt initiation of a Fusion Simulation Project. In 2003, the Office of Fusion Energy Sciences formed a steering committee that developed a project vision, roadmap, and governance concepts [Journal of Fusion Energy 23, 1 (2004)]. The current FSP planning effort involved forty-six physicists, applied mathematicians and computer scientists, from twenty-one institutions, formed into four panels and a coordinating committee. These panels were constituted to consider: Status of Physics Components, Required Computational and Applied Mathematics Tools, Integration and Management of Code Components, and Project Structure and Management. The ideas, reported here, are the products of these panels, working together over several months and culminating in a three-day workshop in May 2007.
International Nuclear Information System (INIS)
2007-01-01
The mission of the Fusion Simulation Project is to develop a predictive capability for the integrated modeling of magnetically confined plasmas. This FSP report adds to the previous activities that defined an approach to integrated modeling in magnetic fusion. These previous activities included a Fusion Energy Sciences Advisory Committee panel that was charged to study integrated simulation in 2002. The report of that panel (Journal of Fusion Energy 20, 135 (2001)) recommended the prompt initiation of a Fusion Simulation Project. In 2003, the Office of Fusion Energy Sciences formed a steering committee that developed a project vision, roadmap, and governance concepts (Journal of Fusion Energy 23, 1 (2004)). The current FSP planning effort involved forty-six physicists, applied mathematicians and computer scientists, from twenty-one institutions, formed into four panels and a coordinating committee. These panels were constituted to consider: Status of Physics Components, Required Computational and Applied Mathematics Tools, Integration and Management of Code Components, and Project Structure and Management. The ideas, reported here, are the products of these panels, working together over several months and culminating in a three-day workshop in May 2007.
International Nuclear Information System (INIS)
Kritz, A.; Keyes, D.
2007-01-01
The mission of the Fusion Simulation Project is to develop a predictive capability for the integrated modeling of magnetically confined plasmas. This FSP report adds to the previous activities that defined an approach to integrated modeling in magnetic fusion. These previous activities included a Fusion Energy Sciences Advisory Committee panel that was charged to study integrated simulation in 2002. The report of that panel [Journal of Fusion Energy 20, 135 (2001)] recommended the prompt initiation of a Fusion Simulation Project. In 2003, the Office of Fusion Energy Sciences formed a steering committee that developed a project vision, roadmap, and governance concepts [Journal of Fusion Energy 23, 1 (2004)]. The current FSP planning effort involved forty-six physicists, applied mathematicians and computer scientists, from twenty-one institutions, formed into four panels and a coordinating committee. These panels were constituted to consider: Status of Physics Components, Required Computational and Applied Mathematics Tools, Integration and Management of Code Components, and Project Structure and Management. The ideas, reported here, are the products of these panels, working together over several months and culminating in a three-day workshop in May 2007
QM/MM MD and Free Energy Simulation Study of Methyl Transfer Processes Catalyzed by PKMTs and PRMTs.
Chu, Yuzhuo; Guo, Hong
2015-09-01
Methyl transfer processes catalyzed by protein lysine methyltransferases (PKMTs) and protein arginine methyltransferases (PRMTs) control important biological events including transcriptional regulation and cell signaling. One important property of these enzymes is that different PKMTs and PRMTs catalyze the formation of different methylated product (product specificity). These different methylation states lead to different biological outcomes. Here, we review the results of quantum mechanics/molecular mechanics molecular dynamics and free energy simulations that have been performed to study the reaction mechanism of PKMTs and PRMTs and the mechanism underlying the product specificity of the methyl transfer processes.
DEFF Research Database (Denmark)
Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit
2012-01-01
Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomistic...... resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates...
Marmor, Rebecca; Jiang, Xiaoqian
2016-01-01
Background Online health community (OHC) moderators help facilitate conversations and provide information to members. However, the necessity of the moderator in helping members achieve goals by providing the support they need remains unclear, with some prior research suggesting that moderation is unnecessary or even harmful for close-knit OHCs. Similarly, members’ perceptions of moderator roles are underexplored. Starting January of 2013, WebMD moderators stopped working for WebMD communities. This event provided an opportunity for us to study the perceived role of moderators in OHCs. Objective We examine the OHC members’ perception on OHC moderators by studying their reactions toward the departure of moderators in their communities. We also analyzed the relative posting activity on OHCs before and after the departure of moderators from the communities among all members and those who discussed moderators’ departures. Methods We applied a mixed-methods approach to study the posts of all 55 moderated WebMD communities by querying the terms relating to discussions surrounding moderators’ disappearance from the WebMD community. We performed open and axial coding and affinity diagramming to thematically analyze patients’ reactions to the disappeared moderators. The number of posts and poster groups (members and moderators) were analyzed over time to understand posting patterns around moderators’ departure. Results Of 821 posts retrieved under 95 threads, a total of 166 open codes were generated. The codes were then grouped into 2 main themes with 6 total subthemes. First, patients attempted to understand why moderators had left and what could be done to fill the void left by the missing moderators. During these discussions, the posts revealed that patients believed that moderators played critical roles in the communities by making the communities vibrant and healthy, finding solutions, and giving medical information. Some patients felt personally attached
Dhindsa, Gurpreet K; Bhowmik, Debsindhu; Goswami, Monojoy; O'Neill, Hugh; Mamontov, Eugene; Sumpter, Bobby G; Hong, Liang; Ganesh, Panchapakesan; Chu, Xiang-Qiang
2016-09-14
Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on ND surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. Our new findings may provide new design principles for safer, improved drug delivery platforms.
Prompers, J.J.; Brüschweiler, R.
2002-01-01
A general framework is presented for the interpretation of NMR relaxation data of proteins. The method, termed isotropic reorientational eigenmode dynamics (iRED), relies on a principal component analysis of the isotropically averaged covariance matrix of the lattice functions of the spin
Comparative MD Simulations Indicate a Dual Role for Arg1323.50 in Dopamine-Dependent D2R Activation.
Directory of Open Access Journals (Sweden)
Ralf C Kling
Full Text Available Residue Arg3.50 belongs to the highly conserved DRY-motif of class A GPCRs, which is located at the bottom of TM3. On the one hand, Arg3.50 has been reported to help stabilize the inactive state of GPCRs, but on the other hand has also been shown to be crucial for stabilizing active receptor conformations and mediating receptor-G protein coupling. The combined results of these studies suggest that the exact function of Arg3.50 is likely to be receptor-dependent and must be characterized independently for every GPCR. Consequently, we now present comparative molecular-dynamics simulations that use our recently described inactive-state and Gα-bound active-state homology models of the dopamine D2 receptor (D2R, which are either bound to dopamine or ligand-free, performed to identify the function of Arg1323.50 in D2R. Our results are consistent with a dynamic model of D2R activation in which Arg1323.50 adopts a dual role, both by stabilizing the inactive-state receptor conformation and enhancing dopamine-dependent D2R-G protein coupling.
International Nuclear Information System (INIS)
Gauden, Piotr A; Terzyk, Artur P; Furmaniak, Sylwester; Zieliński, Wojciech; Włoch, Jerzy; Kowalczyk, Piotr
2014-01-01
The results of systematic studies of organics adsorption from aqueous solutions (at the neutral pH level) in a system of slit-like carbon pores having different sizes and oxygen groups located at the pore mouth are reported. Using molecular dynamics simulations (GROMACS package) the properties of adsorbent–adsorbate (benzene, phenol or paracetamol) as well as adsorbent–water systems are discussed. After the introduction of surface oxygen functionalities, adsorption of organic compounds decreases (in accordance with experimental data) and this is caused by the accumulation of water molecules at pore entrances. The pore blocking effect decreases with the diameter of slits and practically vanishes for widths larger than approx. 0.68 nm. We observed the increase in phenol adsorption with the rise in temperature. Moreover, adsorbed molecules occupy the external surface of the slit pores (the entrances) in the case of oxidized adsorbents. Among the studied molecules benzene, phenol and paracetamol prefer an almost flat orientation and with the rise in the pore width the number of molecules oriented in parallel decreases. The decrease or increase in temperature (with respect to 298 K) leads to insignificant changes of angular orientation of adsorbed molecules. (paper)
Rumolo, G
2017-01-01
The Injector Machine Development (MD) days 2017 were held on 23-24 March, 2017, at CERN with thefollowing main goals:Give a chance to the MD users to present their results and show the relevant progress made in 2016 onseveral fronts.Provide the MD users and the Operation (OP) crews with a general overview on the outcome and theimpact of all ongoing MD activities.Identify the open questions and consequently define - with priorities - a list of machine studies in theinjectors for 2017 (covering the operational beams, LHC Injectors Upgrade, High Luminosity LHC,Physics Beyond Colliders, other projects).Create the opportunity to collect and document the highlights of the 2016 MDs and define the perspectivesfor 2017.Discuss how to make best use of the MD time, in particular let the main MD user express their wishesand see whether/how OP teams can contribute to their fulfilment.
International Nuclear Information System (INIS)
Bhattacharya, Debarati; Rao, T.V. Chandrasekhar; Bhushan, K.G.; Ali, Kawsar; Debnath, A.; Singh, S.; Arya, A.; Bhattacharya, S.; Basu, S.
2015-01-01
Monophasic and homogeneous Ni 10 Zr 7 nanocrystalline alloy films were successfully grown at room temperature by co-sputtering in an indigenously developed three-gun DC/RF magnetron sputtering unit. The films could be produced with long-range crystallographic and chemical order in the alloy, thus overcoming the widely acknowledged inherent proclivity of the glass forming Ni–Zr couple towards amorphization. Crystallinity of these alloys is a desirable feature with regard to improved efficacy in applications such as hydrogen storage, catalytic activity and nuclear reactor engineering, to name a few. Thermal stability of this crystalline phase, being vital for transition to viable applications, was investigated through systematic annealing of the alloy films at 473 K, 673 K and 923 K for various durations. While the films were stable at 473 K, the effect of annealing at 673 K was to create segregation into nanocrystalline Ni (superparamagnetic) and amorphous Ni + Zr (non-magnetic) phases. Detailed analyses of the physical and magnetic structures before and after annealing were performed through several techniques effectual in analyzing stratified configurations and the findings were all consistent with each other. Polarized neutron and X-ray reflectometry, grazing incidence x-ray diffraction, time-of-flight secondary ion mass spectroscopy and X-ray photoelectron spectroscopy were used to gauge phase separation at nanometer length scales. SQUID based magnetometry was used to investigate macroscopic magnetic properties. Simulated annealing performed on this system using molecular dynamic calculations corroborated well with the experimental results. This study provides a thorough understanding of the creation and thermal evolution of a crystalline Ni–Zr alloy. - Highlights: • Nanocrystalline Ni 10 Zr 7 alloy thin films deposited successfully by co-sputtering. • Creation of a crystalline alloy in a binary system with a tendency to amorphize. • Quantitative
Energy Technology Data Exchange (ETDEWEB)
Bhattacharya, Debarati, E-mail: debarati@barc.gov.in [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Rao, T.V. Chandrasekhar; Bhushan, K.G. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Ali, Kawsar [Material Science Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Debnath, A. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Singh, S. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Arya, A. [Material Science Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Bhattacharya, S. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Basu, S. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)
2015-11-15
Monophasic and homogeneous Ni{sub 10}Zr{sub 7} nanocrystalline alloy films were successfully grown at room temperature by co-sputtering in an indigenously developed three-gun DC/RF magnetron sputtering unit. The films could be produced with long-range crystallographic and chemical order in the alloy, thus overcoming the widely acknowledged inherent proclivity of the glass forming Ni–Zr couple towards amorphization. Crystallinity of these alloys is a desirable feature with regard to improved efficacy in applications such as hydrogen storage, catalytic activity and nuclear reactor engineering, to name a few. Thermal stability of this crystalline phase, being vital for transition to viable applications, was investigated through systematic annealing of the alloy films at 473 K, 673 K and 923 K for various durations. While the films were stable at 473 K, the effect of annealing at 673 K was to create segregation into nanocrystalline Ni (superparamagnetic) and amorphous Ni + Zr (non-magnetic) phases. Detailed analyses of the physical and magnetic structures before and after annealing were performed through several techniques effectual in analyzing stratified configurations and the findings were all consistent with each other. Polarized neutron and X-ray reflectometry, grazing incidence x-ray diffraction, time-of-flight secondary ion mass spectroscopy and X-ray photoelectron spectroscopy were used to gauge phase separation at nanometer length scales. SQUID based magnetometry was used to investigate macroscopic magnetic properties. Simulated annealing performed on this system using molecular dynamic calculations corroborated well with the experimental results. This study provides a thorough understanding of the creation and thermal evolution of a crystalline Ni–Zr alloy. - Highlights: • Nanocrystalline Ni{sub 10}Zr{sub 7} alloy thin films deposited successfully by co-sputtering. • Creation of a crystalline alloy in a binary system with a tendency to amorphize.
Developing improved MD codes for understanding processive cellulases
International Nuclear Information System (INIS)
Crowley, M F; Nimlos, M R; Himmel, M E; Uberbacher, E C; Iii, C L Brooks; Walker, R C
2008-01-01
The mechanism of action of cellulose-degrading enzymes is illuminated through a multidisciplinary collaboration that uses molecular dynamics (MD) simulations and expands the capabilities of MD codes to allow simulations of enzymes and substrates on petascale computational facilities. There is a class of glycoside hydrolase enzymes called cellulases that are thought to decrystallize and processively depolymerize cellulose using biochemical processes that are largely not understood. Understanding the mechanisms involved and improving the efficiency of this hydrolysis process through computational models and protein engineering presents a compelling grand challenge. A detailed understanding of cellulose structure, dynamics and enzyme function at the molecular level is required to direct protein engineers to the right modifications or to understand if natural thermodynamic or kinetic limits are in play. Much can be learned about processivity by conducting carefully designed molecular dynamics (MD) simulations of the binding and catalytic domains of cellulases with various substrate configurations, solvation models and thermodynamic protocols. Most of these numerical experiments, however, will require significant modification of existing code and algorithms in order to efficiently use current (terascale) and future (petascale) hardware to the degree of parallelism necessary to simulate a system of the size proposed here. This work will develop MD codes that can efficiently use terascale and petascale systems, not just for simple classical MD simulations, but also for more advanced methods, including umbrella sampling with complex restraints and reaction coordinates, transition path sampling, steered molecular dynamics, and quantum mechanical/molecular mechanical simulations of systems the size of cellulose degrading enzymes acting on cellulose
Directory of Open Access Journals (Sweden)
Haiyan Wang
2014-01-01
Full Text Available Based on silsesquioxanes (SSO derived from the hydrolytic condensation of (γ-glycidyloxypropyltrimethoxysilane (GPMS and titanium tetrabutoxide (TTB, hybrid films on aluminum alloy (AA, film-GPMS-SSO (f-GS and f-GS-TTBi% (f-GSTT5%–25%, i = 5, 10, 15, 20 and 25 wt%, were prepared and tested by electrochemical measurements with typical potentiodynamic polarization curves. The Icorr values of the samples were significantly lower, comparing with the Icorr values of the f-GS, AA and f-GS modified tetraethoxysilane (TEOS in the previous study, which implies that the TTB5%–25% (TiO2 additions in the coatings indeed enhance the electrochemical corrosion resistance. Correlations between the film structures and anticorrosion properties were discussed. To validate the corresponding anticorrosion experiment results, different 3D-amorphous cubic unit cells were employed as models to investigate the self-diffusion coefficient (SDC for SO2, NO2 and H2O molecules by molecular dynamics (MD simulation. All of the SDCs calculated for SO2, NO2 and H2O diffusing in f-GSTT5%–25% cells were less than the SDCs in f-GS. These results validated the corresponding anticorrosion experiment results.
International Nuclear Information System (INIS)
Kadkhodayan, B.; Czerwinski, K.R.; Kreek, S.A.; Hannink, N.J.; Gregorich, K.E.; Lee, D.M.; Nurmia, M.J.; Hoffman, D.C.; Hall, H.L.
1992-01-01
We have measured the half-life and production cross section of the new isotope 253 Md, produced via the 243 Am( 13 C,3n) reaction. Isolation of Md from other activities was accomplished using elution with ammonium α-hydroxyisobutyrate from a cation exchange resin column. Experiments were performed with different irradiation time intervals, but the chemical separation always began and ended at exactly the same length of time after the end of irradiation. All separations with the same irradation lengths were combined and analyzed for growth and decay of the 3.0-d 253 Fm daughter and 20.47-d 253 Es, granddaugther of 253 Md. The amount of 253 Es in each fraction depends on the length of each irradiation and the 253 Md half-life. An increase in the length of irradiation will cause a corresponding increase in the amount of the new isotope 253 Md and hence, in the amount of 253 Es produced, provided the length of irradiations are not very long compared to the half-life of 253 Md. In this way, the Md half-life was estimated to be about 6 minutes with a production cross section of the order of 50 nb. (orig.)
2013-01-01
The physiological responses of silicate-based bioactive glasses (BGs) are known to depend critically on both the P content (nP) of the glass and its silicate network connectivity (N̅BOSi). However, while the bioactivity generally displays a nonmonotonic dependence on nP itself, recent work suggest that it is merely the net orthophosphate content that directly links to the bioactivity. We exploit molecular dynamics (MD) simulations combined with 31P and 29Si solid-state nuclear magnetic resonance (NMR) spectroscopy to explore the quantitative relationships between N̅BOSi, nP, and the silicate and phosphate speciations in a series of Na2O–CaO–SiO2–P2O5 glasses spanning 2.1 ≤ N̅BOSi ≤ 2.9 and variable P2O5 contents up to 6.0 mol %. The fractional population of the orthophosphate groups remains independent of nP at a fixed N̅BOSi-value, but is reduced slightly as N̅BOSi increases. Nevertheless, P remains predominantly as readily released orthophosphate ions, whose content may be altered essentially independently of the network connectivity, thereby offering a route to optimize the glass bioactivity. We discuss the observed composition-structure links in relation to known composition-bioactivity correlations, and define how Na2O–CaO–SiO2–P2O5 compositions exhibiting an optimal bioactivity can be designed by simultaneously altering three key parameters: the silicate network connectivity, the (ortho)phosphate content, and the nNa/nCa molar ratio. PMID:24364818
Sommer, Lisa A M; Janke, J Joel; Bennett, W F Drew; Bürck, Jochen; Ulrich, Anne S; Tieleman, D Peter; Dames, Sonja A
2014-05-08
The multidomain ser/thr kinase "target of rapamycin" (TOR) centrally controls eukaryotic growth and metabolism. The C-terminal FATC domain is important for TOR regulation and was suggested to directly mediate TOR-membrane interactions. Here, we present a detailed characterization of the membrane immersion properties of the oxidized and reduced yeast TOR1 FATC domain (2438-2470 = y1fatc). The immersion depth was characterized by NMR-monitored interaction studies with DPC micelles containing paramagnetically tagged 5- or 16-doxyl stearic acid (5-/16-SASL) and by analyzing the paramagnetic relaxation enhancement (PRE) from Mn(2+) in the solvent. Complementary MD-simulations of micellar systems in the absence and presence of protein showed that 5-/16-SASL can move in the micelle and that 16-SASL can bend such that the doxyl group is close to the headgroup region and not deep in the interior as commonly assumed. Based on oriented CD (OCD) data, the single α-helix of oxidized/reduced y1fatc has an angle to the membrane normal of ∼30-60°/∼35-65° in neutral and ∼5-35°/∼0-30° in negatively charged bilayers. The presented experimentally well-founded models help to better understand how this redox-sensitive peripheral membrane anchor may be part of a network of protein-protein and protein-membrane interactions regulating TOR localization at different cellular membranes. Moreover, the presented work provides a good methodological reference for the structural characterization of other peripherally membrane associating proteins.
... patients may need assisted ventilation to treat respiratory muscle weakness and a pacemaker for cardiac abnormalities. View Full Treatment Information Definition The muscular dystrophies (MD) are a group of more than 30 ...
Long-time atomistic simulations with the Parallel Replica Dynamics method
Perez, Danny
Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.
Priebe, A; Dehning, B; Redaelli, S; Salvachua Ferrando, BM; Sapinski, M; Solfaroli Camillocci, M; Valuch, D
2013-01-01
The fast beam losses in the order of 1 ms are expected to be a potential major luminosity limitation for higher beam energies after the LHC long shutdown (LS1). Therefore a Quench Test is planned in the winter 2013 to estimate the quench limit in this timescale and revise the current models. This experiment was devoted to determination the LHC Transverse Damper (ADT) as a system for fast losses induction. A non-standard operation of the ADT was used to develop the beam oscillation instead of suppressing them. The sign flip method had allowed us to create the fast losses within several LHC turns at 450 GeV during the previous test (26th March 2012). Thus, the ADT could be potentially used for the studies of the UFO ("Unidentied Falling Object") impact on the cold magnets. Verification of the system capability and investigations of the disturbed beam properties were the main objectives of this MD. During the experiment, the pilot bunches of proton beam were excited independently in the horizontal and vertical ...
Nedea, S.V.; Frijns, A.J.H.; Steenhoven, van A.A.; Markvoort, Albert. J.; Hilbers, P.A.J.
2005-01-01
We combine molecular dynamics (MD) and Monte Carlo (MC) simulations to study the properties of gas molecules confined between two hard walls of a microchannel or nanochannel. The coupling between MD and MC simulations is introduced by performing MD near the boundaries for accuracy and MC in the bulk
Methods for Monte Carlo simulations of biomacromolecules.
Vitalis, Andreas; Pappu, Rohit V
2009-01-01
The state-of-the-art for Monte Carlo (MC) simulations of biomacromolecules is reviewed. Available methodologies for sampling conformational equilibria and associations of biomacromolecules in the canonical ensemble, given a continuum description of the solvent environment, are reviewed. Detailed sections are provided dealing with the choice of degrees of freedom, the efficiencies of MC algorithms and algorithmic peculiarities, as well as the optimization of simple movesets. The issue of introducing correlations into elementary MC moves, and the applicability of such methods to simulations of biomacromolecules is discussed. A brief discussion of multicanonical methods and an overview of recent simulation work highlighting the potential of MC methods are also provided. It is argued that MC simulations, while underutilized biomacromolecular simulation community, hold promise for simulations of complex systems and phenomena that span multiple length scales, especially when used in conjunction with implicit solvation models or other coarse graining strategies.
Numerical methods used in simulation
International Nuclear Information System (INIS)
Caseau, Paul; Perrin, Michel; Planchard, Jacques
1978-01-01
The fundamental numerical problem posed by simulation problems is the stability of the resolution diagram. The system of the most used equations is defined, since there is a family of models of increasing complexity with 3, 4 or 5 equations although only models with 3 and 4 equations have been used extensively. After defining what is meant by explicit or implicit, the best established stability results is given for one-dimension problems and then for two-dimension problems. It is shown that two types of discretisation may be defined: four and eight point diagrams (in one or two dimensions) and six and ten point diagrams (in one or two dimensions). To end, some results are given on problems that are not usually treated very much, i.e. non-asymptotic stability and the stability of diagrams based on finite elements [fr
Methods for simulating turbulent phase screen
International Nuclear Information System (INIS)
Zhang Jianzhu; Zhang Feizhou; Wu Yi
2012-01-01
Some methods for simulating turbulent phase screen are summarized, and their characteristics are analyzed by calculating the phase structure function, decomposing phase screens into Zernike polynomials, and simulating laser propagation in the atmosphere. Through analyzing, it is found that, the turbulent high-frequency components are well contained by those phase screens simulated by the FFT method, but the low-frequency components are little contained. The low-frequency components are well contained by screens simulated by Zernike method, but the high-frequency components are not contained enough. The high frequency components contained will be improved by increasing the order of the Zernike polynomial, but they mainly lie in the edge-area. Compared with the two methods above, the fractal method is a better method to simulate turbulent phase screens. According to the radius of the focal spot and the variance of the focal spot jitter, there are limitations in the methods except the fractal method. Combining the FFT and Zernike method or combining the FFT method and self-similar theory to simulate turbulent phase screens is an effective and appropriate way. In general, the fractal method is probably the best way. (authors)
Detector Simulation: Data Treatment and Analysis Methods
Apostolakis, J
2011-01-01
Detector Simulation in 'Data Treatment and Analysis Methods', part of 'Landolt-Börnstein - Group I Elementary Particles, Nuclei and Atoms: Numerical Data and Functional Relationships in Science and Technology, Volume 21B1: Detectors for Particles and Radiation. Part 1: Principles and Methods'. This document is part of Part 1 'Principles and Methods' of Subvolume B 'Detectors for Particles and Radiation' of Volume 21 'Elementary Particles' of Landolt-Börnstein - Group I 'Elementary Particles, Nuclei and Atoms'. It contains the Section '4.1 Detector Simulation' of Chapter '4 Data Treatment and Analysis Methods' with the content: 4.1 Detector Simulation 4.1.1 Overview of simulation 4.1.1.1 Uses of detector simulation 4.1.2 Stages and types of simulation 4.1.2.1 Tools for event generation and detector simulation 4.1.2.2 Level of simulation and computation time 4.1.2.3 Radiation effects and background studies 4.1.3 Components of detector simulation 4.1.3.1 Geometry modeling 4.1.3.2 External fields 4.1.3.3 Intro...
Isogeometric methods for numerical simulation
Bordas, Stéphane
2015-01-01
The book presents the state of the art in isogeometric modeling and shows how the method has advantaged. First an introduction to geometric modeling with NURBS and T-splines is given followed by the implementation into computer software. The implementation in both the FEM and BEM is discussed.
Hofer, Thomas S.; Hünenberger, Philippe H.
2018-06-01
The absolute intrinsic hydration free energy GH+,w a t ◦ of the proton, the surface electric potential jump χwa t ◦ upon entering bulk water, and the absolute redox potential VH+,w a t ◦ of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy. However, this model describes the short-range solvation inaccurately and relies on the choice of arbitrary ion-size parameters. In the present study, both shortcomings are alleviated by performing first-principle calculations of the hydration free energies of the sodium (Na+) and potassium (K+) ions. The calculations rely on thermodynamic integration based on quantum-mechanical molecular-mechanical (QM/MM) molecular dynamics (MD) simulations involving the ion and 2000 water molecules. The ion and its first hydration shell are described using a correlated ab initio method, namely resolution-of-identity second-order Møller-Plesset perturbation (RIMP2). The next hydration shells are described using the extended simple point charge water model (SPC/E). The hydration free energy is first calculated at the MM level and subsequently increased by a quantization term accounting for the transformation to a QM/MM description. It is also corrected for finite-size, approximate-electrostatics, and potential-summation errors, as well as standard-state definition. These computationally intensive simulations provide accurate first-principle estimates for GH+,w a t ◦, χwa t ◦, and VH+,w a t ◦, reported with statistical errors based on a confidence interval of 99%. The values obtained
Howie, Philip V.
1993-04-01
The MD Explorer is an eight-seat twin-turbine engine helicopter which is being developed using integrated product definition (IPD) team methodology. New techniques include NOTAR antitorque system for directional control, a composite fuselage, an all-composite bearingless main rotor, and digital cockpit displays. Three-dimensional CAD models are the basis of the entire Explorer design. Solid models provide vendor with design clarification, removing much of the normal drawing interpretation errors.
Spectral Methods in Numerical Plasma Simulation
DEFF Research Database (Denmark)
Coutsias, E.A.; Hansen, F.R.; Huld, T.
1989-01-01
An introduction is given to the use of spectral methods in numerical plasma simulation. As examples of the use of spectral methods, solutions to the two-dimensional Euler equations in both a simple, doubly periodic region, and on an annulus will be shown. In the first case, the solution is expanded...
Evaluation of structural reliability using simulation methods
Directory of Open Access Journals (Sweden)
Baballëku Markel
2015-01-01
Full Text Available Eurocode describes the 'index of reliability' as a measure of structural reliability, related to the 'probability of failure'. This paper is focused on the assessment of this index for a reinforced concrete bridge pier. It is rare to explicitly use reliability concepts for design of structures, but the problems of structural engineering are better known through them. Some of the main methods for the estimation of the probability of failure are the exact analytical integration, numerical integration, approximate analytical methods and simulation methods. Monte Carlo Simulation is used in this paper, because it offers a very good tool for the estimation of probability in multivariate functions. Complicated probability and statistics problems are solved through computer aided simulations of a large number of tests. The procedures of structural reliability assessment for the bridge pier and the comparison with the partial factor method of the Eurocodes have been demonstrated in this paper.
2-d Simulations of Test Methods
DEFF Research Database (Denmark)
Thrane, Lars Nyholm
2004-01-01
One of the main obstacles for the further development of self-compacting concrete is to relate the fresh concrete properties to the form filling ability. Therefore, simulation of the form filling ability will provide a powerful tool in obtaining this goal. In this paper, a continuum mechanical...... approach is presented by showing initial results from 2-d simulations of the empirical test methods slump flow and L-box. This method assumes a homogeneous material, which is expected to correspond to particle suspensions e.g. concrete, when it remains stable. The simulations have been carried out when...... using both a Newton and Bingham model for characterisation of the rheological properties of the concrete. From the results, it is expected that both the slump flow and L-box can be simulated quite accurately when the model is extended to 3-d and the concrete is characterised according to the Bingham...
Novel Methods for Electromagnetic Simulation and Design
2016-08-03
modeling software that can handle complicated, electrically large objects in a manner that is sufficiently fast to allow design by simulation. 15. SUBJECT...electrically large objects in a manner that is sufficiently fast to allow design by simulation. We also developed new methods for scattering from cavities in a...basis for high fidelity modeling software that can handle complicated, electrically large objects in a manner that is sufficiently fast to allow
MD2036: UFO Dynamics Studies and UFO Fast Detection
Belanger, Philippe; Valette, Matthieu; Lindstrom, Bjorn Hans Filip; Grob, Laura Katharina; Schmidt, Rudiger; Wollmann, Daniel
2017-01-01
UFOs are one of the remaining unknown related to LHC operation. Therefore, improving the understanding of UFO dynamics and validating the developed models against direct beam measurements is of fundamental importance in view of LHC operation at 7 TeV and with HL-LHC beam intensities. If not understood, UFOs could also be a showstopper for future machines such as FCC. This MD demonstrates new methods to study the dynamic behaviour of a calibrated UFO, simulated by the interaction of wire scanners with the beam. The events created during the MD were monitored using diamond BLMs in IR7, providing bunch-by-bunch resolution measurements. The analysis presented herein shows that blown-up bunches can be used to identify the plane of movement of UFOs, that bunch profiles and bunch sizes can be measured with dBLMs with good precision, that simulation of expected losses are in good agreement with measurements for oscillating bunches and that the space resolution of the acquisition system used during the MD is about 10 ...
Matrix method for acoustic levitation simulation.
Andrade, Marco A B; Perez, Nicolas; Buiochi, Flavio; Adamowski, Julio C
2011-08-01
A matrix method is presented for simulating acoustic levitators. A typical acoustic levitator consists of an ultrasonic transducer and a reflector. The matrix method is used to determine the potential for acoustic radiation force that acts on a small sphere in the standing wave field produced by the levitator. The method is based on the Rayleigh integral and it takes into account the multiple reflections that occur between the transducer and the reflector. The potential for acoustic radiation force obtained by the matrix method is validated by comparing the matrix method results with those obtained by the finite element method when using an axisymmetric model of a single-axis acoustic levitator. After validation, the method is applied in the simulation of a noncontact manipulation system consisting of two 37.9-kHz Langevin-type transducers and a plane reflector. The manipulation system allows control of the horizontal position of a small levitated sphere from -6 mm to 6 mm, which is done by changing the phase difference between the two transducers. The horizontal position of the sphere predicted by the matrix method agrees with the horizontal positions measured experimentally with a charge-coupled device camera. The main advantage of the matrix method is that it allows simulation of non-symmetric acoustic levitators without requiring much computational effort.
A close examination of the structure and dynamics of HC(NH2)2PbI3by MD simulations and group theory
Carignano, M. A.; Saeed, Y.; Aravindh, S. Assa; Roqan, Iman S.; Even, J.; Katan, C.
2016-01-01
The formamidinium lead iodide hybrid perovskite is studied using first principles molecular dynamics simulations and further analyzed using group theory. The simulations are performed on large supercells containing 768 atoms under isothermal
Simulation teaching method in Engineering Optics
Lu, Qieni; Wang, Yi; Li, Hongbin
2017-08-01
We here introduce a pedagogical method of theoretical simulation as one major means of the teaching process of "Engineering Optics" in course quality improvement action plan (Qc) in our school. Students, in groups of three to five, complete simulations of interference, diffraction, electromagnetism and polarization of light; each student is evaluated and scored in light of his performance in the interviews between the teacher and the student, and each student can opt to be interviewed many times until he is satisfied with his score and learning. After three years of Qc practice, the remarkable teaching and learning effect is obatined. Such theoretical simulation experiment is a very valuable teaching method worthwhile for physical optics which is highly theoretical and abstruse. This teaching methodology works well in training students as to how to ask questions and how to solve problems, which can also stimulate their interest in research learning and their initiative to develop their self-confidence and sense of innovation.
Hybrid Method Simulation of Slender Marine Structures
DEFF Research Database (Denmark)
Christiansen, Niels Hørbye
This present thesis consists of an extended summary and five appended papers concerning various aspects of the implementation of a hybrid method which combines classical simulation methods and artificial neural networks. The thesis covers three main topics. Common for all these topics...... only recognize patterns similar to those comprised in the data used to train the network. Fatigue life evaluation of marine structures often considers simulations of more than a hundred different sea states. Hence, in order for this method to be useful, the training data must be arranged so...... that a single neural network can cover all relevant sea states. The applicability and performance of the present hybrid method is demonstrated on a numerical model of a mooring line attached to a floating offshore platform. The second part of the thesis demonstrates how sequential neural networks can be used...
A Simulation Method Measuring Psychomotor Nursing Skills.
McBride, Helena; And Others
1981-01-01
The development of a simulation technique to evaluate performance of psychomotor skills in an undergraduate nursing program is described. This method is used as one admission requirement to an alternate route nursing program. With modifications, any health profession could use this technique where psychomotor skills performance is important.…
An Efficient Simulation Method for Rare Events
Rached, Nadhir B.
2015-01-07
Estimating the probability that a sum of random variables (RVs) exceeds a given threshold is a well-known challenging problem. Closed-form expressions for the sum distribution do not generally exist, which has led to an increasing interest in simulation approaches. A crude Monte Carlo (MC) simulation is the standard technique for the estimation of this type of probability. However, this approach is computationally expensive, especially when dealing with rare events. Variance reduction techniques are alternative approaches that can improve the computational efficiency of naive MC simulations. We propose an Importance Sampling (IS) simulation technique based on the well-known hazard rate twisting approach, that presents the advantage of being asymptotically optimal for any arbitrary RVs. The wide scope of applicability of the proposed method is mainly due to our particular way of selecting the twisting parameter. It is worth observing that this interesting feature is rarely satisfied by variance reduction algorithms whose performances were only proven under some restrictive assumptions. It comes along with a good efficiency, illustrated by some selected simulation results comparing the performance of our method with that of an algorithm based on a conditional MC technique.
An Efficient Simulation Method for Rare Events
Rached, Nadhir B.; Benkhelifa, Fatma; Kammoun, Abla; Alouini, Mohamed-Slim; Tempone, Raul
2015-01-01
Estimating the probability that a sum of random variables (RVs) exceeds a given threshold is a well-known challenging problem. Closed-form expressions for the sum distribution do not generally exist, which has led to an increasing interest in simulation approaches. A crude Monte Carlo (MC) simulation is the standard technique for the estimation of this type of probability. However, this approach is computationally expensive, especially when dealing with rare events. Variance reduction techniques are alternative approaches that can improve the computational efficiency of naive MC simulations. We propose an Importance Sampling (IS) simulation technique based on the well-known hazard rate twisting approach, that presents the advantage of being asymptotically optimal for any arbitrary RVs. The wide scope of applicability of the proposed method is mainly due to our particular way of selecting the twisting parameter. It is worth observing that this interesting feature is rarely satisfied by variance reduction algorithms whose performances were only proven under some restrictive assumptions. It comes along with a good efficiency, illustrated by some selected simulation results comparing the performance of our method with that of an algorithm based on a conditional MC technique.
Simulation methods for nuclear production scheduling
International Nuclear Information System (INIS)
Miles, W.T.; Markel, L.C.
1975-01-01
Recent developments and applications of simulation methods for use in nuclear production scheduling and fuel management are reviewed. The unique characteristics of the nuclear fuel cycle as they relate to the overall optimization of a mixed nuclear-fossil system in both the short-and mid-range time frame are described. Emphasis is placed on the various formulations and approaches to the mid-range planning problem, whose objective is the determination of an optimal (least cost) system operation strategy over a multi-year planning horizon. The decomposition of the mid-range problem into power system simulation, reactor core simulation and nuclear fuel management optimization, and system integration models is discussed. Present utility practices, requirements, and research trends are described. 37 references
Petascale molecular dynamics simulation using the fast multipole method on K computer
Ohno, Yousuke; Yokota, Rio; Koyama, Hiroshi; Morimoto, Gentaro; Hasegawa, Aki; Masumoto, Gen; Okimoto, Noriaki; Hirano, Yoshinori; Ibeid, Huda; Narumi, Tetsu; Taiji, Makoto
2014-01-01
In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.
Petascale molecular dynamics simulation using the fast multipole method on K computer
Ohno, Yousuke
2014-10-01
In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.
The ABCs of molecular dynamics simulations on B-DNA, circa 2012
Indian Academy of Sciences (India)
2012-06-25
Jun 25, 2012 ... Introduction ... methods and applications of MD simulations to nucleic acids. ... access to high-performance computing, all-atom MD on DNA ... Specifically, the focus in this article is (a) ... of MD on DNA using AMBER came with the development ..... python-based tool for managing this task on widely.
Lagrangian numerical methods for ocean biogeochemical simulations
Paparella, Francesco; Popolizio, Marina
2018-05-01
We propose two closely-related Lagrangian numerical methods for the simulation of physical processes involving advection, reaction and diffusion. The methods are intended to be used in settings where the flow is nearly incompressible and the Péclet numbers are so high that resolving all the scales of motion is unfeasible. This is commonplace in ocean flows. Our methods consist in augmenting the method of characteristics, which is suitable for advection-reaction problems, with couplings among nearby particles, producing fluxes that mimic diffusion, or unresolved small-scale transport. The methods conserve mass, obey the maximum principle, and allow to tune the strength of the diffusive terms down to zero, while avoiding unwanted numerical dissipation effects.
Simulation and the Monte Carlo method
Rubinstein, Reuven Y
2016-01-01
Simulation and the Monte Carlo Method, Third Edition reflects the latest developments in the field and presents a fully updated and comprehensive account of the major topics that have emerged in Monte Carlo simulation since the publication of the classic First Edition over more than a quarter of a century ago. While maintaining its accessible and intuitive approach, this revised edition features a wealth of up-to-date information that facilitates a deeper understanding of problem solving across a wide array of subject areas, such as engineering, statistics, computer science, mathematics, and the physical and life sciences. The book begins with a modernized introduction that addresses the basic concepts of probability, Markov processes, and convex optimization. Subsequent chapters discuss the dramatic changes that have occurred in the field of the Monte Carlo method, with coverage of many modern topics including: Markov Chain Monte Carlo, variance reduction techniques such as the transform likelihood ratio...
Simulating colloid hydrodynamics with lattice Boltzmann methods
International Nuclear Information System (INIS)
Cates, M E; Stratford, K; Adhikari, R; Stansell, P; Desplat, J-C; Pagonabarraga, I; Wagner, A J
2004-01-01
We present a progress report on our work on lattice Boltzmann methods for colloidal suspensions. We focus on the treatment of colloidal particles in binary solvents and on the inclusion of thermal noise. For a benchmark problem of colloids sedimenting and becoming trapped by capillary forces at a horizontal interface between two fluids, we discuss the criteria for parameter selection, and address the inevitable compromise between computational resources and simulation accuracy
An improved method for simulating radiographs
International Nuclear Information System (INIS)
Laguna, G.W.
1986-01-01
The parameters involved in generating actual radiographs and what can and cannot be modeled are examined in this report. Using the spectral distribution of the radiation source and the mass absorption curve for the material comprising the part to be modeled, the actual amount of radiation that would pass through the part and reach the film is determined. This method increases confidence in the results of the simulation and enables the modeling of parts made of multiple materials
Spectral methods in numerical plasma simulation
International Nuclear Information System (INIS)
Coutsias, E.A.; Hansen, F.R.; Huld, T.; Knorr, G.; Lynov, J.P.
1989-01-01
An introduction is given to the use of spectral methods in numerical plasma simulation. As examples of the use of spectral methods, solutions to the two-dimensional Euler equations in both a simple, doubly periodic region, and on an annulus will be shown. In the first case, the solution is expanded in a two-dimensional Fourier series, while a Chebyshev-Fourier expansion is employed in the second case. A new, efficient algorithm for the solution of Poisson's equation on an annulus is introduced. Problems connected to aliasing and to short wavelength noise generated by gradient steepening are discussed. (orig.)
Electromagnetic simulation using the FDTD method
Sullivan, Dennis M
2013-01-01
A straightforward, easy-to-read introduction to the finite-difference time-domain (FDTD) method Finite-difference time-domain (FDTD) is one of the primary computational electrodynamics modeling techniques available. Since it is a time-domain method, FDTD solutions can cover a wide frequency range with a single simulation run and treat nonlinear material properties in a natural way. Written in a tutorial fashion, starting with the simplest programs and guiding the reader up from one-dimensional to the more complex, three-dimensional programs, this book provides a simple, yet comp
International Nuclear Information System (INIS)
Wang, J.; Gutierre, M.S.
2010-01-01
This paper presents results of a molecular dynamics simulation study of dehydrated 2:1 clay minerals using the Parrinello-Rahman constant-pressure molecular dynamics method. The method is capable of simulating a system under the most general applied stress conditions by considering the changes of MD cell size and shape. Given the advantage of the method, it is the major goal of the paper to investigate the influence of imposed cell boundary conditions on the molecular structural transformation of 2:1 clay minerals under different normal pressures. Simulation results show that the degrees of freedom of the simulation cell (i.e., whether the cell size or shape change is allowed) determines the final equilibrated crystal structure of clay minerals. Both the MD method and the static method have successfully revealed unforeseen structural transformations of clay minerals upon relaxation under different normal pressures. It is found that large shear distortions of clay minerals occur when full allowance is given to the cell size and shape change. A complete elimination of the interlayer spacing is observed in a static simulation. However, when only the cell size change is allowed, interlayer spacing is retained, but large internal shear stresses also exist.
Rishworth, Susan K
2012-01-01
The purpose of this historical article is to demonstrate, as the biography of Verina Morton Jones, MD, is uncovered, the difficulties inherent in researching original source material on the lives of 19th- and early 20th-century African American physicians as well as the great benefits derived from doing this research. The procedures used include basic archival research and close examination of published materials about her in the past, in conjunction with oral history. Original correspondence from Dr Morton Jones to her niece and nephew is used to illustrate events in her life and the thoughts and attitudes she expressed. Some of these thoughts and attitudes reflect those current situations in which African Americans found themselves, and others are quite unique, no doubt owing to her privileged position in the African American community. The principle conclusions reached include the great benefits derived from doing this kind of research, as difficult and time-consuming as that may be, with the enhanced knowledge and appreciation of the heritage of African American physicians, and insights into American social history during this period.
Varmus, H E
1995-06-01
On November 19, 1993, the Senate approved the nomination of Harold E. Varmus, MD, as Director of the National Institutes of Health (NIH). Varmus, who received the 1989 Nobel Prize in Medicine, brought unquestioned credentials as a scientist to the NIH. Despite his limited background as an administrator, Varmus has received high marks from most observers for improving the morale of NIH staffers and implementing streamlined procedures in the grant review process. His tenure has not been free of controversy, however. Many clinical researchers have long felt there is a bias in NIH study sections against patient-oriented research. A recent study sponsored by the Division of Research Grants confirmed the lower success rate of patient-oriented research proposals, but the outcome of these findings remains unclear. Faced with mounting political pressure for a balanced budget, and the resultant reduction of funding to many branches of government, Varmus has been a strong voice for non-targeted investigator initiated research. Interviewed in his office in Building One on the NIH campus in Bethesda, Maryland, Varmus discussed the state of patient oriented research, the evolving role of the NIH in supporting science, and just where the money to pay for it should be found.
An Efficient Hybrid DSMC/MD Algorithm for Accurate Modeling of Micro Gas Flows
Liang, Tengfei
2013-01-01
Aiming at simulating micro gas flows with accurate boundary conditions, an efficient hybrid algorithmis developed by combining themolecular dynamics (MD) method with the direct simulationMonte Carlo (DSMC)method. The efficiency comes from the fact that theMD method is applied only within the gas-wall interaction layer, characterized by the cut-off distance of the gas-solid interaction potential, to resolve accurately the gas-wall interaction process, while the DSMC method is employed in the remaining portion of the flow field to efficiently simulate rarefied gas transport outside the gas-wall interaction layer. A unique feature about the present scheme is that the coupling between the two methods is realized by matching the molecular velocity distribution function at the DSMC/MD interface, hence there is no need for one-toone mapping between a MD gas molecule and a DSMC simulation particle. Further improvement in efficiency is achieved by taking advantage of gas rarefaction inside the gas-wall interaction layer and by employing the "smart-wall model" proposed by Barisik et al. The developed hybrid algorithm is validated on two classical benchmarks namely 1-D Fourier thermal problem and Couette shear flow problem. Both the accuracy and efficiency of the hybrid algorithm are discussed. As an application, the hybrid algorithm is employed to simulate thermal transpiration coefficient in the free-molecule regime for a system with atomically smooth surface. Result is utilized to validate the coefficients calculated from the pure DSMC simulation with Maxwell and Cercignani-Lampis gas-wall interaction models. ©c 2014 Global-Science Press.
Meshless Method for Simulation of Compressible Flow
Nabizadeh Shahrebabak, Ebrahim
In the present age, rapid development in computing technology and high speed supercomputers has made numerical analysis and computational simulation more practical than ever before for large and complex cases. Numerical simulations have also become an essential means for analyzing the engineering problems and the cases that experimental analysis is not practical. There are so many sophisticated and accurate numerical schemes, which do these simulations. The finite difference method (FDM) has been used to solve differential equation systems for decades. Additional numerical methods based on finite volume and finite element techniques are widely used in solving problems with complex geometry. All of these methods are mesh-based techniques. Mesh generation is an essential preprocessing part to discretize the computation domain for these conventional methods. However, when dealing with mesh-based complex geometries these conventional mesh-based techniques can become troublesome, difficult to implement, and prone to inaccuracies. In this study, a more robust, yet simple numerical approach is used to simulate problems in an easier manner for even complex problem. The meshless, or meshfree, method is one such development that is becoming the focus of much research in the recent years. The biggest advantage of meshfree methods is to circumvent mesh generation. Many algorithms have now been developed to help make this method more popular and understandable for everyone. These algorithms have been employed over a wide range of problems in computational analysis with various levels of success. Since there is no connectivity between the nodes in this method, the challenge was considerable. The most fundamental issue is lack of conservation, which can be a source of unpredictable errors in the solution process. This problem is particularly evident in the presence of steep gradient regions and discontinuities, such as shocks that frequently occur in high speed compressible flow
Czech Academy of Sciences Publication Activity Database
Krepl, Miroslav; Clery, A.; Blatter, M.; Allain, F.H.T.; Šponer, Jiří
2016-01-01
Roč. 44, č. 13 (2016), s. 6452-6470 ISSN 0305-1048 Institutional support: RVO:68081707 Keywords : molecular- dynamics simulations * particle mesh ewald * pre-ribosomal-rna Subject RIV: BO - Biophysics Impact factor: 10.162, year: 2016
A new method for simulating human emotions
Institute of Scientific and Technical Information of China (English)
无
2003-01-01
How to make machines express emotions would be instrumental in establishing a completely new paradigm for man ma-chine interaction. A new method for simulating and assessing artificial psychology has been developed for the research of the emo-tion robot. The human psychology activity is regarded as a Markov process. An emotion space and psychology model is constructedbased on Markov process. The conception of emotion entropy is presented to assess the artificial emotion complexity. The simulatingresults play up to human psychology activity. This model can also be applied to consumer-friendly human-computer interfaces, andinteractive video etc.
Mora Osorio, Camilo Andrés; González Barrios, Andrés Fernando
2016-12-07
Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium. Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces. Multiple MD of the twenty classic amino acids located at the interface of rectangular simulation boxes with a dodecane-water medium were performed. A GCM to calculate the free energy of entire peptides is then proposed. The method uses the summation of the Gibbs free energy of each amino acid adjusted in function of its presence or absence in the chain as well as its hydrophobic characteristics. Validation of the equation was performed with twenty-one peptides all simulated using MD in dodecane-water rectangular boxes in previous work, obtaining an average relative error of 16%.
Comparison of validation methods for forming simulations
Schug, Alexander; Kapphan, Gabriel; Bardl, Georg; Hinterhölzl, Roland; Drechsler, Klaus
2018-05-01
The forming simulation of fibre reinforced thermoplastics could reduce the development time and improve the forming results. But to take advantage of the full potential of the simulations it has to be ensured that the predictions for material behaviour are correct. For that reason, a thorough validation of the material model has to be conducted after characterising the material. Relevant aspects for the validation of the simulation are for example the outer contour, the occurrence of defects and the fibre paths. To measure these features various methods are available. Most relevant and also most difficult to measure are the emerging fibre orientations. For that reason, the focus of this study was on measuring this feature. The aim was to give an overview of the properties of different measuring systems and select the most promising systems for a comparison survey. Selected were an optical, an eddy current and a computer-assisted tomography system with the focus on measuring the fibre orientations. Different formed 3D parts made of unidirectional glass fibre and carbon fibre reinforced thermoplastics were measured. Advantages and disadvantages of the tested systems were revealed. Optical measurement systems are easy to use, but are limited to the surface plies. With an eddy current system also lower plies can be measured, but it is only suitable for carbon fibres. Using a computer-assisted tomography system all plies can be measured, but the system is limited to small parts and challenging to evaluate.
Directory of Open Access Journals (Sweden)
Lanlan Li
Full Text Available Bisphenol A (BPA can interact with nuclear receptors and affect the normal function of nuclear receptors in very low doses, which causes BPA to be one of the most controversial endocrine disruptors. However, the detailed molecular mechanism about how BPA interferes the normal function of nuclear receptors is still undiscovered. Herein, molecular dynamics simulations were performed to explore the detailed interaction mechanism between BPA with three typical nuclear receptors, including hERα, hERRγ and hPPARγ. The simulation results and calculated binding free energies indicate that BPA can bind to these three nuclear receptors. The binding affinities of BPA were slightly lower than that of E2 to these three receptors. The simulation results proved that the binding process was mainly driven by direct hydrogen bond and hydrophobic interactions. In addition, structural analysis suggested that BPA could interact with these nuclear receptors by mimicking the action of natural hormone and keeping the nuclear receptors in active conformations. The present work provided the structural evidence to recognize BPA as an endocrine disruptor and would be important guidance for seeking safer substitutions of BPA.
Directory of Open Access Journals (Sweden)
Sara Y. Cheng
2016-06-01
Full Text Available This data article supports the research article entitled “Maximally Asymmetric Transbilayer Distribution of Anionic Lipids Alters the Structure and interaction with Lipids of an Amyloidogenic Protein Dimer Bound to the Membrane Surface” [1]. We describe supporting data on the binding kinetics, time evolution of secondary structure, and residue-contact maps of a surface-absorbed beta-amyloid dimer protein on different membrane surfaces. We further demonstrate the sorting of annular and non-annular regions of the protein/lipid bilayer simulation systems, and the correlation of lipid-number mismatch and surface area per lipid mismatch of asymmetric lipid membranes.
Molecular Simulation towards Efficient and Representative Subsurface Reservoirs Modeling
Kadoura, Ahmad Salim
2016-01-01
This dissertation focuses on the application of Monte Carlo (MC) molecular simulation and Molecular Dynamics (MD) in modeling thermodynamics and flow of subsurface reservoir fluids. At first, MC molecular simulation is proposed as a promising method
Odinokov, A. V.; Leontyev, I. V.; Basilevsky, M. V.; Petrov, N. Ch.
2011-01-01
Potentials of mean force (PMF) are calculated for two model ion pairs in two non-aqueous solvents. Standard non-polarizable molecular dynamics simulation (NPMD) and approximate polarizable simulation (PMD) are implemented and compared as tools for monitoring PMF profiles. For the polar solvent (dimethylsulfoxide, DMSO) the PMF generated in terms of the NPMD reproduces fairly well the refined PMD-PMF profile. For the non-polar solvent (benzene) the conventional NPMD computation proves to be deficient. The validity of the correction found in terms of the approximate PMD approach is verified by its comparison with the result of the explicit PMD computation in benzene. The shapes of the PMF profiles in DMSO and in benzene are quite different. In DMSO, owing to dielectric screening, the PMF presents a flat plot with a shallow minimum positioned in the vicinity of the van der Waals contact of the ion pair. For the benzene case, the observed minimum proves to be unexpectedly deep, which manifests the formation of a tightly-binded contact ion pair. This remarkable effect arises owing to the strong electrostatic interaction that is incompletely screened by a non-polar medium. The PMFs for the binary benzene/DMSO mixtures display intermediate behaviour depending on the DMSO content.
A close examination of the structure and dynamics of HC(NH2)2PbI3by MD simulations and group theory
Carignano, M. A.
2016-06-22
The formamidinium lead iodide hybrid perovskite is studied using first principles molecular dynamics simulations and further analyzed using group theory. The simulations are performed on large supercells containing 768 atoms under isothermal and fully anisotropic isobaric conditions. Two trajectories, one at 300 K and another at 450 K, were extended for over 50 ps in order to perform a detailed assessment of the rotational dynamics of organic cations. The characteristic rotations of the cation are analyzed by defining two rotation axes. It is found that the formamidinium molecules rotate preferentially around the direction parallel to the line connecting the two nitrogen atoms. The rotational dynamics shows some characteristics already observed in methylammonium lead iodide, like the heterogeneous dynamics at room temperature that disappears at 450 K. The orientational probability of the molecules is explored in terms of an expansion in cubic harmonics up to the 12th order. It reveals a strong directionality at room temperature that relaxes when increasing the temperature. These findings are further rationalized using Landau and group theories suggesting a mixed displacive/order-disorder structural instability at lower temperatures.
Wettability of graphitic-carbon and silicon surfaces: MD modeling and theoretical analysis
International Nuclear Information System (INIS)
Ramos-Alvarado, Bladimir; Kumar, Satish; Peterson, G. P.
2015-01-01
The wettability of graphitic carbon and silicon surfaces was numerically and theoretically investigated. A multi-response method has been developed for the analysis of conventional molecular dynamics (MD) simulations of droplets wettability. The contact angle and indicators of the quality of the computations are tracked as a function of the data sets analyzed over time. This method of analysis allows accurate calculations of the contact angle obtained from the MD simulations. Analytical models were also developed for the calculation of the work of adhesion using the mean-field theory, accounting for the interfacial entropy changes. A calibration method is proposed to provide better predictions of the respective contact angles under different solid-liquid interaction potentials. Estimations of the binding energy between a water monomer and graphite match those previously reported. In addition, a breakdown in the relationship between the binding energy and the contact angle was observed. The macroscopic contact angles obtained from the MD simulations were found to match those predicted by the mean-field model for graphite under different wettability conditions, as well as the contact angles of Si(100) and Si(111) surfaces. Finally, an assessment of the effect of the Lennard-Jones cutoff radius was conducted to provide guidelines for future comparisons between numerical simulations and analytical models of wettability
Directory of Open Access Journals (Sweden)
Rohit S Bavi
2013-02-01
Full Text Available Modified nucleic acid bases are most commonly found in tRNA. These may contain modifications from simple methylation to addition of bulky groups. Methylation of the four canonical nucleotide bases at a wide variety of positions is particularly prominent among the known modification. Methylation of N2 group of guanine is a relatively common modification in tRNA and rRNA. N2-methylguanosine (m2G is the second most often encountered nucleoside in E. coli tRNAs. N2, N2-dimethylguanosine (m22G is found in the majority of eukaryotic tRNAs and involved in forming base pair interactions with adjacent bases. Hence, in order to understand the structural significance of these methylated nucleic acid bases we have carried out molecular dynamics simulation to see the salvation effect. The results obtained shows iso-energetic conformational behaviors for m2G and m22G. The simulation trajectory of m2G shows regular periodical fluctuations suggesting that m2G is equally stable as either s-cis or s-trans rotamers. The two rotamers of m2G may interact canonically or non-canonically with opposite base as s-trans m2G26:C/A/U44 and s-cis m2G26:A/U44. The free rotations around the C-N bond could be the possible reason for these iso-energetic conformations. Dimethylation of G has almost no influence on base pairing with either A or U. Thus, these results reveal that modified nucleosides m2G and m22G may play an important role to prevent tRNA from adopting the unusual mitochondrial like conformation.
Rare event simulation using Monte Carlo methods
Rubino, Gerardo
2009-01-01
In a probabilistic model, a rare event is an event with a very small probability of occurrence. The forecasting of rare events is a formidable task but is important in many areas. For instance a catastrophic failure in a transport system or in a nuclear power plant, the failure of an information processing system in a bank, or in the communication network of a group of banks, leading to financial losses. Being able to evaluate the probability of rare events is therefore a critical issue. Monte Carlo Methods, the simulation of corresponding models, are used to analyze rare events. This book sets out to present the mathematical tools available for the efficient simulation of rare events. Importance sampling and splitting are presented along with an exposition of how to apply these tools to a variety of fields ranging from performance and dependability evaluation of complex systems, typically in computer science or in telecommunications, to chemical reaction analysis in biology or particle transport in physics. ...
Computational Simulations and the Scientific Method
Kleb, Bil; Wood, Bill
2005-01-01
As scientific simulation software becomes more complicated, the scientific-software implementor's need for component tests from new model developers becomes more crucial. The community's ability to follow the basic premise of the Scientific Method requires independently repeatable experiments, and model innovators are in the best position to create these test fixtures. Scientific software developers also need to quickly judge the value of the new model, i.e., its cost-to-benefit ratio in terms of gains provided by the new model and implementation risks such as cost, time, and quality. This paper asks two questions. The first is whether other scientific software developers would find published component tests useful, and the second is whether model innovators think publishing test fixtures is a feasible approach.
Directory of Open Access Journals (Sweden)
Shixiong Lua
Full Text Available T46I is the second mutation on the hVAPB MSP domain which was recently identified from non-Brazilian kindred to cause a familial amyotrophic lateral sclerosis (ALS. Here using CD, NMR and molecular dynamics (MD simulations, we characterized the structure, stability, dynamics and binding capacity of the T46I-MSP domain. The results reveal: 1 unlike P56S which we previously showed to completely eliminate the native MSP structure, T46I leads to no significant disruption of the native secondary and tertiary structures, as evidenced from its far-UV CD spectrum, as well as Cα and Cβ NMR chemical shifts. 2 Nevertheless, T46I does result in a reduced thermodynamic stability and loss of the cooperative urea-unfolding transition. As such, the T46I-MSP domain is more prone to aggregation than WT at high protein concentrations and temperatures in vitro, which may become more severe in the crowded cellular environments. 3 T46I only causes a 3-fold affinity reduction to the Nir2 peptide, but a significant elimination of its binding to EphA4. 4 EphA4 and Nir2 peptide appear to have overlapped binding interfaces on the MSP domain, which strongly implies that two signaling networks may have a functional interplay in vivo. 5 As explored by both H/D exchange and MD simulations, the MSP domain is very dynamic, with most loop residues and many residues on secondary structures highly fluctuated or/and exposed to bulk solvent. Although T46I does not alter overall dynamics, it does trigger increased dynamics of several local regions of the MSP domain which are implicated in binding to EphA4 and Nir2 peptide. Our study provides the structural and dynamic understanding of the T46I-causing ALS; and strongly highlights the possibility that the interplay of two signaling networks mediated by the FFAT-containing proteins and Eph receptors may play a key role in ALS pathogenesis.
Sobieraj, M; Krzyśko, K A; Jarmuła, A; Kalinowski, M W; Lesyng, B; Prokopowicz, M; Cieśla, J; Gojdź, A; Kierdaszuk, B
2015-04-01
Predicting FRET pathways in proteins using computer simulation techniques is very important for reliable interpretation of experimental data. A novel and relatively simple methodology has been developed and applied to purine nucleoside phosphorylase (PNP) complexed with a fluorescent ligand - formycin A (FA). FRET occurs between an excited Tyr residue (D*) and FA (A). This study aims to interpret experimental data that, among others, suggests the absence of FRET for the PNPF159A mutant in complex with FA, based on novel theoretical methodology. MD simulations for the protein molecule containing D*, and complexed with A, are carried out. Interactions of D* with its molecular environment are accounted by including changes of the ESP charges in S1, compared to S0, and computed at the SCF-CI level. FRET probability W F depends on the inverse six-power of the D*-A distance, R da . The orientational factor 0 < k(2) < 4 between D* and A is computed and included in the analysis. Finally W F is time-averaged over the MD trajectories resulting in its mean value. The red-shift of the tyrosinate anion emission and thus lack of spectral overlap integral and thermal energy dissipation are the reasons for the FRET absence in the studied mutants at pH 7 and above. The presence of the tyrosinate anion results in a competitive energy dissipation channel and red-shifted emission, thus in consequence in the absence of FRET. These studies also indicate an important role of the phenyl ring of Phe159 for FRET in the wild-type PNP, which does not exist in the Ala159 mutant, and for the effective association of PNP with FA. In a more general context, our observations point out very interesting and biologically important properties of the tyrosine residue in its excited state, which may undergo spontaneous deprotonation in the biomolecular systems, resulting further in unexpected physical and/or biological phenomena. Until now, this observation has not been widely discussed in the
Benay, G; Wipff, G
2013-01-31
Bistriazinyl-phenantroline "BTPhen" ligands L display the remarkable feature to complex trivalent lanthanide and actinide ions, with a marked selectivity for the latter. We report on molecular dynamics studies of tetrasubstituted X(4)BTPhens: L(4+) (X = (+)Et(3)NCH(2)-), L(4-) (X = (-)SO(3)Ph-), and L(0) (X = CyMe(4)) and their complexes with Eu(III) in binary octanol/water solutions. Changes in free energies upon interface crossing are also calculated for typical solutes by potential of mean force PMF simulations. The ligands and their complexes partition, as expected, to either the aqueous or the oil phase, depending on the "solubilizing" group X. Furthermore, most of them are found to be surface active. The water-soluble L(4+) and L(4-) ligands and their (L)Eu(NO(3))(3) complexes adsorb at the aqueous side of the interface, more with L(4-) than with L(4+). The oil soluble ligand L(0) is not surface active in its endo-endo form but adsorbs on the oil side of the interface in its most polar endo-exo form, as well as in its protonated L(0)H(+) and complexed (L(0))Eu(NO(3))(3) states. Furthermore, comparing PMFs of the Eu(III) complexes with and without nitric acid shows that acidifying the aqueous phase has different effects, depending on the ligand charge. In particular, acid promotes the Eu(III) extraction by L(0) via the (L(0))(2)Eu(NO(3))(2+) complex, as observed experimentally. Overall, the results point to the importance of interfacial adsorption for the liquid-liquid extraction of trivalent lanthanide and actinide cations by BTPhens and analogues.
Yang, Guangjie; Zhang, Fangrong; Deng, Linfang; Chen, Chang; Cheng, Zhongzhe; Huang, Jiangeng; Liu, Jiangyun; Jiang, Hongliang
2016-09-01
Mucuna pruriens, an ancient Indian herbal medicine containing levodopa, is widely used for Parkinson's disease. In order to simultaneously determine levodopa and 1,1-dimethyl-3-carboxy-6,7-dihydroxy-1,2,3,4-tetrahydroisoquinoline (MD01) in rat plasma, an improved LC-MS/MS method was developed and validated for a pharmacokinetic study in rats orally administered levodopa or Mucuna pruriens extract (MPE). Elimination of matrix effect and improvement of extraction recovery were achieved through systematic optimization of reversed-phase and hydrophilic interaction chromatographic conditions together with sample clean-up procedures. A satisfactory chromatographic performance was obtained with a Thermo Aquasil C18 column (50 × 2.1 mm, 3 µm) using acetonitrile and water containing 0.2% formic acid as mobile phases. Futhermore, sodium metabisulfite and formic acid were used as stabilizers in neat solutions as well as rat plasma. The method was validated in a dynamic range of 20.0-10,000 ng/mL for levodopa and MD01; the intra- and inter-day precision and accuracy were acceptable. The method was successfully utilized to determine the levodopa level in plasma samples of rats administered levodopa or MPE. Pharmacokinetic results showed that an increase in the AUC of levodopa was observed in rats following oral administration of multiple doses of MPE. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.
Directory of Open Access Journals (Sweden)
Kaushikbhai C. Parmar
2017-04-01
Full Text Available Simulation gives different results when using different methods for the same simulation. Autodesk Moldflow Simulation software provide two different facilities for creating mold for the simulation of injection molding process. Mold can be created inside the Moldflow or it can be imported as CAD file. The aim of this paper is to study the difference in the simulation results like mold temperature part temperature deflection in different direction time for the simulation and coolant temperature for this two different methods.
International Nuclear Information System (INIS)
Hulet, E.K.; Wild, J.F.; Lougheed, R.W.; Baisden, P.A.; Landrum, J.H.; Dougan, R.J.; Mustafa, M.; Ghiorso, A.; Nitschke, J.M.
1979-01-01
The mass and kinetic energy distributions of fission fragments from the spontaneous fission of th newly discovered nuclide 259 Md were obtained. 259 Md was identified as the E. C. daughter of 259 No, and was found to decay entirely (> 95%) by spontaneous fission with a 95-min half-life. From the kinetic energies measured for 397 pairs of coincident fragments, a mass distribution was derived that is symmetric with sigma = 13 amu. 259 Md, together with 258 Fm and 259 Fm, form a select group of three nuclides whose mass division in spontaneous fission is highly symmetric. Unlike the total-kinetic-energy (TKE) distributions of 258 Fm and 259 Fm, which peak at approx. = to 240 MeV, this distribution for 259 Md is broad and is 50 MeV lower in energy. Analysis of the mass and energy distributions shows that events near mass symmetry also exhibit a broad TKE distribution, with one-third of the symmetric events having TKEs less than 200 MeV. The associated of low TKEs with symmetric mass division in the fission of very heavy actinides is anomalous and inconsistent with theories based upon the emergence of fragment shells near the scission point. Either three-body fragmentation or peculiar fragment shapes are assumed as the cause for the large consumption of Coulomb energy observed for a significant fraction of symmetric fissions in 259 Md. 6 figures
International Nuclear Information System (INIS)
Onodera, T; Tsuboi, H; Hatakeyama, N; Endou, A; Miyamoto, A; Miura, R; Takaba, H; Suzuki, A; Kubo, M
2010-01-01
Tribology at the atomistic and molecular levels has been theoretically studied by a classical molecular dynamics (MD) method. However, this method inherently cannot simulate the tribochemical reaction dynamics because it does not consider the electrons in nature. Although the first-principles based MD method has recently been used for understanding the chemical reaction dynamics of several molecules in the tribology field, the method cannot simulate the tribochemical reaction dynamics of a large complex system including solid surfaces and interfaces due to its huge computation costs. On the other hand, we have developed a quantum chemical MD tribochemical simulator on the basis of a hybrid tight-binding quantum chemical/classical MD method. In the simulator, the central part of the chemical reaction dynamics is calculated by the tight-binding quantum chemical MD method, and the remaining part is calculated by the classical MD method. Therefore, the developed tribochemical simulator realizes the study on tribochemical reaction dynamics of a large complex system, which cannot be treated by using the conventional classical MD or the first-principles MD methods. In this paper, we review our developed quantum chemical MD tribochemical simulator and its application to the tribochemical reaction dynamics of a few lubricant additives
Hybrid classical/quantum simulation for infrared spectroscopy of water
Maekawa, Yuki; Sasaoka, Kenji; Ube, Takuji; Ishiguro, Takashi; Yamamoto, Takahiro
2018-05-01
We have developed a hybrid classical/quantum simulation method to calculate the infrared (IR) spectrum of water. The proposed method achieves much higher accuracy than conventional classical molecular dynamics (MD) simulations at a much lower computational cost than ab initio MD simulations. The IR spectrum of water is obtained as an ensemble average of the eigenvalues of the dynamical matrix constructed by ab initio calculations, using the positions of oxygen atoms that constitute water molecules obtained from the classical MD simulation. The calculated IR spectrum is in excellent agreement with the experimental IR spectrum.
Numerical methods in simulation of resistance welding
DEFF Research Database (Denmark)
Nielsen, Chris Valentin; Martins, Paulo A.F.; Zhang, Wenqi
2015-01-01
Finite element simulation of resistance welding requires coupling betweenmechanical, thermal and electrical models. This paper presents the numerical models and theircouplings that are utilized in the computer program SORPAS. A mechanical model based onthe irreducible flow formulation is utilized...... a resistance welding point of view, the most essential coupling between the above mentioned models is the heat generation by electrical current due to Joule heating. The interaction between multiple objects is anothercritical feature of the numerical simulation of resistance welding because it influences...... thecontact area and the distribution of contact pressure. The numerical simulation of resistancewelding is illustrated by a spot welding example that includes subsequent tensile shear testing...
Virtual Crowds Methods, Simulation, and Control
Pelechano, Nuria; Allbeck, Jan
2008-01-01
There are many applications of computer animation and simulation where it is necessary to model virtual crowds of autonomous agents. Some of these applications include site planning, education, entertainment, training, and human factors analysis for building evacuation. Other applications include simulations of scenarios where masses of people gather, flow, and disperse, such as transportation centers, sporting events, and concerts. Most crowd simulations include only basic locomotive behaviors possibly coupled with a few stochastic actions. Our goal in this survey is to establish a baseline o
MD 2179: Scraping of oﬀ-momentum halo after injection
Garcia Morales, Hector; Patecki, Marcin; Wretborn, Sven Joel; CERN. Geneva. ATS Department
2018-01-01
In this MD, a beam scraping was performed using the momentum primary collimator in IR3 where dispersion is high. A second scraping was performed using a TCSG in IR7 where dispersion is almost negligible. In such a way, we aim to disentangle the contribution of oﬀ-momentum particles to halo population. These scrapings will provide useful information to better understand the usual oﬀ-momentum losses we see at the start of the ramp. The MD results would also be used to benchmark simulations of oﬀ-momentum beam losses in order to gain conﬁdence in simulation models.
Collaborative simulation method with spatiotemporal synchronization process control
Zou, Yisheng; Ding, Guofu; Zhang, Weihua; Zhang, Jian; Qin, Shengfeng; Tan, John Kian
2016-10-01
When designing a complex mechatronics system, such as high speed trains, it is relatively difficult to effectively simulate the entire system's dynamic behaviors because it involves multi-disciplinary subsystems. Currently,a most practical approach for multi-disciplinary simulation is interface based coupling simulation method, but it faces a twofold challenge: spatial and time unsynchronizations among multi-directional coupling simulation of subsystems. A new collaborative simulation method with spatiotemporal synchronization process control is proposed for coupling simulating a given complex mechatronics system across multiple subsystems on different platforms. The method consists of 1) a coupler-based coupling mechanisms to define the interfacing and interaction mechanisms among subsystems, and 2) a simulation process control algorithm to realize the coupling simulation in a spatiotemporal synchronized manner. The test results from a case study show that the proposed method 1) can certainly be used to simulate the sub-systems interactions under different simulation conditions in an engineering system, and 2) effectively supports multi-directional coupling simulation among multi-disciplinary subsystems. This method has been successfully applied in China high speed train design and development processes, demonstrating that it can be applied in a wide range of engineering systems design and simulation with improved efficiency and effectiveness.
Math-Based Simulation Tools and Methods
National Research Council Canada - National Science Library
Arepally, Sudhakar
2007-01-01
.... The following methods are reviewed: matrix operations, ordinary and partial differential system of equations, Lagrangian operations, Fourier transforms, Taylor Series, Finite Difference Methods, implicit and explicit finite element...
Connelly, Laura; Arce, Fernando Teran; Jang, Hyunbum; Capone, Ricardo; Kotler, Samuel A.; Ramachandran, Srinivasan; Kagan, Bruce L.; Nussinov, Ruth; Lal, Ratnesh
2012-01-01
Alzheimer’s disease (AD) is a protein misfolding disease characterized by a build-up of β-amyloid (Aβ) peptide as senile plaques, uncontrolled neurodegeneration, and memory loss. AD pathology is linked to the destabilization of cellular ionic homeostasis and involves Aβ peptide-plasma membrane interactions. In principle, there are two possible ways through which disturbance of the ionic homeostasis can take place: directly, where the Aβ peptide either inserts into the membrane and creates ion-conductive pores or destabilizes the membrane organization; or, indirectly, where the Aβ peptide interacts with existing cell membrane receptors. To distinguish between these two possible types of Aβ-membrane interactions, we took advantage of the biochemical tenet that ligand-receptor interactions are stereospecific; L-amino acid peptides, but not their D-counterparts, bind to cell membrane receptors. However, with respect to the ion channel-mediated mechanism, like L-amino acids, D-amino acid peptides will also form ion channel-like structures. Using atomic force microscopy (AFM) we imaged the structures of both D- and L-enantiomers of the full length Aβ1-42 when reconstituted in lipid bilayers. AFM imaging shows that both L- and D-Aβ isomers form similar channel-like structures. Molecular dynamics (MD) simulations support the AFM imaged 3D structures. Earlier we have shown that D-Aβ1-42 channels conduct ions similarly to their L-counter parts. Taken together, our results support the direct mechanism of Aβ ion channel-mediated destabilization of ionic homeostasis rather than the indirect mechanism through Aβ interaction with membrane receptors. PMID:22217000
A method for ensemble wildland fire simulation
Mark A. Finney; Isaac C. Grenfell; Charles W. McHugh; Robert C. Seli; Diane Trethewey; Richard D. Stratton; Stuart Brittain
2011-01-01
An ensemble simulation system that accounts for uncertainty in long-range weather conditions and two-dimensional wildland fire spread is described. Fuel moisture is expressed based on the energy release component, a US fire danger rating index, and its variation throughout the fire season is modeled using time series analysis of historical weather data. This analysis...
Synergistic Applications of MD and NMR for the Study of Biological Systems
Directory of Open Access Journals (Sweden)
Olivier Fisette
2012-01-01
same time, theoretical and computational approaches gain in reliability and their field of application widens. In this short paper, we discuss recent advances in the areas of solution nuclear magnetic resonance (NMR spectroscopy and molecular dynamics (MD simulations that were made possible by the combination of both methods, that is, through their synergistic use. We present the main NMR observables and parameters that can be computed from simulations, and how they are used in a variety of complementary applications, including dynamics studies, model-free analysis, force field validation, and structural studies.
Directory of Open Access Journals (Sweden)
Abbas Doulani
2010-03-01
Full Text Available The present study seeks to examine the status of research methods employed in dissertations submitted by graduates of Tabriz University of Medical Sciences. The study also examined the impact factors. Using content analysis, the research methods were divided into four groups: historical, descriptive, empirical and literature review. The distributions for each method were calculated on the basis of gender, graduate level, citations, time frame and fields of study. Samples were chosen randomly from among the dissertations available at faculty libraries at TUMS. 390 dissertations were selected. Findings demonstrated that gender did not influence the choice of research method. With exception of Nursing faculty, graduate level proved to be an prominent factor when choosing research method. All types of citations (books, journals, online and non-printed sources were identified as another significant factor impacting pushing towards any given research method. With exception of Hygiene and Food Faculty, the time factor affected the research method selection process as well. Finally, given their different research characteristics, the field of studies investigated also contributed to both the scope and direction of research methods chosen.
Interactive methods for exploring particle simulation data
Energy Technology Data Exchange (ETDEWEB)
Co, Christopher S.; Friedman, Alex; Grote, David P.; Vay, Jean-Luc; Bethel, E. Wes; Joy, Kenneth I.
2004-05-01
In this work, we visualize high-dimensional particle simulation data using a suite of scatter plot-based visualizations coupled with interactive selection tools. We use traditional 2D and 3D projection scatter plots as well as a novel oriented disk rendering style to convey various information about the data. Interactive selection tools allow physicists to manually classify ''interesting'' sets of particles that are highlighted across multiple, linked views of the data. The power of our application is the ability to correspond new visual representations of the simulation data with traditional, well understood visualizations. This approach supports the interactive exploration of the high-dimensional space while promoting discovery of new particle behavior.
Hospital Registration Process Reengineering Using Simulation Method
Directory of Open Access Journals (Sweden)
Qiang Su
2010-01-01
Full Text Available With increasing competition, many healthcare organizations have undergone tremendous reform in the last decade aiming to increase efficiency, decrease waste, and reshape the way that care is delivered. This study focuses on the operational efficiency improvement of hospital’s registration process. The operational efficiency related factors including the service process, queue strategy, and queue parameters were explored systematically and illustrated with a case study. Guided by the principle of business process reengineering (BPR, a simulation approach was employed for process redesign and performance optimization. As a result, the queue strategy is changed from multiple queues and multiple servers to single queue and multiple servers with a prepare queue. Furthermore, through a series of simulation experiments, the length of the prepare queue and the corresponding registration process efficiency was quantitatively evaluated and optimized.
Numerical simulation methods for electron and ion optics
International Nuclear Information System (INIS)
Munro, Eric
2011-01-01
This paper summarizes currently used techniques for simulation and computer-aided design in electron and ion beam optics. Topics covered include: field computation, methods for computing optical properties (including Paraxial Rays and Aberration Integrals, Differential Algebra and Direct Ray Tracing), simulation of Coulomb interactions, space charge effects in electron and ion sources, tolerancing, wave optical simulations and optimization. Simulation examples are presented for multipole aberration correctors, Wien filter monochromators, imaging energy filters, magnetic prisms, general curved axis systems and electron mirrors.
Benchmarking HRA methods against different NPP simulator data
International Nuclear Information System (INIS)
Petkov, Gueorgui; Filipov, Kalin; Velev, Vladimir; Grigorov, Alexander; Popov, Dimiter; Lazarov, Lazar; Stoichev, Kosta
2008-01-01
The paper presents both international and Bulgarian experience in assessing HRA methods, underlying models approaches for their validation and verification by benchmarking HRA methods against different NPP simulator data. The organization, status, methodology and outlooks of the studies are described
Math-Based Simulation Tools and Methods
National Research Council Canada - National Science Library
Arepally, Sudhakar
2007-01-01
...: HMMWV 30-mph Rollover Test, Soldier Gear Effects, Occupant Performance in Blast Effects, Anthropomorphic Test Device, Human Models, Rigid Body Modeling, Finite Element Methods, Injury Criteria...
Particle-transport simulation with the Monte Carlo method
International Nuclear Information System (INIS)
Carter, L.L.; Cashwell, E.D.
1975-01-01
Attention is focused on the application of the Monte Carlo method to particle transport problems, with emphasis on neutron and photon transport. Topics covered include sampling methods, mathematical prescriptions for simulating particle transport, mechanics of simulating particle transport, neutron transport, and photon transport. A literature survey of 204 references is included. (GMT)
Real-time hybrid simulation using the convolution integral method
International Nuclear Information System (INIS)
Kim, Sung Jig; Christenson, Richard E; Wojtkiewicz, Steven F; Johnson, Erik A
2011-01-01
This paper proposes a real-time hybrid simulation method that will allow complex systems to be tested within the hybrid test framework by employing the convolution integral (CI) method. The proposed CI method is potentially transformative for real-time hybrid simulation. The CI method can allow real-time hybrid simulation to be conducted regardless of the size and complexity of the numerical model and for numerical stability to be ensured in the presence of high frequency responses in the simulation. This paper presents the general theory behind the proposed CI method and provides experimental verification of the proposed method by comparing the CI method to the current integration time-stepping (ITS) method. Real-time hybrid simulation is conducted in the Advanced Hazard Mitigation Laboratory at the University of Connecticut. A seismically excited two-story shear frame building with a magneto-rheological (MR) fluid damper is selected as the test structure to experimentally validate the proposed method. The building structure is numerically modeled and simulated, while the MR damper is physically tested. Real-time hybrid simulation using the proposed CI method is shown to provide accurate results
Simulation of tunneling construction methods of the Cisumdawu toll road
Abduh, Muhamad; Sukardi, Sapto Nugroho; Ola, Muhammad Rusdian La; Ariesty, Anita; Wirahadikusumah, Reini D.
2017-11-01
Simulation can be used as a tool for planning and analysis of a construction method. Using simulation technique, a contractor could design optimally resources associated with a construction method and compare to other methods based on several criteria, such as productivity, waste, and cost. This paper discusses the use of simulation using Norwegian Method of Tunneling (NMT) for a 472-meter tunneling work in the Cisumdawu Toll Road project. Primary and secondary data were collected to provide useful information for simulation as well as problems that may be faced by the contractor. The method was modelled using the CYCLONE and then simulated using the WebCYCLONE. The simulation could show the duration of the project from the duration model of each work tasks which based on literature review, machine productivity, and several assumptions. The results of simulation could also show the total cost of the project that was modeled based on journal construction & building unit cost and online websites of local and international suppliers. The analysis of the advantages and disadvantages of the method was conducted based on its, wastes, and cost. The simulation concluded the total cost of this operation is about Rp. 900,437,004,599 and the total duration of the tunneling operation is 653 days. The results of the simulation will be used for a recommendation to the contractor before the implementation of the already selected tunneling operation.
Interval sampling methods and measurement error: a computer simulation.
Wirth, Oliver; Slaven, James; Taylor, Matthew A
2014-01-01
A simulation study was conducted to provide a more thorough account of measurement error associated with interval sampling methods. A computer program simulated the application of momentary time sampling, partial-interval recording, and whole-interval recording methods on target events randomly distributed across an observation period. The simulation yielded measures of error for multiple combinations of observation period, interval duration, event duration, and cumulative event duration. The simulations were conducted up to 100 times to yield measures of error variability. Although the present simulation confirmed some previously reported characteristics of interval sampling methods, it also revealed many new findings that pertain to each method's inherent strengths and weaknesses. The analysis and resulting error tables can help guide the selection of the most appropriate sampling method for observation-based behavioral assessments. © Society for the Experimental Analysis of Behavior.
Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding.
Directory of Open Access Journals (Sweden)
Aruna Rajan
2010-04-01
Full Text Available Recent advances in computing technology have enabled microsecond long all-atom molecular dynamics (MD simulations of biological systems. Methods that can distill the salient features of such large trajectories are now urgently needed. Conventional clustering methods used to analyze MD trajectories suffer from various setbacks, namely (i they are not data driven, (ii they are unstable to noise and changes in cut-off parameters such as cluster radius and cluster number, and (iii they do not reduce the dimensionality of the trajectories, and hence are unsuitable for finding collective coordinates. We advocate the application of principal component analysis (PCA and a non-metric multidimensional scaling (nMDS method to reduce MD trajectories and overcome the drawbacks of clustering. To illustrate the superiority of nMDS over other methods in reducing data and reproducing salient features, we analyze three complete villin headpiece folding trajectories. Our analysis suggests that the folding process of the villin headpiece is structurally heterogeneous.
The frontal method in hydrodynamics simulations
Walters, R.A.
1980-01-01
The frontal solution method has proven to be an effective means of solving the matrix equations resulting from the application of the finite element method to a variety of problems. In this study, several versions of the frontal method were compared in efficiency for several hydrodynamics problems. Three basic modifications were shown to be of value: 1. Elimination of equations with boundary conditions beforehand, 2. Modification of the pivoting procedures to allow dynamic management of the equation size, and 3. Storage of the eliminated equations in a vector. These modifications are sufficiently general to be applied to other classes of problems. ?? 1980.
Multiple time-scale methods in particle simulations of plasmas
International Nuclear Information System (INIS)
Cohen, B.I.
1985-01-01
This paper surveys recent advances in the application of multiple time-scale methods to particle simulation of collective phenomena in plasmas. These methods dramatically improve the efficiency of simulating low-frequency kinetic behavior by allowing the use of a large timestep, while retaining accuracy. The numerical schemes surveyed provide selective damping of unwanted high-frequency waves and preserve numerical stability in a variety of physics models: electrostatic, magneto-inductive, Darwin and fully electromagnetic. The paper reviews hybrid simulation models, the implicitmoment-equation method, the direct implicit method, orbit averaging, and subcycling
Natural tracer test simulation by stochastic particle tracking method
International Nuclear Information System (INIS)
Ackerer, P.; Mose, R.; Semra, K.
1990-01-01
Stochastic particle tracking methods are well adapted to 3D transport simulations where discretization requirements of other methods usually cannot be satisfied. They do need a very accurate approximation of the velocity field. The described code is based on the mixed hybrid finite element method (MHFEM) to calculated the piezometric and velocity field. The random-walk method is used to simulate mass transport. The main advantages of the MHFEM over FD or FE are the simultaneous calculation of pressure and velocity, which are considered as unknowns; the possibility of interpolating velocities everywhere; and the continuity of the normal component of the velocity vector from one element to another. For these reasons, the MHFEM is well adapted for particle tracking methods. After a general description of the numerical methods, the model is used to simulate the observations made during the Twin Lake Tracer Test in 1983. A good match is found between observed and simulated heads and concentrations. (Author) (12 refs., 4 figs.)
Factorization method for simulating QCD at finite density
International Nuclear Information System (INIS)
Nishimura, Jun
2003-01-01
We propose a new method for simulating QCD at finite density. The method is based on a general factorization property of distribution functions of observables, and it is therefore applicable to any system with a complex action. The so-called overlap problem is completely eliminated by the use of constrained simulations. We test this method in a Random Matrix Theory for finite density QCD, where we are able to reproduce the exact results for the quark number density. (author)
Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins
Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru
2014-03-01
A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.
Evaluation of full-scope simulator testing methods
Energy Technology Data Exchange (ETDEWEB)
Feher, M P; Moray, N; Senders, J W; Biron, K [Human Factors North Inc., Toronto, ON (Canada)
1995-03-01
This report discusses the use of full scope nuclear power plant simulators in licensing examinations for Unit First Operators of CANDU reactors. The existing literature is reviewed, and an annotated bibliography of the more important sources provided. Since existing methods are judged inadequate, conceptual bases for designing a system for licensing are discussed, and a method proposed which would make use of objective scoring methods based on data collection in full-scope simulators. A field trial of such a method is described. The practicality of such a method is critically discussed and possible advantages of subjective methods of evaluation considered. (author). 32 refs., 1 tab., 4 figs.
Evaluation of full-scope simulator testing methods
International Nuclear Information System (INIS)
Feher, M.P.; Moray, N.; Senders, J.W.; Biron, K.
1995-03-01
This report discusses the use of full scope nuclear power plant simulators in licensing examinations for Unit First Operators of CANDU reactors. The existing literature is reviewed, and an annotated bibliography of the more important sources provided. Since existing methods are judged inadequate, conceptual bases for designing a system for licensing are discussed, and a method proposed which would make use of objective scoring methods based on data collection in full-scope simulators. A field trial of such a method is described. The practicality of such a method is critically discussed and possible advantages of subjective methods of evaluation considered. (author). 32 refs., 1 tab., 4 figs
Sidler, Dominik; Schwaninger, Arthur; Riniker, Sereina
2016-10-21
In molecular dynamics (MD) simulations, free-energy differences are often calculated using free energy perturbation or thermodynamic integration (TI) methods. However, both techniques are only suited to calculate free-energy differences between two end states. Enveloping distribution sampling (EDS) presents an attractive alternative that allows to calculate multiple free-energy differences in a single simulation. In EDS, a reference state is simulated which "envelopes" the end states. The challenge of this methodology is the determination of optimal reference-state parameters to ensure equal sampling of all end states. Currently, the automatic determination of the reference-state parameters for multiple end states is an unsolved issue that limits the application of the methodology. To resolve this, we have generalised the replica-exchange EDS (RE-EDS) approach, introduced by Lee et al. [J. Chem. Theory Comput. 10, 2738 (2014)] for constant-pH MD simulations. By exchanging configurations between replicas with different reference-state parameters, the complexity of the parameter-choice problem can be substantially reduced. A new robust scheme to estimate the reference-state parameters from a short initial RE-EDS simulation with default parameters was developed, which allowed the calculation of 36 free-energy differences between nine small-molecule inhibitors of phenylethanolamine N-methyltransferase from a single simulation. The resulting free-energy differences were in excellent agreement with values obtained previously by TI and two-state EDS simulations.
Constraint methods that accelerate free-energy simulations of biomolecules.
Perez, Alberto; MacCallum, Justin L; Coutsias, Evangelos A; Dill, Ken A
2015-12-28
Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann's law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.
International Nuclear Information System (INIS)
Ishimoto, Takayoshi; Koyama, Michihisa
2012-01-01
Graphical abstract: Molecular dynamics method based on multi-component molecular orbital method was applied to basic hydrogen bonding systems, H 5 O 2 + , and its isotopomers (D 5 O 2 + andT 5 O 2 + ). Highlights: ► Molecular dynamics method with nuclear quantum effect was developed. ► Multi-component molecular orbital method was used as ab initio MO calculation. ► Developed method applied to basic hydrogen bonding system, H 5 O 2 + , and isotopomers. ► O ⋯ O vibrational stretching reflected to the distribution of protonic wavefunctions. ► H/D/T isotope effect was also analyzed. - Abstract: We propose a molecular dynamics (MD) method based on the multi-component molecular orbital (MC M O) method, which takes into account the quantum effect of proton directly, for the detailed analyses of proton transfer in hydrogen bonding system. The MC M O based MD (MC M O-MD) method is applied to the basic structures, H 5 O 2 + (called “Zundel ion”), and its isotopomers (D 5 O 2 + andT 5 O 2 + ). We clearly demonstrate the geometrical difference of hydrogen bonded O ⋯ O distance induced by H/D/T isotope effect because the O ⋯ O in H-compound was longer than that in D- or T-compound. We also find the strong relation between stretching vibration of O ⋯ O and the distribution of hydrogen bonded protonic wavefunction because the protonic wavefunction tends to delocalize when the O ⋯ O distance becomes short during the dynamics. Our proposed MC M O-MD simulation is expected as a powerful tool to analyze the proton dynamics in hydrogen bonding systems.
New method of fast simulation for a hadron calorimeter response
International Nuclear Information System (INIS)
Kul'chitskij, Yu.; Sutiak, J.; Tokar, S.; Zenis, T.
2003-01-01
In this work we present the new method of a fast Monte-Carlo simulation of a hadron calorimeter response. It is based on the three-dimensional parameterization of the hadronic shower obtained from the ATLAS TILECAL test beam data and GEANT simulations. A new approach of including the longitudinal fluctuations of hadronic shower is described. The obtained results of the fast simulation are in good agreement with the TILECAL experimental data
Daylighting simulation: methods, algorithms, and resources
Energy Technology Data Exchange (ETDEWEB)
Carroll, William L.
1999-12-01
This document presents work conducted as part of Subtask C, ''Daylighting Design Tools'', Subgroup C2, ''New Daylight Algorithms'', of the IEA SHC Task 21 and the ECBCS Program Annex 29 ''Daylight in Buildings''. The search for and collection of daylighting analysis methods and algorithms led to two important observations. First, there is a wide range of needs for different types of methods to produce a complete analysis tool. These include: Geometry; Light modeling; Characterization of the natural illumination resource; Materials and components properties, representations; and Usability issues (interfaces, interoperability, representation of analysis results, etc). Second, very advantageously, there have been rapid advances in many basic methods in these areas, due to other forces. They are in part driven by: The commercial computer graphics community (commerce, entertainment); The lighting industry; Architectural rendering and visualization for projects; and Academia: Course materials, research. This has led to a very rich set of information resources that have direct applicability to the small daylighting analysis community. Furthermore, much of this information is in fact available online. Because much of the information about methods and algorithms is now online, an innovative reporting strategy was used: the core formats are electronic, and used to produce a printed form only secondarily. The electronic forms include both online WWW pages and a downloadable .PDF file with the same appearance and content. Both electronic forms include live primary and indirect links to actual information sources on the WWW. In most cases, little additional commentary is provided regarding the information links or citations that are provided. This in turn allows the report to be very concise. The links are expected speak for themselves. The report consists of only about 10+ pages, with about 100+ primary links, but
A particle-based method for granular flow simulation
Chang, Yuanzhang; Bao, Kai; Zhu, Jian; Wu, Enhua
2012-01-01
We present a new particle-based method for granular flow simulation. In the method, a new elastic stress term, which is derived from a modified form of the Hooke's law, is included in the momentum governing equation to handle the friction of granular materials. Viscosity force is also added to simulate the dynamic friction for the purpose of smoothing the velocity field and further maintaining the simulation stability. Benefiting from the Lagrangian nature of the SPH method, large flow deformation can be well handled easily and naturally. In addition, a signed distance field is also employed to enforce the solid boundary condition. The experimental results show that the proposed method is effective and efficient for handling the flow of granular materials, and different kinds of granular behaviors can be well simulated by adjusting just one parameter. © 2012 Science China Press and Springer-Verlag Berlin Heidelberg.
Research on Monte Carlo simulation method of industry CT system
International Nuclear Information System (INIS)
Li Junli; Zeng Zhi; Qui Rui; Wu Zhen; Li Chunyan
2010-01-01
There are a series of radiation physical problems in the design and production of industry CT system (ICTS), including limit quality index analysis; the effect of scattering, efficiency of detectors and crosstalk to the system. Usually the Monte Carlo (MC) Method is applied to resolve these problems. Most of them are of little probability, so direct simulation is very difficult, and existing MC methods and programs can't meet the needs. To resolve these difficulties, particle flux point auto-important sampling (PFPAIS) is given on the basis of auto-important sampling. Then, on the basis of PFPAIS, a particular ICTS simulation method: MCCT is realized. Compared with existing MC methods, MCCT is proved to be able to simulate the ICTS more exactly and effectively. Furthermore, the effects of all kinds of disturbances of ICTS are simulated and analyzed by MCCT. To some extent, MCCT can guide the research of the radiation physical problems in ICTS. (author)
A simple method for potential flow simulation of cascades
Indian Academy of Sciences (India)
vortex panel method to simulate potential flow in cascades is presented. The cascade ... The fluid loading on the blades, such as the normal force and pitching moment, may ... of such discrete infinite array singularities along the blade surface.
A particle-based method for granular flow simulation
Chang, Yuanzhang
2012-03-16
We present a new particle-based method for granular flow simulation. In the method, a new elastic stress term, which is derived from a modified form of the Hooke\\'s law, is included in the momentum governing equation to handle the friction of granular materials. Viscosity force is also added to simulate the dynamic friction for the purpose of smoothing the velocity field and further maintaining the simulation stability. Benefiting from the Lagrangian nature of the SPH method, large flow deformation can be well handled easily and naturally. In addition, a signed distance field is also employed to enforce the solid boundary condition. The experimental results show that the proposed method is effective and efficient for handling the flow of granular materials, and different kinds of granular behaviors can be well simulated by adjusting just one parameter. © 2012 Science China Press and Springer-Verlag Berlin Heidelberg.
Comparing three methods for participatory simulation of hospital work systems
DEFF Research Database (Denmark)
Broberg, Ole; Andersen, Simone Nyholm
Summative Statement: This study compared three participatory simulation methods using different simulation objects: Low resolution table-top setup using Lego figures, full scale mock-ups, and blueprints using Lego figures. It was concluded the three objects by differences in fidelity and affordance...... scenarios using the objects. Results: Full scale mock-ups significantly addressed the local space and technology/tool elements of a work system. In contrast, the table-top simulation object addressed the organizational issues of the future work system. The blueprint based simulation addressed...
Forest canopy BRDF simulation using Monte Carlo method
Huang, J.; Wu, B.; Zeng, Y.; Tian, Y.
2006-01-01
Monte Carlo method is a random statistic method, which has been widely used to simulate the Bidirectional Reflectance Distribution Function (BRDF) of vegetation canopy in the field of visible remote sensing. The random process between photons and forest canopy was designed using Monte Carlo method.
Simulation methods of nuclear electromagnetic pulse effects in integrated circuits
International Nuclear Information System (INIS)
Cheng Jili; Liu Yuan; En Yunfei; Fang Wenxiao; Wei Aixiang; Yang Yuanzhen
2013-01-01
In the paper the ways to compute the response of transmission line (TL) illuminated by electromagnetic pulse (EMP) were introduced firstly, which include finite-difference time-domain (FDTD) and trans-mission line matrix (TLM); then the feasibility of electromagnetic topology (EMT) in ICs nuclear electromagnetic pulse (NEMP) effect simulation was discussed; in the end, combined with the methods computing the response of TL, a new method of simulate the transmission line in IC illuminated by NEMP was put forward. (authors)
An introduction to computer simulation methods applications to physical systems
Gould, Harvey; Christian, Wolfgang
2007-01-01
Now in its third edition, this book teaches physical concepts using computer simulations. The text incorporates object-oriented programming techniques and encourages readers to develop good programming habits in the context of doing physics. Designed for readers at all levels , An Introduction to Computer Simulation Methods uses Java, currently the most popular programming language. Introduction, Tools for Doing Simulations, Simulating Particle Motion, Oscillatory Systems, Few-Body Problems: The Motion of the Planets, The Chaotic Motion of Dynamical Systems, Random Processes, The Dynamics of Many Particle Systems, Normal Modes and Waves, Electrodynamics, Numerical and Monte Carlo Methods, Percolation, Fractals and Kinetic Growth Models, Complex Systems, Monte Carlo Simulations of Thermal Systems, Quantum Systems, Visualization and Rigid Body Dynamics, Seeing in Special and General Relativity, Epilogue: The Unity of Physics For all readers interested in developing programming habits in the context of doing phy...
Motion simulation of hydraulic driven safety rod using FSI method
International Nuclear Information System (INIS)
Jung, Jaeho; Kim, Sanghaun; Yoo, Yeonsik; Cho, Yeonggarp; Kim, Jong In
2013-01-01
Hydraulic driven safety rod which is one of them is being developed by Division for Reactor Mechanical Engineering, KAERI. In this paper the motion of this rod is simulated by fluid structure interaction (FSI) method before manufacturing for design verification and pump sizing. A newly designed hydraulic driven safety rod which is one of reactivity control mechanism is simulated using FSI method for design verification and pump sizing. The simulation is done in CFD domain with UDF. The pressure drop is changed slightly by flow rates. It means that the pressure drop is mainly determined by weight of moving part. The simulated velocity of piston is linearly proportional to flow rates so the pump can be sized easily according to the rising and drop time requirement of the safety rod using the simulation results
Cavity Voltage Phase Modulation MD
Mastoridis, Themistoklis; Molendijk, John; Timko, Helga; CERN. Geneva. ATS Department
2016-01-01
The LHC RF/LLRF system is currently configured for extremely stable RF voltage to minimize transient beam loading effects. The present scheme cannot be extended beyond nominal beam current since the demanded power would exceed the peak klystron power and lead to saturation. A new scheme has therefore been proposed: for beam currents above nominal (and possibly earlier), the cavity phase modulation by the beam will not be corrected (transient beam loading), but the strong RF feedback and One-Turn Delay feedback will still be active for loop and beam stability in physics. To achieve this, the voltage set point will be adapted for each bunch. The goal of this MD was to test a new algorithm that would adjust the voltage set point to achieve the cavity phase modulation that would minimize klystron forward power.
A simulation method for lightning surge response of switching power
International Nuclear Information System (INIS)
Wei, Ming; Chen, Xiang
2013-01-01
In order to meet the need of protection design for lighting surge, a prediction method of lightning electromagnetic pulse (LEMP) response which is based on system identification is presented. Experiments of switching power's surge injection were conducted, and the input and output data were sampled, de-noised and de-trended. In addition, the model of energy coupling transfer function was obtained by system identification method. Simulation results show that the system identification method can predict the surge response of linear circuit well. The method proposed in the paper provided a convenient and effective technology for simulation of lightning effect.
Real time simulation method for fast breeder reactors dynamics
International Nuclear Information System (INIS)
Miki, Tetsushi; Mineo, Yoshiyuki; Ogino, Takamichi; Kishida, Koji; Furuichi, Kenji.
1985-01-01
The development of multi-purpose real time simulator models with suitable plant dynamics was made; these models can be used not only in training operators but also in designing control systems, operation sequences and many other items which must be studied for the development of new type reactors. The prototype fast breeder reactor ''Monju'' is taken as an example. Analysis is made on various factors affecting the accuracy and computer load of its dynamic simulation. A method is presented which determines the optimum number of nodes in distributed systems and time steps. The oscillations due to the numerical instability are observed in the dynamic simulation of evaporators with a small number of nodes, and a method to cancel these oscillations is proposed. It has been verified through the development of plant dynamics simulation codes that these methods can provide efficient real time dynamics models of fast breeder reactors. (author)
Simulation of plume dynamics by the Lattice Boltzmann Method
Mora, Peter; Yuen, David A.
2017-09-01
The Lattice Boltzmann Method (LBM) is a semi-microscopic method to simulate fluid mechanics by modelling distributions of particles moving and colliding on a lattice. We present 2-D simulations using the LBM of a fluid in a rectangular box being heated from below, and cooled from above, with a Rayleigh of Ra = 108, similar to current estimates of the Earth's mantle, and a Prandtl number of 5000. At this Prandtl number, the flow is found to be in the non-inertial regime where the inertial terms denoted I ≪ 1. Hence, the simulations presented lie within the regime of relevance for geodynamical problems. We obtain narrow upwelling plumes with mushroom heads and chutes of downwelling fluid as expected of a flow in the non-inertial regime. The method developed demonstrates that the LBM has great potential for simulating thermal convection and plume dynamics relevant to geodynamics, albeit with some limitations.
Method of simulating dose reduction for digital radiographic systems
International Nuclear Information System (INIS)
Baath, M.; Haakansson, M.; Tingberg, A.; Maansson, L. G.
2005-01-01
The optimisation of image quality vs. radiation dose is an important task in medical imaging. To obtain maximum validity of the optimisation, it must be based on clinical images. Images at different dose levels can then either be obtained by collecting patient images at the different dose levels sought to investigate - including additional exposures and permission from an ethical committee - or by manipulating images to simulate different dose levels. The aim of the present work was to develop a method of simulating dose reduction for digital radiographic systems. The method uses information about the detective quantum efficiency and noise power spectrum at the original and simulated dose levels to create an image containing filtered noise. When added to the original image this results in an image with noise which, in terms of frequency content, agrees with the noise present in an image collected at the simulated dose level. To increase the validity, the method takes local dose variations in the original image into account. The method was tested on a computed radiography system and was shown to produce images with noise behaviour similar to that of images actually collected at the simulated dose levels. The method can, therefore, be used to modify an image collected at one dose level so that it simulates an image of the same object collected at any lower dose level. (authors)
A tool for simulating parallel branch-and-bound methods
Golubeva, Yana; Orlov, Yury; Posypkin, Mikhail
2016-01-01
The Branch-and-Bound method is known as one of the most powerful but very resource consuming global optimization methods. Parallel and distributed computing can efficiently cope with this issue. The major difficulty in parallel B&B method is the need for dynamic load redistribution. Therefore design and study of load balancing algorithms is a separate and very important research topic. This paper presents a tool for simulating parallel Branchand-Bound method. The simulator allows one to run load balancing algorithms with various numbers of processors, sizes of the search tree, the characteristics of the supercomputer's interconnect thereby fostering deep study of load distribution strategies. The process of resolution of the optimization problem by B&B method is replaced by a stochastic branching process. Data exchanges are modeled using the concept of logical time. The user friendly graphical interface to the simulator provides efficient visualization and convenient performance analysis.
A tool for simulating parallel branch-and-bound methods
Directory of Open Access Journals (Sweden)
Golubeva Yana
2016-01-01
Full Text Available The Branch-and-Bound method is known as one of the most powerful but very resource consuming global optimization methods. Parallel and distributed computing can efficiently cope with this issue. The major difficulty in parallel B&B method is the need for dynamic load redistribution. Therefore design and study of load balancing algorithms is a separate and very important research topic. This paper presents a tool for simulating parallel Branchand-Bound method. The simulator allows one to run load balancing algorithms with various numbers of processors, sizes of the search tree, the characteristics of the supercomputer’s interconnect thereby fostering deep study of load distribution strategies. The process of resolution of the optimization problem by B&B method is replaced by a stochastic branching process. Data exchanges are modeled using the concept of logical time. The user friendly graphical interface to the simulator provides efficient visualization and convenient performance analysis.
Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.
Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao
2018-02-01
Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Published by Elsevier Ltd.
Ghaffour, Noreddine
2016-09-01
An integrated forward osmosis-membrane distillation (FO-MD) module and systems and methods incorporating the module is disclosed providing higher efficiencies and using less energy. The FO-MD module is osmotically and thermally isolated. The isolation can prevent mixing of FO draw solution/FO permeate and MD feed, and minimize dilution of FO draw solution and cooling of MD feed. The module provides MD feed solution and FO draw solution streams that flow in the same module but are separated by an isolation barrier. The osmotically and thermally isolated FO-MD integrated module, systems and methods offer higher driving forces of both FO and MD processes, higher recovery, and wider application than previously proposed hybrid FO- MD systems.
Ghaffour, NorEddine; Francis, Lijo; Li, Zhenyu; Valladares, Rodrigo; Alsaadi, Ahmad S.; Ghdaib, Muhannad Abu; Amy, Gary L.
2016-01-01
An integrated forward osmosis-membrane distillation (FO-MD) module and systems and methods incorporating the module is disclosed providing higher efficiencies and using less energy. The FO-MD module is osmotically and thermally isolated. The isolation can prevent mixing of FO draw solution/FO permeate and MD feed, and minimize dilution of FO draw solution and cooling of MD feed. The module provides MD feed solution and FO draw solution streams that flow in the same module but are separated by an isolation barrier. The osmotically and thermally isolated FO-MD integrated module, systems and methods offer higher driving forces of both FO and MD processes, higher recovery, and wider application than previously proposed hybrid FO- MD systems.
Plasma simulations using the Car-Parrinello method
International Nuclear Information System (INIS)
Clerouin, J.; Zerah, G.; Benisti, D.; Hansen, J.P.
1990-01-01
A simplified version of the Car-Parrinello method, based on the Thomas-Fermi (local density) functional for the electrons, is adapted to the simulation of the ionic dynamics in dense plasmas. The method is illustrated by an explicit application to a degenerate one-dimensional hydrogen plasma
Nonequilibrium relaxation method – An alternative simulation strategy
Indian Academy of Sciences (India)
One well-established simulation strategy to study the thermal phases and transitions of a given microscopic model system is the so-called equilibrium method, in which one first realizes the equilibrium ensemble of a finite system and then extrapolates the results to infinite system. This equilibrium method traces over the ...
A direct simulation method for flows with suspended paramagnetic particles
Kang, T.G.; Hulsen, M.A.; Toonder, den J.M.J.; Anderson, P.D.; Meijer, H.E.H.
2008-01-01
A direct numerical simulation method based on the Maxwell stress tensor and a fictitious domain method has been developed to solve flows with suspended paramagnetic particles. The numerical scheme enables us to take into account both hydrodynamic and magnetic interactions between particles in a
DRK methods for time-domain oscillator simulation
Sevat, M.F.; Houben, S.H.M.J.; Maten, ter E.J.W.; Di Bucchianico, A.; Mattheij, R.M.M.; Peletier, M.A.
2006-01-01
This paper presents a new Runge-Kutta type integration method that is well-suited for time-domain simulation of oscillators. A unique property of the new method is that its damping characteristics can be controlled by a continuous parameter.
The afforestation problem: a heuristic method based on simulated annealing
DEFF Research Database (Denmark)
Vidal, Rene Victor Valqui
1992-01-01
This paper presents the afforestation problem, that is the location and design of new forest compartments to be planted in a given area. This optimization problem is solved by a two-step heuristic method based on simulated annealing. Tests and experiences with this method are also presented....
Multilevel panel method for wind turbine rotor flow simulations
van Garrel, Arne
2016-01-01
Simulation methods of wind turbine aerodynamics currently in use mainly fall into two categories: the first is the group of traditional low-fidelity engineering models and the second is the group of computationally expensive CFD methods based on the Navier-Stokes equations. For an engineering
LOMEGA: a low frequency, field implicit method for plasma simulation
International Nuclear Information System (INIS)
Barnes, D.C.; Kamimura, T.
1982-04-01
Field implicit methods for low frequency plasma simulation by the LOMEGA (Low OMEGA) codes are described. These implicit field methods may be combined with particle pushing algorithms using either Lorentz force or guiding center force models to study two-dimensional, magnetized, electrostatic plasmas. Numerical results for ωsub(e)deltat>>1 are described. (author)
Performance evaluation of sea surface simulation methods for target detection
Xia, Renjie; Wu, Xin; Yang, Chen; Han, Yiping; Zhang, Jianqi
2017-11-01
With the fast development of sea surface target detection by optoelectronic sensors, machine learning has been adopted to improve the detection performance. Many features can be learned from training images by machines automatically. However, field images of sea surface target are not sufficient as training data. 3D scene simulation is a promising method to address this problem. For ocean scene simulation, sea surface height field generation is the key point to achieve high fidelity. In this paper, two spectra-based height field generation methods are evaluated. Comparison between the linear superposition and linear filter method is made quantitatively with a statistical model. 3D ocean scene simulating results show the different features between the methods, which can give reference for synthesizing sea surface target images with different ocean conditions.
Clinical simulation as an evaluation method in health informatics
DEFF Research Database (Denmark)
Jensen, Sanne
2016-01-01
Safe work processes and information systems are vital in health care. Methods for design of health IT focusing on patient safety are one of many initiatives trying to prevent adverse events. Possible patient safety hazards need to be investigated before health IT is integrated with local clinical...... work practice including other technology and organizational structure. Clinical simulation is ideal for proactive evaluation of new technology for clinical work practice. Clinical simulations involve real end-users as they simulate the use of technology in realistic environments performing realistic...... tasks. Clinical simulation study assesses effects on clinical workflow and enables identification and evaluation of patient safety hazards before implementation at a hospital. Clinical simulation also offers an opportunity to create a space in which healthcare professionals working in different...
Architecture oriented modeling and simulation method for combat mission profile
Directory of Open Access Journals (Sweden)
CHEN Xia
2017-05-01
Full Text Available In order to effectively analyze the system behavior and system performance of combat mission profile, an architecture-oriented modeling and simulation method is proposed. Starting from the architecture modeling,this paper describes the mission profile based on the definition from National Military Standard of China and the US Department of Defense Architecture Framework(DoDAFmodel, and constructs the architecture model of the mission profile. Then the transformation relationship between the architecture model and the agent simulation model is proposed to form the mission profile executable model. At last,taking the air-defense mission profile as an example,the agent simulation model is established based on the architecture model,and the input and output relations of the simulation model are analyzed. It provides method guidance for the combat mission profile design.
A nondissipative simulation method for the drift kinetic equation
International Nuclear Information System (INIS)
Watanabe, Tomo-Hiko; Sugama, Hideo; Sato, Tetsuya
2001-07-01
With the aim to study the ion temperature gradient (ITG) driven turbulence, a nondissipative kinetic simulation scheme is developed and comprehensively benchmarked. The new simulation method preserving the time-reversibility of basic kinetic equations can successfully reproduce the analytical solutions of asymmetric three-mode ITG equations which are extended to provide a more general reference for benchmarking than the previous work [T.-H. Watanabe, H. Sugama, and T. Sato: Phys. Plasmas 7 (2000) 984]. It is also applied to a dissipative three-mode system, and shows a good agreement with the analytical solution. The nondissipative simulation result of the ITG turbulence accurately satisfies the entropy balance equation. Usefulness of the nondissipative method for the drift kinetic simulations is confirmed in comparisons with other dissipative schemes. (author)
Adaptive implicit method for thermal compositional reservoir simulation
Energy Technology Data Exchange (ETDEWEB)
Agarwal, A.; Tchelepi, H.A. [Society of Petroleum Engineers, Richardson, TX (United States)]|[Stanford Univ., Palo Alto (United States)
2008-10-15
As the global demand for oil increases, thermal enhanced oil recovery techniques are becoming increasingly important. Numerical reservoir simulation of thermal methods such as steam assisted gravity drainage (SAGD) is complex and requires a solution of nonlinear mass and energy conservation equations on a fine reservoir grid. The most currently used technique for solving these equations is the fully IMplicit (FIM) method which is unconditionally stable, allowing for large timesteps in simulation. However, it is computationally expensive. On the other hand, the method known as IMplicit pressure explicit saturations, temperature and compositions (IMPEST) is computationally inexpensive, but it is only conditionally stable and restricts the timestep size. To improve the balance between the timestep size and computational cost, the thermal adaptive IMplicit (TAIM) method uses stability criteria and a switching algorithm, where some simulation variables such as pressure, saturations, temperature, compositions are treated implicitly while others are treated with explicit schemes. This presentation described ongoing research on TAIM with particular reference to thermal displacement processes such as the stability criteria that dictate the maximum allowed timestep size for simulation based on the von Neumann linear stability analysis method; the switching algorithm that adapts labeling of reservoir variables as implicit or explicit as a function of space and time; and, complex physical behaviors such as heat and fluid convection, thermal conduction and compressibility. Key numerical results obtained by enhancing Stanford's General Purpose Research Simulator (GPRS) were also presented along with a list of research challenges. 14 refs., 2 tabs., 11 figs., 1 appendix.
Activity coefficients from molecular simulations using the OPAS method
Kohns, Maximilian; Horsch, Martin; Hasse, Hans
2017-10-01
A method for determining activity coefficients by molecular dynamics simulations is presented. It is an extension of the OPAS (osmotic pressure for the activity of the solvent) method in previous work for studying the solvent activity in electrolyte solutions. That method is extended here to study activities of all components in mixtures of molecular species. As an example, activity coefficients in liquid mixtures of water and methanol are calculated for 298.15 K and 323.15 K at 1 bar using molecular models from the literature. These dense and strongly interacting mixtures pose a significant challenge to existing methods for determining activity coefficients by molecular simulation. It is shown that the new method yields accurate results for the activity coefficients which are in agreement with results obtained with a thermodynamic integration technique. As the partial molar volumes are needed in the proposed method, the molar excess volume of the system water + methanol is also investigated.
The discovery of 260Md and the decay properties of 258Fm, 258m,gMd and 259Md
International Nuclear Information System (INIS)
Lougheed, R.W.; Hulet, E.K.; Dougan, R.J.; Wild, J.F.; Dupzyk, R.J.; Henderson, C.M.; Moody, K.J.; Hahn, R.L.; Suemmerer, K.; Bethune, G.
1986-01-01
We have discovered a new neutron-rich isotope, 260 Md, from 18 O and 22 Ne bombardments of 254 Es. We observed a spontaneous-fission (SF) activity with a half-life of 32 days in electromagnetically separated fractions with mass number 260 from these bombardments and we measured the mass and kinetic energy distributions of this SF activity. The mass distribution was symmetric with the principal energy peak at a total kinetic energy (TKE) of 234 MeV, similar to previous observations for heavy fermium isotopes. Surprisingly, we also observed a smaller symmetric component with a TKE of 195 MeV. We interpret these two peaks in the TKE distribution as arising from two types of fission in the same nucleus, or bimodal fission. The observed fission activity may be either from the SF decay of 260 Md or from 260 Fm which would arise from electron-capture (EC) decay of 260 Md. We have eliminated the possible β - decay of 260 Md by measuring β - -SF time correlations for the decay of 260 Md and we plan to determine whether 260 Md decays by EC by measuring time correlations between fermium X-rays and SF events. We also measured various properties of the heavy fermium and mendelevium isotopes and obtained 1. more accurate cross-sections for the neutron-rich mendelevium isotopes which we use to predict the production rates of yet undiscovered nuclides, 2. improved half-life measurements for 258m,g Md and 259 Md, 3. confirmation of the EC decay of 258m Md by measurement of the fermium X-rays preceding the SF decay of 258 Fm and 4. very substantially improved mass and TKE distributions for the SF decay of 258 Fm and 259 Md. (orig.)
Simulation of the acoustic wave propagation using a meshless method
Directory of Open Access Journals (Sweden)
Bajko J.
2017-01-01
Full Text Available This paper presents numerical simulations of the acoustic wave propagation phenomenon modelled via Linearized Euler equations. A meshless method based on collocation of the strong form of the equation system is adopted. Moreover, the Weighted least squares method is used for local approximation of derivatives as well as stabilization technique in a form of spatial ltering. The accuracy and robustness of the method is examined on several benchmark problems.
Numerical simulation methods for wave propagation through optical waveguides
International Nuclear Information System (INIS)
Sharma, A.
1993-01-01
The simulation of the field propagation through waveguides requires numerical solutions of the Helmholtz equation. For this purpose a method based on the principle of orthogonal collocation was recently developed. The method is also applicable to nonlinear pulse propagation through optical fibers. Some of the salient features of this method and its application to both linear and nonlinear wave propagation through optical waveguides are discussed in this report. 51 refs, 8 figs, 2 tabs
Advance in research on aerosol deposition simulation methods
International Nuclear Information System (INIS)
Liu Keyang; Li Jingsong
2011-01-01
A comprehensive analysis of the health effects of inhaled toxic aerosols requires exact data on airway deposition. A knowledge of the effect of inhaled drugs is essential to the optimization of aerosol drug delivery. Sophisticated analytical deposition models can be used for the computation of total, regional and generation specific deposition efficiencies. The continuously enhancing computer seem to allow us to study the particle transport and deposition in more and more realistic airway geometries with the help of computational fluid dynamics (CFD) simulation method. In this article, the trends in aerosol deposition models and lung models, and the methods for achievement of deposition simulations are also reviewed. (authors)
Finite element method for simulation of the semiconductor devices
International Nuclear Information System (INIS)
Zikatanov, L.T.; Kaschiev, M.S.
1991-01-01
An iterative method for solving the system of nonlinear equations of the drift-diffusion representation for the simulation of the semiconductor devices is worked out. The Petrov-Galerkin method is taken for the discretization of these equations using the bilinear finite elements. It is shown that the numerical scheme is a monotonous one and there are no oscillations of the solutions in the region of p-n transition. The numerical calculations of the simulation of one semiconductor device are presented. 13 refs.; 3 figs
Reliability analysis of neutron transport simulation using Monte Carlo method
International Nuclear Information System (INIS)
Souza, Bismarck A. de; Borges, Jose C.
1995-01-01
This work presents a statistical and reliability analysis covering data obtained by computer simulation of neutron transport process, using the Monte Carlo method. A general description of the method and its applications is presented. Several simulations, corresponding to slowing down and shielding problems have been accomplished. The influence of the physical dimensions of the materials and of the sample size on the reliability level of results was investigated. The objective was to optimize the sample size, in order to obtain reliable results, optimizing computation time. (author). 5 refs, 8 figs
Tutorial: Determination of thermal boundary resistance by molecular dynamics simulations
Liang, Zhi; Hu, Ming
2018-05-01
Due to the high surface-to-volume ratio of nanostructured components in microelectronics and other advanced devices, the thermal resistance at material interfaces can strongly affect the overall thermal behavior in these devices. Therefore, the thermal boundary resistance, R, must be taken into account in the thermal analysis of nanoscale structures and devices. This article is a tutorial on the determination of R and the analysis of interfacial thermal transport via molecular dynamics (MD) simulations. In addition to reviewing the commonly used equilibrium and non-equilibrium MD models for the determination of R, we also discuss several MD simulation methods which can be used to understand interfacial thermal transport behavior. To illustrate how these MD models work for various interfaces, we will show several examples of MD simulation results on thermal transport across solid-solid, solid-liquid, and solid-gas interfaces. The advantages and drawbacks of a few other MD models such as approach-to-equilibrium MD and first-principles MD are also discussed.
First thoughts on MD priorities for 2012
Zimmermann, F; Assmann, R
2012-01-01
In 2012, 22 days of beam time will be allocated for LHC MDs. In this paper, after recalling the 2011 LHC MD experience, the MD rrequests for 2012 are reviewed. Three primary MD themes for 2012 can be identified: 1)pushing performance in 2012, 2)preparing for 2014/15, and 3)towards maximum luminosity. Example topics include emittance growth in collision or enhanced satellites for theme 1), 25 ns operation for 2), and ATS optics for 3). Structures lists of MD requests and topics for each theme as well as some initial thoughts on the MD priorities are presented. For certain topics, "start-of-fill MDs" are proposed in order to most efficiently use of the available beam time.
International Nuclear Information System (INIS)
Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako
2008-01-01
We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases. TM and MA were partly supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan.MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE
MONTE CARLO METHOD AND APPLICATION IN @RISK SIMULATION SYSTEM
Directory of Open Access Journals (Sweden)
Gabriela Ižaríková
2015-12-01
Full Text Available The article is an example of using the software simulation @Risk designed for simulation in Microsoft Excel spread sheet, demonstrated the possibility of its usage in order to show a universal method of solving problems. The simulation is experimenting with computer models based on the real production process in order to optimize the production processes or the system. The simulation model allows performing a number of experiments, analysing them, evaluating, optimizing and afterwards applying the results to the real system. A simulation model in general is presenting modelling system by using mathematical formulations and logical relations. In the model is possible to distinguish controlled inputs (for instance investment costs and random outputs (for instance demand, which are by using a model transformed into outputs (for instance mean value of profit. In case of a simulation experiment at the beginning are chosen controlled inputs and random (stochastic outputs are generated randomly. Simulations belong into quantitative tools, which can be used as a support for a decision making.
Energy Technology Data Exchange (ETDEWEB)
HOLM,ELIZABETH A.; BATTAILE,CORBETT C.; BUCHHEIT,THOMAS E.; FANG,HUEI ELIOT; RINTOUL,MARK DANIEL; VEDULA,VENKATA R.; GLASS,S. JILL; KNOROVSKY,GERALD A.; NEILSEN,MICHAEL K.; WELLMAN,GERALD W.; SULSKY,DEBORAH; SHEN,YU-LIN; SCHREYER,H. BUCK
2000-04-01
Computational materials simulations have traditionally focused on individual phenomena: grain growth, crack propagation, plastic flow, etc. However, real materials behavior results from a complex interplay between phenomena. In this project, the authors explored methods for coupling mesoscale simulations of microstructural evolution and micromechanical response. In one case, massively parallel (MP) simulations for grain evolution and microcracking in alumina stronglink materials were dynamically coupled. In the other, codes for domain coarsening and plastic deformation in CuSi braze alloys were iteratively linked. this program provided the first comparison of two promising ways to integrate mesoscale computer codes. Coupled microstructural/micromechanical codes were applied to experimentally observed microstructures for the first time. In addition to the coupled codes, this project developed a suite of new computational capabilities (PARGRAIN, GLAD, OOF, MPM, polycrystal plasticity, front tracking). The problem of plasticity length scale in continuum calculations was recognized and a solution strategy was developed. The simulations were experimentally validated on stockpile materials.
Simulation methods with extended stability for stiff biochemical Kinetics
Directory of Open Access Journals (Sweden)
Rué Pau
2010-08-01
Full Text Available Abstract Background With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (biochemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA. The key quantity is the step size, or waiting time, τ, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where τ can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called τ-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as τ grows. Results In this paper we extend Poisson τ-leap methods to a general class of Runge-Kutta (RK τ-leap methods. We show that with the proper selection of the coefficients, the variance of the extended τ-leap can be well-behaved, leading to significantly larger step sizes. Conclusions The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original τ-leap method. The approach paves the way to explore new multiscale methods to simulate (biochemical systems.
Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi
2017-10-12
Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.
High viscosity fluid simulation using particle-based method
Chang, Yuanzhang
2011-03-01
We present a new particle-based method for high viscosity fluid simulation. In the method, a new elastic stress term, which is derived from a modified form of the Hooke\\'s law, is included in the traditional Navier-Stokes equation to simulate the movements of the high viscosity fluids. Benefiting from the Lagrangian nature of Smoothed Particle Hydrodynamics method, large flow deformation can be well handled easily and naturally. In addition, in order to eliminate the particle deficiency problem near the boundary, ghost particles are employed to enforce the solid boundary condition. Compared with Finite Element Methods with complicated and time-consuming remeshing operations, our method is much more straightforward to implement. Moreover, our method doesn\\'t need to store and compare to an initial rest state. The experimental results show that the proposed method is effective and efficient to handle the movements of highly viscous flows, and a large variety of different kinds of fluid behaviors can be well simulated by adjusting just one parameter. © 2011 IEEE.
Computerized simulation methods for dose reduction, in radiodiagnosis
International Nuclear Information System (INIS)
Brochi, M.A.C.
1990-01-01
The present work presents computational methods that allow the simulation of any situation encountered in diagnostic radiology. Parameters of radiographic techniques that yield a standard radiographic image, previously chosen, and so could compare the dose of radiation absorbed by the patient is studied. Initially the method was tested on a simple system composed of 5.0 cm of water and 1.0 mm of aluminium and, after verifying experimentally its validity, it was applied in breast and arm fracture radiographs. It was observed that the choice of the filter material is not an important factor, because analogous behaviours were presented by aluminum, iron, copper, gadolinium, and other filters. A method of comparison of materials based on the spectral match is shown. Both the results given by this simulation method and the experimental measurements indicate an equivalence of brass and copper, both more efficient than aluminium, in terms of exposition time, but not of dose. (author)
Simulation of quantum systems by the tomography Monte Carlo method
International Nuclear Information System (INIS)
Bogdanov, Yu I
2007-01-01
A new method of statistical simulation of quantum systems is presented which is based on the generation of data by the Monte Carlo method and their purposeful tomography with the energy minimisation. The numerical solution of the problem is based on the optimisation of the target functional providing a compromise between the maximisation of the statistical likelihood function and the energy minimisation. The method does not involve complicated and ill-posed multidimensional computational procedures and can be used to calculate the wave functions and energies of the ground and excited stationary sates of complex quantum systems. The applications of the method are illustrated. (fifth seminar in memory of d.n. klyshko)
Vectorization of a particle simulation method for hypersonic rarefied flow
Mcdonald, Jeffrey D.; Baganoff, Donald
1988-01-01
An efficient particle simulation technique for hypersonic rarefied flows is presented at an algorithmic and implementation level. The implementation is for a vector computer architecture, specifically the Cray-2. The method models an ideal diatomic Maxwell molecule with three translational and two rotational degrees of freedom. Algorithms are designed specifically for compatibility with fine grain parallelism by reducing the number of data dependencies in the computation. By insisting on this compatibility, the method is capable of performing simulation on a much larger scale than previously possible. A two-dimensional simulation of supersonic flow over a wedge is carried out for the near-continuum limit where the gas is in equilibrium and the ideal solution can be used as a check on the accuracy of the gas model employed in the method. Also, a three-dimensional, Mach 8, rarefied flow about a finite-span flat plate at a 45 degree angle of attack was simulated. It utilized over 10 to the 7th particles carried through 400 discrete time steps in less than one hour of Cray-2 CPU time. This problem was chosen to exhibit the capability of the method in handling a large number of particles and a true three-dimensional geometry.
A multiscale quantum mechanics/electromagnetics method for device simulations.
Yam, ChiYung; Meng, Lingyi; Zhang, Yu; Chen, GuanHua
2015-04-07
Multiscale modeling has become a popular tool for research applying to different areas including materials science, microelectronics, biology, chemistry, etc. In this tutorial review, we describe a newly developed multiscale computational method, incorporating quantum mechanics into electronic device modeling with the electromagnetic environment included through classical electrodynamics. In the quantum mechanics/electromagnetics (QM/EM) method, the regions of the system where active electron scattering processes take place are treated quantum mechanically, while the surroundings are described by Maxwell's equations and a semiclassical drift-diffusion model. The QM model and the EM model are solved, respectively, in different regions of the system in a self-consistent manner. Potential distributions and current densities at the interface between QM and EM regions are employed as the boundary conditions for the quantum mechanical and electromagnetic simulations, respectively. The method is illustrated in the simulation of several realistic systems. In the case of junctionless field-effect transistors, transfer characteristics are obtained and a good agreement between experiments and simulations is achieved. Optical properties of a tandem photovoltaic cell are studied and the simulations demonstrate that multiple QM regions are coupled through the classical EM model. Finally, the study of a carbon nanotube-based molecular device shows the accuracy and efficiency of the QM/EM method.
A mixed finite element method for particle simulation in lasertron
International Nuclear Information System (INIS)
Le Meur, G.
1987-03-01
A particle simulation code is being developed with the aim to treat the motion of charged particles in electromagnetic devices, such as Lasertron. The paper describes the use of mixed finite element methods in computing the field components, without derivating them from scalar or vector potentials. Graphical results are shown
A simulation based engineering method to support HAZOP studies
DEFF Research Database (Denmark)
Enemark-Rasmussen, Rasmus; Cameron, David; Angelo, Per Bagge
2012-01-01
the conventional HAZOP procedure. The method systematically generates failure scenarios by considering process equipment deviations with pre-defined failure modes. The effect of failure scenarios is then evaluated using dynamic simulations -in this study the K-Spice® software used. The consequences of each failure...
Vectorization of a particle simulation method for hypersonic rarefied flow
International Nuclear Information System (INIS)
Mcdonald, J.D.; Baganoff, D.
1988-01-01
An efficient particle simulation technique for hypersonic rarefied flows is presented at an algorithmic and implementation level. The implementation is for a vector computer architecture, specifically the Cray-2. The method models an ideal diatomic Maxwell molecule with three translational and two rotational degrees of freedom. Algorithms are designed specifically for compatibility with fine grain parallelism by reducing the number of data dependencies in the computation. By insisting on this compatibility, the method is capable of performing simulation on a much larger scale than previously possible. A two-dimensional simulation of supersonic flow over a wedge is carried out for the near-continuum limit where the gas is in equilibrium and the ideal solution can be used as a check on the accuracy of the gas model employed in the method. Also, a three-dimensional, Mach 8, rarefied flow about a finite-span flat plate at a 45 degree angle of attack was simulated. It utilized over 10 to the 7th particles carried through 400 discrete time steps in less than one hour of Cray-2 CPU time. This problem was chosen to exhibit the capability of the method in handling a large number of particles and a true three-dimensional geometry. 14 references
Correction of measured multiplicity distributions by the simulated annealing method
International Nuclear Information System (INIS)
Hafidouni, M.
1993-01-01
Simulated annealing is a method used to solve combinatorial optimization problems. It is used here for the correction of the observed multiplicity distribution from S-Pb collisions at 200 GeV/c per nucleon. (author) 11 refs., 2 figs
Kinematics and simulation methods to determine the target thickness
International Nuclear Information System (INIS)
Rosales, P.; Aguilar, E.F.; Martinez Q, E.
2001-01-01
Making use of the kinematics and of the particles energy loss two methods for calculating the thickness of a target are described. Through a computer program and other of simulation in which parameters obtained experimentally are used. Several values for a 12 C target thickness were obtained. It is presented a comparison of the obtained values with each one of the used programs. (Author)
A mixed finite element method for particle simulation in Lasertron
International Nuclear Information System (INIS)
Le Meur, G.
1987-01-01
A particle simulation code is being developed with the aim to treat the motion of charged particles in electromagnetic devices, such as Lasertron. The paper describes the use of mixed finite element methods in computing the field components, without derivating them from scalar or vector potentials. Graphical results are shown
Dynamical simulation of heavy ion collisions; VUU and QMD method
International Nuclear Information System (INIS)
Niita, Koji
1992-01-01
We review two simulation methods based on the Vlasov-Uehling-Uhlenbeck (VUU) equation and Quantum Molecular Dynamics (QMD), which are the most widely accepted theoretical framework for the description of intermediate-energy heavy-ion reactions. We show some results of the calculations and compare them with the experimental data. (author)
Simulating water hammer with corrective smoothed particle method
Hou, Q.; Kruisbrink, A.C.H.; Tijsseling, A.S.; Keramat, A.
2012-01-01
The corrective smoothed particle method (CSPM) is used to simulate water hammer. The spatial derivatives in the water-hammer equations are approximated by a corrective kernel estimate. For the temporal derivatives, the Euler-forward time integration algorithm is employed. The CSPM results are in
STUDY ON SIMULATION METHOD OF AVALANCHE : FLOW ANALYSIS OF AVALANCHE USING PARTICLE METHOD
塩澤, 孝哉
2015-01-01
In this paper, modeling for the simulation of the avalanche by a particle method is discussed. There are two kinds of the snow avalanches, one is the surface avalanche which shows a smoke-like flow, and another is the total-layer avalanche which shows a flow like Bingham fluid. In the simulation of the surface avalanche, the particle method in consideration of a rotation resistance model is used. The particle method by Bingham fluid is used in the simulation of the total-layer avalanche. At t...
Efficient method for transport simulations in quantum cascade lasers
Directory of Open Access Journals (Sweden)
Maczka Mariusz
2017-01-01
Full Text Available An efficient method for simulating quantum transport in quantum cascade lasers is presented. The calculations are performed within a simple approximation inspired by Büttiker probes and based on a finite model for semiconductor superlattices. The formalism of non-equilibrium Green’s functions is applied to determine the selected transport parameters in a typical structure of a terahertz laser. Results were compared with those obtained for a infinite model as well as other methods described in literature.
A method of simulating and visualizing nuclear reactions
International Nuclear Information System (INIS)
Atwood, C.H.; Paul, K.M.
1994-01-01
Teaching nuclear reactions to students is difficult because the mechanisms are complex and directly visualizing them is impossible. As a teaching tool, the authors have developed a method of simulating nuclear reactions using colliding water droplets. Videotaping of the collisions, taken with a high shutter speed camera and run frame-by-frame, shows details of the collisions that are analogous to nuclear reactions. The method for colliding the water drops and videotaping the collisions are shown
International Nuclear Information System (INIS)
Wu, Jian-Chun; Feng, Qi-Jie; Liu, Xian-Kun; Zhan, Chang-Yong; Zou, Yu; Liu, Yao-Guang
2016-01-01
A multiscale sequence of simulation should be used to predict properties of materials under irradiation. Binary collision theory and molecular dynamics (MDs) method are commonly used to characterize the displacement cascades induced by neutrons in a material. In order to reduce the clock time spent for the MD simulation of damages induced by high-energy primary knock-on atoms (PKAs), the damage zones were split into sub-cascade according to the sub-cascade formation criteria. Two well-known codes, Geant4 and TRIM, were used to simulate high-energy PKA-induced cascades in B_4C and then produce the secondary knock-on atom (SKA) energy spectrum. It has been found that both high-energy primary knock-on B and C atoms move a long range in the boron carbide. These atoms produce sub-cascades at the tip of trajectory. The energy received by most of the SKAs is <10 keV, which can be used as input to reduce the clock time spent for MD simulation.
Meshfree simulation of avalanches with the Finite Pointset Method (FPM)
Michel, Isabel; Kuhnert, Jörg; Kolymbas, Dimitrios
2017-04-01
Meshfree methods are the numerical method of choice in case of applications which are characterized by strong deformations in conjunction with free surfaces or phase boundaries. In the past the meshfree Finite Pointset Method (FPM) developed by Fraunhofer ITWM (Kaiserslautern, Germany) has been successfully applied to problems in computational fluid dynamics such as water crossing of cars, water turbines, and hydraulic valves. Most recently the simulation of granular flows, e.g. soil interaction with cars (rollover), has also been tackled. This advancement is the basis for the simulation of avalanches. Due to the generalized finite difference formulation in FPM, the implementation of different material models is quite simple. We will demonstrate 3D simulations of avalanches based on the Drucker-Prager yield criterion as well as the nonlinear barodesy model. The barodesy model (Division of Geotechnical and Tunnel Engineering, University of Innsbruck, Austria) describes the mechanical behavior of soil by an evolution equation for the stress tensor. The key feature of successful and realistic simulations of avalanches - apart from the numerical approximation of the occurring differential operators - is the choice of the boundary conditions (slip, no-slip, friction) between the different phases of the flow as well as the geometry. We will discuss their influences for simplified one- and two-phase flow examples. This research is funded by the German Research Foundation (DFG) and the FWF Austrian Science Fund.
Same Content, Different Methods: Comparing Lecture, Engaged Classroom, and Simulation.
Raleigh, Meghan F; Wilson, Garland Anthony; Moss, David Alan; Reineke-Piper, Kristen A; Walden, Jeffrey; Fisher, Daniel J; Williams, Tracy; Alexander, Christienne; Niceler, Brock; Viera, Anthony J; Zakrajsek, Todd
2018-02-01
There is a push to use classroom technology and active teaching methods to replace didactic lectures as the most prevalent format for resident education. This multisite collaborative cohort study involving nine residency programs across the United States compared a standard slide-based didactic lecture, a facilitated group discussion via an engaged classroom, and a high-fidelity, hands-on simulation scenario for teaching the topic of acute dyspnea. The primary outcome was knowledge retention at 2 to 4 weeks. Each teaching method was assigned to three different residency programs in the collaborative according to local resources. Learning objectives were determined by faculty. Pre- and posttest questions were validated and utilized as a measurement of knowledge retention. Each site administered the pretest, taught the topic of acute dyspnea utilizing their assigned method, and administered a posttest 2 to 4 weeks later. Differences between the groups were compared using paired t-tests. A total of 146 residents completed the posttest, and scores increased from baseline across all groups. The average score increased 6% in the standard lecture group (n=47), 11% in the engaged classroom (n=53), and 9% in the simulation group (n=56). The differences in improvement between engaged classroom and simulation were not statistically significant. Compared to standard lecture, both engaged classroom and high-fidelity simulation were associated with a statistically significant improvement in knowledge retention. Knowledge retention after engaged classroom and high-fidelity simulation did not significantly differ. More research is necessary to determine if different teaching methods result in different levels of comfort and skill with actual patient care.
Czech Academy of Sciences Publication Activity Database
Mládek, Arnošt; Banáš, P.; Jurečka, P.; Otyepka, M.; Zgarbová, M.; Šponer, Jiří
2014-01-01
Roč. 10, č. 1 (2014), s. 463-480 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GAP208/12/1878; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : DENSITY-FUNCTIONAL THEORY * SUGAR-PHOSPHATE BACKBONE * QUANTUM-CHEMICAL CALCULATIONS Subject RIV: BO - Biophysics Impact factor: 5.498, year: 2014
Modified network simulation model with token method of bus access
Directory of Open Access Journals (Sweden)
L.V. Stribulevich
2013-08-01
Full Text Available Purpose. To study the characteristics of the local network with the marker method of access to the bus its modified simulation model was developed. Methodology. Defining characteristics of the network is carried out on the developed simulation model, which is based on the state diagram-layer network station with the mechanism of processing priorities, both in steady state and in the performance of control procedures: the initiation of a logical ring, the entrance and exit of the station network with a logical ring. Findings. A simulation model, on the basis of which can be obtained the dependencies of the application the maximum waiting time in the queue for different classes of access, and the reaction time usable bandwidth on the data rate, the number of network stations, the generation rate applications, the number of frames transmitted per token holding time, frame length was developed. Originality. The technique of network simulation reflecting its work in the steady condition and during the control procedures, the mechanism of priority ranking and handling was proposed. Practical value. Defining network characteristics in the real-time systems on railway transport based on the developed simulation model.
Thermal shale fracturing simulation using the Cohesive Zone Method (CZM)
Enayatpour, Saeid; van Oort, Eric; Patzek, Tadeusz
2018-01-01
Extensive research has been conducted over the past two decades to improve hydraulic fracturing methods used for hydrocarbon recovery from tight reservoir rocks such as shales. Our focus in this paper is on thermal fracturing of such tight rocks to enhance hydraulic fracturing efficiency. Thermal fracturing is effective in generating small fractures in the near-wellbore zone - or in the vicinity of natural or induced fractures - that may act as initiation points for larger fractures. Previous analytical and numerical results indicate that thermal fracturing in tight rock significantly enhances rock permeability, thereby enhancing hydrocarbon recovery. Here, we present a more powerful way of simulating the initiation and propagation of thermally induced fractures in tight formations using the Cohesive Zone Method (CZM). The advantages of CZM are: 1) CZM simulation is fast compared to similar models which are based on the spring-mass particle method or Discrete Element Method (DEM); 2) unlike DEM, rock material complexities such as scale-dependent failure behavior can be incorporated in a CZM simulation; 3) CZM is capable of predicting the extent of fracture propagation in rock, which is more difficult to determine in a classic finite element approach. We demonstrate that CZM delivers results for the challenging fracture propagation problem of similar accuracy to the eXtended Finite Element Method (XFEM) while reducing complexity and computational effort. Simulation results for thermal fracturing in the near-wellbore zone show the effect of stress anisotropy in fracture propagation in the direction of the maximum horizontal stress. It is shown that CZM can be used to readily obtain the extent and the pattern of induced thermal fractures.
Thermal shale fracturing simulation using the Cohesive Zone Method (CZM)
Enayatpour, Saeid
2018-05-17
Extensive research has been conducted over the past two decades to improve hydraulic fracturing methods used for hydrocarbon recovery from tight reservoir rocks such as shales. Our focus in this paper is on thermal fracturing of such tight rocks to enhance hydraulic fracturing efficiency. Thermal fracturing is effective in generating small fractures in the near-wellbore zone - or in the vicinity of natural or induced fractures - that may act as initiation points for larger fractures. Previous analytical and numerical results indicate that thermal fracturing in tight rock significantly enhances rock permeability, thereby enhancing hydrocarbon recovery. Here, we present a more powerful way of simulating the initiation and propagation of thermally induced fractures in tight formations using the Cohesive Zone Method (CZM). The advantages of CZM are: 1) CZM simulation is fast compared to similar models which are based on the spring-mass particle method or Discrete Element Method (DEM); 2) unlike DEM, rock material complexities such as scale-dependent failure behavior can be incorporated in a CZM simulation; 3) CZM is capable of predicting the extent of fracture propagation in rock, which is more difficult to determine in a classic finite element approach. We demonstrate that CZM delivers results for the challenging fracture propagation problem of similar accuracy to the eXtended Finite Element Method (XFEM) while reducing complexity and computational effort. Simulation results for thermal fracturing in the near-wellbore zone show the effect of stress anisotropy in fracture propagation in the direction of the maximum horizontal stress. It is shown that CZM can be used to readily obtain the extent and the pattern of induced thermal fractures.
Hybrid numerical methods for multiscale simulations of subsurface biogeochemical processes
International Nuclear Information System (INIS)
Scheibe, T D; Tartakovsky, A M; Tartakovsky, D M; Redden, G D; Meakin, P
2007-01-01
Many subsurface flow and transport problems of importance today involve coupled non-linear flow, transport, and reaction in media exhibiting complex heterogeneity. In particular, problems involving biological mediation of reactions fall into this class of problems. Recent experimental research has revealed important details about the physical, chemical, and biological mechanisms involved in these processes at a variety of scales ranging from molecular to laboratory scales. However, it has not been practical or possible to translate detailed knowledge at small scales into reliable predictions of field-scale phenomena important for environmental management applications. A large assortment of numerical simulation tools have been developed, each with its own characteristic scale. Important examples include 1. molecular simulations (e.g., molecular dynamics); 2. simulation of microbial processes at the cell level (e.g., cellular automata or particle individual-based models); 3. pore-scale simulations (e.g., lattice-Boltzmann, pore network models, and discrete particle methods such as smoothed particle hydrodynamics); and 4. macroscopic continuum-scale simulations (e.g., traditional partial differential equations solved by finite difference or finite element methods). While many problems can be effectively addressed by one of these models at a single scale, some problems may require explicit integration of models across multiple scales. We are developing a hybrid multi-scale subsurface reactive transport modeling framework that integrates models with diverse representations of physics, chemistry and biology at different scales (sub-pore, pore and continuum). The modeling framework is being designed to take advantage of advanced computational technologies including parallel code components using the Common Component Architecture, parallel solvers, gridding, data and workflow management, and visualization. This paper describes the specific methods/codes being used at each
Discrete Particle Method for Simulating Hypervelocity Impact Phenomena
Directory of Open Access Journals (Sweden)
Erkai Watson
2017-04-01
Full Text Available In this paper, we introduce a computational model for the simulation of hypervelocity impact (HVI phenomena which is based on the Discrete Element Method (DEM. Our paper constitutes the first application of DEM to the modeling and simulating of impact events for velocities beyond 5 kms-1. We present here the results of a systematic numerical study on HVI of solids. For modeling the solids, we use discrete spherical particles that interact with each other via potentials. In our numerical investigations we are particularly interested in the dynamics of material fragmentation upon impact. We model a typical HVI experiment configuration where a sphere strikes a thin plate and investigate the properties of the resulting debris cloud. We provide a quantitative computational analysis of the resulting debris cloud caused by impact and a comprehensive parameter study by varying key parameters of our model. We compare our findings from the simulations with recent HVI experiments performed at our institute. Our findings are that the DEM method leads to very stable, energy–conserving simulations of HVI scenarios that map the experimental setup where a sphere strikes a thin plate at hypervelocity speed. Our chosen interaction model works particularly well in the velocity range where the local stresses caused by impact shock waves markedly exceed the ultimate material strength.
Experiences using DAKOTA stochastic expansion methods in computational simulations.
Energy Technology Data Exchange (ETDEWEB)
Templeton, Jeremy Alan; Ruthruff, Joseph R.
2012-01-01
Uncertainty quantification (UQ) methods bring rigorous statistical connections to the analysis of computational and experiment data, and provide a basis for probabilistically assessing margins associated with safety and reliability. The DAKOTA toolkit developed at Sandia National Laboratories implements a number of UQ methods, which are being increasingly adopted by modeling and simulation teams to facilitate these analyses. This report disseminates results as to the performance of DAKOTA's stochastic expansion methods for UQ on a representative application. Our results provide a number of insights that may be of interest to future users of these methods, including the behavior of the methods in estimating responses at varying probability levels, and the expansion levels for the methodologies that may be needed to achieve convergence.
Quantum control with NMR methods: Application to quantum simulations
International Nuclear Information System (INIS)
Negrevergne, Camille
2002-01-01
Manipulating information according to quantum laws allows improvements in the efficiency of the way we treat certain problems. Liquid state Nuclear Magnetic Resonance methods allow us to initialize, manipulate and read the quantum state of a system of coupled spins. These methods have been used to realize an experimental small Quantum Information Processor (QIP) able to process information through around hundred elementary operations. One of the main themes of this work was to design, optimize and validate reliable RF-pulse sequences used to 'program' the QIP. Such techniques have been used to run a quantum simulation algorithm for anionic systems. Some experimental results have been obtained on the determination of Eigen energies and correlation function for a toy problem consisting of fermions on a lattice, showing an experimental proof of principle for such quantum simulations. (author) [fr
From fuel cells to batteries: Synergies, scales and simulation methods
Bessler, Wolfgang G.
2011-01-01
The recent years have shown a dynamic growth of battery research and development activities both in academia and industry, supported by large governmental funding initiatives throughout the world. A particular focus is being put on lithium-based battery technologies. This situation provides a stimulating environment for the fuel cell modeling community, as there are considerable synergies in the modeling and simulation methods for fuel cells and batteries. At the same time, batter...
Ayalew Tegegn', MD,McommH, Meseret Yazachew”, MD, MPH
African Journals Online (AJOL)
METHODS: A cross-sectional study was conducted in 12 public health facilities ..... and total treatment delay should be reduced to reverse the ... appointment for re-evaluation, which as a result to Jimma University for logistic and other support.
Multi-Device to Multi-Device (MD2MD Content-Centric Networking Based on Multi-RAT Device
Directory of Open Access Journals (Sweden)
Cheolhoon Kim
2017-11-01
Full Text Available This paper proposes a method whereby a device can transmit and receive information using a beacon, and also describes application scenarios for the proposed method. In a multi-device to multi-device (MD2MD content-centric networking (CCN environment, the main issue involves searching for and connecting to nearby devices. However, if a device can’t find another device that satisfies its requirements, the connection is delayed due to the repetition of processes. It is possible to rapidly connect to a device without repetition through the selection of the optimal device using the proposed method. Consequently, the proposed method and scenarios are advantageous in that they enable efficient content identification and delivery in a content-centric Internet of Things (IoT environment, in which multiple mobile devices coexist.
Application of subset simulation methods to dynamic fault tree analysis
International Nuclear Information System (INIS)
Liu Mengyun; Liu Jingquan; She Ding
2015-01-01
Although fault tree analysis has been implemented in the nuclear safety field over the past few decades, it was recently criticized for the inability to model the time-dependent behaviors. Several methods are proposed to overcome this disadvantage, and dynamic fault tree (DFT) has become one of the research highlights. By introducing additional dynamic gates, DFT is able to describe the dynamic behaviors like the replacement of spare components or the priority of failure events. Using Monte Carlo simulation (MCS) approach to solve DFT has obtained rising attention, because it can model the authentic behaviors of systems and avoid the limitations in the analytical method. In this paper, it provides an overview and MCS information for DFT analysis, including the sampling of basic events and the propagation rule for logic gates. When calculating rare-event probability, large amount of simulations in standard MCS are required. To improve the weakness, subset simulation (SS) approach is applied. Using the concept of conditional probability and Markov Chain Monte Carlo (MCMC) technique, the SS method is able to accelerate the efficiency of exploring the failure region. Two cases are tested to illustrate the performance of SS approach, and the numerical results suggest that it gives high efficiency when calculating complicated systems with small failure probabilities. (author)
A computer method for simulating the decay of radon daughters
International Nuclear Information System (INIS)
Hartley, B.M.
1988-01-01
The analytical equations representing the decay of a series of radioactive atoms through a number of daughter products are well known. These equations are for an idealized case in which the expectation value of the number of atoms which decay in a certain time can be represented by a smooth curve. The real curve of the total number of disintegrations from a radioactive species consists of a series of Heaviside step functions, with the steps occurring at the time of the disintegration. The disintegration of radioactive atoms is said to be random but this random behaviour is such that a single species forms an ensemble of which the times of disintegration give a geometric distribution. Numbers which have a geometric distribution can be generated by computer and can be used to simulate the decay of one or more radioactive species. A computer method is described for simulating such decay of radioactive atoms and this method is applied specifically to the decay of the short half life daughters of radon 222 and the emission of alpha particles from polonium 218 and polonium 214. Repeating the simulation of the decay a number of times provides a method for investigating the statistical uncertainty inherent in methods for measurement of exposure to radon daughters. This statistical uncertainty is difficult to investigate analytically since the time of decay of an atom of polonium 218 is not independent of the time of decay of subsequent polonium 214. The method is currently being used to investigate the statistical uncertainties of a number of commonly used methods for the counting of alpha particles from radon daughters and the calculations of exposure
Etesami, S. Alireza; Asadi, Ebrahim
2018-01-01
Availability of a reliable interatomic potential is one of the major challenges in utilizing molecular dynamics (MD) for simulations of metals at near the melting temperatures and melting point (MP). Here, we propose a novel approach to address this challenge in the concept of modified-embedded-atom (MEAM) interatomic potential; also, we apply the approach on iron, nickel, copper, and aluminum as case studies. We propose adding experimentally available high temperature elastic constants and MP of the element to the list of typical low temperature properties used for the development of MD interatomic potential parameters. We show that the proposed approach results in a reasonable agreement between the MD calculations of melting properties such as latent heat, expansion in melting, liquid structure factor, and solid-liquid interface stiffness and their experimental/computational counterparts. Then, we present the physical properties of mentioned elements near melting temperatures using the new MEAM parameters. We observe that the behavior of elastic constants, heat capacity and thermal linear expansion coefficient at room temperature compared to MP follows an empirical linear relation (α±β × MP) for transition metals. Furthermore, a linear relation between the tetragonal shear modulus and the enthalpy change from room temperature to MP is observed for face-centered cubic materials.
Atmosphere Re-Entry Simulation Using Direct Simulation Monte Carlo (DSMC Method
Directory of Open Access Journals (Sweden)
Francesco Pellicani
2016-05-01
Full Text Available Hypersonic re-entry vehicles aerothermodynamic investigations provide fundamental information to other important disciplines like materials and structures, assisting the development of thermal protection systems (TPS efficient and with a low weight. In the transitional flow regime, where thermal and chemical equilibrium is almost absent, a new numerical method for such studies has been introduced, the direct simulation Monte Carlo (DSMC numerical technique. The acceptance and applicability of the DSMC method have increased significantly in the 50 years since its invention thanks to the increase in computer speed and to the parallel computing. Anyway, further verification and validation efforts are needed to lead to its greater acceptance. In this study, the Monte Carlo simulator OpenFOAM and Sparta have been studied and benchmarked against numerical and theoretical data for inert and chemically reactive flows and the same will be done against experimental data in the near future. The results show the validity of the data found with the DSMC. The best setting of the fundamental parameters used by a DSMC simulator are presented for each software and they are compared with the guidelines deriving from the theory behind the Monte Carlo method. In particular, the number of particles per cell was found to be the most relevant parameter to achieve valid and optimized results. It is shown how a simulation with a mean value of one particle per cell gives sufficiently good results with very low computational resources. This achievement aims to reconsider the correct investigation method in the transitional regime where both the direct simulation Monte Carlo (DSMC and the computational fluid-dynamics (CFD can work, but with a different computational effort.
A particle finite element method for machining simulations
Sabel, Matthias; Sator, Christian; Müller, Ralf
2014-07-01
The particle finite element method (PFEM) appears to be a convenient technique for machining simulations, since the geometry and topology of the problem can undergo severe changes. In this work, a short outline of the PFEM-algorithm is given, which is followed by a detailed description of the involved operations. The -shape method, which is used to track the topology, is explained and tested by a simple example. Also the kinematics and a suitable finite element formulation are introduced. To validate the method simple settings without topological changes are considered and compared to the standard finite element method for large deformations. To examine the performance of the method, when dealing with separating material, a tensile loading is applied to a notched plate. This investigation includes a numerical analysis of the different meshing parameters, and the numerical convergence is studied. With regard to the cutting simulation it is found that only a sufficiently large number of particles (and thus a rather fine finite element discretisation) leads to converged results of process parameters, such as the cutting force.
Multigrid Methods for Fully Implicit Oil Reservoir Simulation
Molenaar, J.
1996-01-01
In this paper we consider the simultaneous flow of oil and water in reservoir rock. This displacement process is modeled by two basic equations: the material balance or continuity equations and the equation of motion (Darcy's law). For the numerical solution of this system of nonlinear partial differential equations there are two approaches: the fully implicit or simultaneous solution method and the sequential solution method. In the sequential solution method the system of partial differential equations is manipulated to give an elliptic pressure equation and a hyperbolic (or parabolic) saturation equation. In the IMPES approach the pressure equation is first solved, using values for the saturation from the previous time level. Next the saturations are updated by some explicit time stepping method; this implies that the method is only conditionally stable. For the numerical solution of the linear, elliptic pressure equation multigrid methods have become an accepted technique. On the other hand, the fully implicit method is unconditionally stable, but it has the disadvantage that in every time step a large system of nonlinear algebraic equations has to be solved. The most time-consuming part of any fully implicit reservoir simulator is the solution of this large system of equations. Usually this is done by Newton's method. The resulting systems of linear equations are then either solved by a direct method or by some conjugate gradient type method. In this paper we consider the possibility of applying multigrid methods for the iterative solution of the systems of nonlinear equations. There are two ways of using multigrid for this job: either we use a nonlinear multigrid method or we use a linear multigrid method to deal with the linear systems that arise in Newton's method. So far only a few authors have reported on the use of multigrid methods for fully implicit simulations. Two-level FAS algorithm is presented for the black-oil equations, and linear multigrid for
Radon movement simulation in overburden by the 'Scattered Packet Method'
International Nuclear Information System (INIS)
Marah, H.; Sabir, A.; Hlou, L.; Tayebi, M.
1998-01-01
The analysis of Radon ( 222 Rn) movement in overburden needs the resolution of the General Equation of Transport in porous medium, involving diffusion and convection. Generally this equation was derived and solved analytically. The 'Scattered Packed Method' is a recent mathematical method of resolution, initially developed for the electrons movements in the semiconductors studies. In this paper, we have adapted this method to simulate radon emanation in porous medium. The keys parameters are the radon concentration at the source, the diffusion coefficient, and the geometry. To show the efficiency of this method, several cases of increasing complexity are considered. This model allows to follow the migration, in the time and space, of radon produced as a function of the characteristics of the studied site. Forty soil radon measurements were taken from a North Moroccan fault. Forward modeling of the radon anomalies produces satisfactory fits of the observed data and allows the overburden thickness determination. (author)
Evaluation of null-point detection methods on simulation data
Olshevsky, Vyacheslav; Fu, Huishan; Vaivads, Andris; Khotyaintsev, Yuri; Lapenta, Giovanni; Markidis, Stefano
2014-05-01
We model the measurements of artificial spacecraft that resemble the configuration of CLUSTER propagating in the particle-in-cell simulation of turbulent magnetic reconnection. The simulation domain contains multiple isolated X-type null-points, but the majority are O-type null-points. Simulations show that current pinches surrounded by twisted fields, analogous to laboratory pinches, are formed along the sequences of O-type nulls. In the simulation, the magnetic reconnection is mainly driven by the kinking of the pinches, at spatial scales of several ion inertial lentghs. We compute the locations of magnetic null-points and detect their type. When the satellites are separated by the fractions of ion inertial length, as it is for CLUSTER, they are able to locate both the isolated null-points, and the pinches. We apply the method to the real CLUSTER data and speculate how common are pinches in the magnetosphere, and whether they play a dominant role in the dissipation of magnetic energy.
A molecular dynamics simulation code ISIS
International Nuclear Information System (INIS)
Kambayashi, Shaw
1992-06-01
Computer simulation based on the molecular dynamics (MD) method has become an important tool complementary to experiments and theoretical calculations in a wide range of scientific fields such as physics, chemistry, biology, and so on. In the MD method, the Newtonian equations-of-motion of classical particles are integrated numerically to reproduce a phase-space trajectory of the system. In the 1980's, several new techniques have been developed for simulation at constant-temperature and/or constant-pressure in convenient to compare result of computer simulation with experimental results. We first summarize the MD method for both microcanonical and canonical simulations. Then, we present and overview of a newly developed ISIS (Isokinetic Simulation of Soft-spheres) code and its performance on various computers including vector processors. The ISIS code has a capability to make a MD simulation under constant-temperature condition by using the isokinetic constraint method. The equations-of-motion is integrated by a very accurate fifth-order finite differential algorithm. The bookkeeping method is also utilized to reduce the computational time. Furthermore, the ISIS code is well adopted for vector processing: Speedup ratio ranged from 16 to 24 times is obtained on a VP2600/10 vector processor. (author)
Chen, Yunjie; Roux, Benoît
2014-09-21
Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct
Chen, Yunjie; Roux, Benoît
2014-09-01
Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct
Structure of Cu64.5Zr35.5 metallic glass by reverse Monte Carlo simulations
International Nuclear Information System (INIS)
Fang, X. W.; Huang, Li; Wang, C. Z.; Ho, K. M.; Ding, Z. J.
2014-01-01
Reverse Monte Carlo simulations (RMC) have been widely used to generate three dimensional (3D) atomistic models for glass systems. To examine the reliability of the method for metallic glass, we use RMC to predict the atomic configurations of a “known” structure from molecular dynamics (MD) simulations, and then compare the structure obtained from the RMC with the target structure from MD. We show that when the structure factors and partial pair correlation functions from the MD simulations are used as inputs for RMC simulations, the 3D atomistic structure of the glass obtained from the RMC gives the short- and medium-range order in good agreement with those from the target structure by the MD simulation. These results suggest that 3D atomistic structure model of the metallic glass alloys can be reasonably well reproduced by RMC method with a proper choice of input constraints
International Nuclear Information System (INIS)
Berthiau, G.
1995-10-01
The circuit design problem consists in determining acceptable parameter values (resistors, capacitors, transistors geometries ...) which allow the circuit to meet various user given operational criteria (DC consumption, AC bandwidth, transient times ...). This task is equivalent to a multidimensional and/or multi objective optimization problem: n-variables functions have to be minimized in an hyper-rectangular domain ; equality constraints can be eventually specified. A similar problem consists in fitting component models. In this way, the optimization variables are the model parameters and one aims at minimizing a cost function built on the error between the model response and the data measured on the component. The chosen optimization method for this kind of problem is the simulated annealing method. This method, provided by the combinatorial optimization domain, has been adapted and compared with other global optimization methods for the continuous variables problems. An efficient strategy of variables discretization and a set of complementary stopping criteria have been proposed. The different parameters of the method have been adjusted with analytical functions of which minima are known, classically used in the literature. Our simulated annealing algorithm has been coupled with an open electrical simulator SPICE-PAC of which the modular structure allows the chaining of simulations required by the circuit optimization process. We proposed, for high-dimensional problems, a partitioning technique which ensures proportionality between CPU-time and variables number. To compare our method with others, we have adapted three other methods coming from combinatorial optimization domain - the threshold method, a genetic algorithm and the Tabu search method - The tests have been performed on the same set of test functions and the results allow a first comparison between these methods applied to continuous optimization variables. Finally, our simulated annealing program
A fast mollified impulse method for biomolecular atomistic simulations
Energy Technology Data Exchange (ETDEWEB)
Fath, L., E-mail: lukas.fath@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Hochbruck, M., E-mail: marlis.hochbruck@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Singh, C.V., E-mail: chandraveer.singh@utoronto.ca [Department of Materials Science & Engineering, University of Toronto (Canada)
2017-03-15
Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice–ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.
Numerical method for IR background and clutter simulation
Quaranta, Carlo; Daniele, Gina; Balzarotti, Giorgio
1997-06-01
The paper describes a fast and accurate algorithm of IR background noise and clutter generation for application in scene simulations. The process is based on the hypothesis that background might be modeled as a statistical process where amplitude of signal obeys to the Gaussian distribution rule and zones of the same scene meet a correlation function with exponential form. The algorithm allows to provide an accurate mathematical approximation of the model and also an excellent fidelity with reality, that appears from a comparison with images from IR sensors. The proposed method shows advantages with respect to methods based on the filtering of white noise in time or frequency domain as it requires a limited number of computation and, furthermore, it is more accurate than the quasi random processes. The background generation starts from a reticule of few points and by means of growing rules the process is extended to the whole scene of required dimension and resolution. The statistical property of the model are properly maintained in the simulation process. The paper gives specific attention to the mathematical aspects of the algorithm and provides a number of simulations and comparisons with real scenes.
Viscoelastic Earthquake Cycle Simulation with Memory Variable Method
Hirahara, K.; Ohtani, M.
2017-12-01
There have so far been no EQ (earthquake) cycle simulations, based on RSF (rate and state friction) laws, in viscoelastic media, except for Kato (2002), who simulated cycles on a 2-D vertical strike-slip fault, and showed nearly the same cycles as those in elastic cases. The viscoelasticity could, however, give more effects on large dip-slip EQ cycles. In a boundary element approach, stress is calculated using a hereditary integral of stress relaxation function and slip deficit rate, where we need the past slip rates, leading to huge computational costs. This is a cause for almost no simulations in viscoelastic media. We have investigated the memory variable method utilized in numerical computation of wave propagation in dissipative media (e.g., Moczo and Kristek, 2005). In this method, introducing memory variables satisfying 1st order differential equations, we need no hereditary integrals in stress calculation and the computational costs are the same order of those in elastic cases. Further, Hirahara et al. (2012) developed the iterative memory variable method, referring to Taylor et al. (1970), in EQ cycle simulations in linear viscoelastic media. In this presentation, first, we introduce our method in EQ cycle simulations and show the effect of the linear viscoelasticity on stick-slip cycles in a 1-DOF block-SLS (standard linear solid) model, where the elastic spring of the traditional block-spring model is replaced by SLS element and we pull, in a constant rate, the block obeying RSF law. In this model, the memory variable stands for the displacement of the dash-pot in SLS element. The use of smaller viscosity reduces the recurrence time to a minimum value. The smaller viscosity means the smaller relaxation time, which makes the stress recovery quicker, leading to the smaller recurrence time. Second, we show EQ cycles on a 2-D dip-slip fault with the dip angel of 20 degrees in an elastic layer with thickness of 40 km overriding a Maxwell viscoelastic half
Amyloid oligomer structure characterization from simulations: A general method
Energy Technology Data Exchange (ETDEWEB)
Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France); Li, Mai Suan [Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw (Poland); Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France); Institut Universitaire de France, 103 Bvd Saint-Germain, 75005 Paris (France)
2014-03-07
Amyloid oligomers and plaques are composed of multiple chemically identical proteins. Therefore, one of the first fundamental problems in the characterization of structures from simulations is the treatment of the degeneracy, i.e., the permutation of the molecules. Second, the intramolecular and intermolecular degrees of freedom of the various molecules must be taken into account. Currently, the well-known dihedral principal component analysis method only considers the intramolecular degrees of freedom, and other methods employing collective variables can only describe intermolecular degrees of freedom at the global level. With this in mind, we propose a general method that identifies all the structures accurately. The basis idea is that the intramolecular and intermolecular states are described in terms of combinations of single-molecule and double-molecule states, respectively, and the overall structures of oligomers are the product basis of the intramolecular and intermolecular states. This way, the degeneracy is automatically avoided. The method is illustrated on the conformational ensemble of the tetramer of the Alzheimer's peptide Aβ{sub 9−40}, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.
Limitations in simulator time-based human reliability analysis methods
International Nuclear Information System (INIS)
Wreathall, J.
1989-01-01
Developments in human reliability analysis (HRA) methods have evolved slowly. Current methods are little changed from those of almost a decade ago, particularly in the use of time-reliability relationships. While these methods were suitable as an interim step, the time (and the need) has come to specify the next evolution of HRA methods. As with any performance-oriented data source, power plant simulator data have no direct connection to HRA models. Errors reported in data are normal deficiencies observed in human performance; failures are events modeled in probabilistic risk assessments (PRAs). Not all errors cause failures; not all failures are caused by errors. Second, the times at which actions are taken provide no measure of the likelihood of failures to act correctly within an accident scenario. Inferences can be made about human reliability, but they must be made with great care. Specific limitations are discussed. Simulator performance data are useful in providing qualitative evidence of the variety of error types and their potential influences on operating systems. More work is required to combine recent developments in the psychology of error with the qualitative data collected at stimulators. Until data become openly available, however, such an advance will not be practical
Hardware-in-the-loop grid simulator system and method
Fox, John Curtiss; Collins, Edward Randolph; Rigas, Nikolaos
2017-05-16
A hardware-in-the-loop (HIL) electrical grid simulation system and method that combines a reactive divider with a variable frequency converter to better mimic and control expected and unexpected parameters in an electrical grid. The invention provides grid simulation in a manner to allow improved testing of variable power generators, such as wind turbines, and their operation once interconnected with an electrical grid in multiple countries. The system further comprises an improved variable fault reactance (reactive divider) capable of providing a variable fault reactance power output to control a voltage profile, therein creating an arbitrary recovery voltage. The system further comprises an improved isolation transformer designed to isolate zero-sequence current from either a primary or secondary winding in a transformer or pass the zero-sequence current from a primary to a secondary winding.
Simulating condensation on microstructured surfaces using Lattice Boltzmann Method
Alexeev, Alexander; Vasyliv, Yaroslav
2017-11-01
We simulate a single component fluid condensing on 2D structured surfaces with different wettability. To simulate the two phase fluid, we use the athermal Lattice Boltzmann Method (LBM) driven by a pseudopotential force. The pseudopotential force results in a non-ideal equation of state (EOS) which permits liquid-vapor phase change. To account for thermal effects, the athermal LBM is coupled to a finite volume discretization of the temperature evolution equation obtained using a thermal energy rate balance for the specific internal energy. We use the developed model to probe the effect of surface structure and surface wettability on the condensation rate in order to identify microstructure topographies promoting condensation. Financial support is acknowledged from Kimberly-Clark.
'Odontologic dosimetric card' experiments and simulations using Monte Carlo methods
International Nuclear Information System (INIS)
Menezes, C.J.M.; Lima, R. de A.; Peixoto, J.E.; Vieira, J.W.
2008-01-01
The techniques for data processing, combined with the development of fast and more powerful computers, makes the Monte Carlo methods one of the most widely used tools in the radiation transport simulation. For applications in diagnostic radiology, this method generally uses anthropomorphic phantoms to evaluate the absorbed dose to patients during exposure. In this paper, some Monte Carlo techniques were used to simulation of a testing device designed for intra-oral X-ray equipment performance evaluation called Odontologic Dosimetric Card (CDO of 'Cartao Dosimetrico Odontologico' in Portuguese) for different thermoluminescent detectors. This paper used two computational models of exposition RXD/EGS4 and CDO/EGS4. In the first model, the simulation results are compared with experimental data obtained in the similar conditions. The second model, it presents the same characteristics of the testing device studied (CDO). For the irradiations, the X-ray spectra were generated by the IPEM report number 78, spectrum processor. The attenuated spectrum was obtained for IEC 61267 qualities and various additional filters for a Pantak 320 X-ray industrial equipment. The results obtained for the study of the copper filters used in the determination of the kVp were compared with experimental data, validating the model proposed for the characterization of the CDO. The results shower of the CDO will be utilized in quality assurance programs in order to guarantee that the equipment fulfill the requirements of the Norm SVS No. 453/98 MS (Brazil) 'Directives of Radiation Protection in Medical and Dental Radiodiagnostic'. We conclude that the EGS4 is a suitable code Monte Carlo to simulate thermoluminescent dosimeters and experimental procedures employed in the routine of the quality control laboratory in diagnostic radiology. (author)
Adaptive mesh refinement and adjoint methods in geophysics simulations
Burstedde, Carsten
2013-04-01
It is an ongoing challenge to increase the resolution that can be achieved by numerical geophysics simulations. This applies to considering sub-kilometer mesh spacings in global-scale mantle convection simulations as well as to using frequencies up to 1 Hz in seismic wave propagation simulations. One central issue is the numerical cost, since for three-dimensional space discretizations, possibly combined with time stepping schemes, a doubling of resolution can lead to an increase in storage requirements and run time by factors between 8 and 16. A related challenge lies in the fact that an increase in resolution also increases the dimensionality of the model space that is needed to fully parametrize the physical properties of the simulated object (a.k.a. earth). Systems that exhibit a multiscale structure in space are candidates for employing adaptive mesh refinement, which varies the resolution locally. An example that we found well suited is the mantle, where plate boundaries and fault zones require a resolution on the km scale, while deeper area can be treated with 50 or 100 km mesh spacings. This approach effectively reduces the number of computational variables by several orders of magnitude. While in this case it is possible to derive the local adaptation pattern from known physical parameters, it is often unclear what are the most suitable criteria for adaptation. We will present the goal-oriented error estimation procedure, where such criteria are derived from an objective functional that represents the observables to be computed most accurately. Even though this approach is well studied, it is rarely used in the geophysics community. A related strategy to make finer resolution manageable is to design methods that automate the inference of model parameters. Tweaking more than a handful of numbers and judging the quality of the simulation by adhoc comparisons to known facts and observations is a tedious task and fundamentally limited by the turnaround times
Sánchez-Pérez, J F; Marín, F; Morales, J L; Cánovas, M; Alhama, F
2018-01-01
Mathematical models simulating different and representative engineering problem, atomic dry friction, the moving front problems and elastic and solid mechanics are presented in the form of a set of non-linear, coupled or not coupled differential equations. For different parameters values that influence the solution, the problem is numerically solved by the network method, which provides all the variables of the problems. Although the model is extremely sensitive to the above parameters, no assumptions are considered as regards the linearization of the variables. The design of the models, which are run on standard electrical circuit simulation software, is explained in detail. The network model results are compared with common numerical methods or experimental data, published in the scientific literature, to show the reliability of the model.
2018-01-01
Mathematical models simulating different and representative engineering problem, atomic dry friction, the moving front problems and elastic and solid mechanics are presented in the form of a set of non-linear, coupled or not coupled differential equations. For different parameters values that influence the solution, the problem is numerically solved by the network method, which provides all the variables of the problems. Although the model is extremely sensitive to the above parameters, no assumptions are considered as regards the linearization of the variables. The design of the models, which are run on standard electrical circuit simulation software, is explained in detail. The network model results are compared with common numerical methods or experimental data, published in the scientific literature, to show the reliability of the model. PMID:29518121
Simulation of Rossi-α method with analog Monte-Carlo method
International Nuclear Information System (INIS)
Lu Yuzhao; Xie Qilin; Song Lingli; Liu Hangang
2012-01-01
The analog Monte-Carlo code for simulating Rossi-α method based on Geant4 was developed. The prompt neutron decay constant α of six metal uranium configurations in Oak Ridge National Laboratory were calculated. α was also calculated by Burst-Neutron method and the result was consistent with the result of Rossi-α method. There is the difference between results of analog Monte-Carlo simulation and experiment, and the reasons for the difference is the gaps between uranium layers. The influence of gaps decrease as the sub-criticality deepens. The relative difference between results of analog Monte-Carlo simulation and experiment changes from 19% to 0.19%. (authors)
Reduction Methods for Real-time Simulations in Hybrid Testing
DEFF Research Database (Denmark)
Andersen, Sebastian
2016-01-01
Hybrid testing constitutes a cost-effective experimental full scale testing method. The method was introduced in the 1960's by Japanese researchers, as an alternative to conventional full scale testing and small scale material testing, such as shake table tests. The principle of the method...... is performed on a glass fibre reinforced polymer composite box girder. The test serves as a pilot test for prospective real-time tests on a wind turbine blade. The Taylor basis is implemented in the test, used to perform the numerical simulations. Despite of a number of introduced errors in the real...... is to divide a structure into a physical substructure and a numerical substructure, and couple these in a test. If the test is conducted in real-time it is referred to as real time hybrid testing. The hybrid testing concept has developed significantly since its introduction in the 1960', both with respect...
Directory of Open Access Journals (Sweden)
Schuetz CA
2015-06-01
Full Text Available Charles Andy Schuetz,1 Siew Hwa Ong,2 Matthias Blüher3 1Evidera Inc., Bethesda, MD, USA; 2Novartis Pharma AG, Basel, Switzerland; 3Department of Medicine, University of Leipzig, Leipzig, Germany Introduction: Dipeptidyl peptidase-4 (DPP-4 inhibitors are a class of oral antidiabetic agents for the treatment of type 2 diabetes mellitus, which lower blood glucose without causing severe hypoglycemia. However, the first cardiovascular (CV safety trials have only recently reported their results, and our understanding of these therapies remains incomplete. Using clinical trial simulations, we estimated the effectiveness of DPP-4 inhibitors in preventing major adverse cardiovascular events (MACE in a population like that enrolled in the SAVOR-TIMI (the Saxagliptin Assessment of Vascular Outcomes Recorded in Patients with Diabetes Mellitus – Thrombolysis in Myocardial Infarction 53 trial. Methods: We used the Archimedes Model to simulate a clinical trial of individuals (N=11,000 with diagnosed type 2 diabetes and elevated CV risk, based on established disease or multiple risk factors. The DPP-4 class was modeled with a meta-analysis of HbA1c and weight change, pooling results from published trials of alogliptin, linagliptin, saxagliptin, sitagliptin, and vildagliptin. The study treatments were added-on to standard care, and outcomes were tracked for 20 years. Results: The DPP-4 class was associated with an HbA1c drop of 0.66% (0.71%, 0.62% and a weight drop of 0.14 (-0.07, 0.36 kg. These biomarker improvements produced a relative risk (RR for MACE at 5 years of 0.977 (0.968, 0.986. The number needed to treat to prevent one occurrence of MACE at 5 years was 327 (233, 550 in the elevated CV risk population. Conclusion: Consistent with recent trial publications, our analysis indicates that DPP-4 inhibitors do not increase the risk of MACE relative to the standard of care. This study provides insights about the long-term benefits of DPP-4 inhibitors and
MD 1691: Active halo control using tune ripple at injection
Garcia Morales, Hector; Bruce, Roderik; Redaelli, Stefano; Fitterer, Miriam; Fiascaris, Maria; Nisbet, David; Thiesen, Hugues; Valentino, Gianluca; Xu, Chen; CERN. Geneva. ATS Department
2017-01-01
In this MD we performed halo excitation through tune ripple. This consists in an excitation that introduces new resonance sidebands around the existing resonance lines. In presence of sufficient detuning with amplitude, these sidebands can in principle affect only the dynamics of the halo particles at large amplitudes. Tune ripple was induced through a current modulation of the warm trim quadrupoles in IR7. This is the first time this method is experimentally tested at the LHC.
Jun, Gyuchan T; Morris, Zoe; Eldabi, Tillal; Harper, Paul; Naseer, Aisha; Patel, Brijesh; Clarkson, John P
2011-05-19
There is an increasing recognition that modelling and simulation can assist in the process of designing health care policies, strategies and operations. However, the current use is limited and answers to questions such as what methods to use and when remain somewhat underdeveloped. The aim of this study is to provide a mechanism for decision makers in health services planning and management to compare a broad range of modelling and simulation methods so that they can better select and use them or better commission relevant modelling and simulation work. This paper proposes a modelling and simulation method comparison and selection tool developed from a comprehensive literature review, the research team's extensive expertise and inputs from potential users. Twenty-eight different methods were identified, characterised by their relevance to different application areas, project life cycle stages, types of output and levels of insight, and four input resources required (time, money, knowledge and data). The characterisation is presented in matrix forms to allow quick comparison and selection. This paper also highlights significant knowledge gaps in the existing literature when assessing the applicability of particular approaches to health services management, where modelling and simulation skills are scarce let alone money and time. A modelling and simulation method comparison and selection tool is developed to assist with the selection of methods appropriate to supporting specific decision making processes. In particular it addresses the issue of which method is most appropriate to which specific health services management problem, what the user might expect to be obtained from the method, and what is required to use the method. In summary, we believe the tool adds value to the scarce existing literature on methods comparison and selection.
Rapid simulation of spatial epidemics: a spectral method.
Brand, Samuel P C; Tildesley, Michael J; Keeling, Matthew J
2015-04-07
Spatial structure and hence the spatial position of host populations plays a vital role in the spread of infection. In the majority of situations, it is only possible to predict the spatial spread of infection using simulation models, which can be computationally demanding especially for large population sizes. Here we develop an approximation method that vastly reduces this computational burden. We assume that the transmission rates between individuals or sub-populations are determined by a spatial transmission kernel. This kernel is assumed to be isotropic, such that the transmission rate is simply a function of the distance between susceptible and infectious individuals; as such this provides the ideal mechanism for modelling localised transmission in a spatial environment. We show that the spatial force of infection acting on all susceptibles can be represented as a spatial convolution between the transmission kernel and a spatially extended 'image' of the infection state. This representation allows the rapid calculation of stochastic rates of infection using fast-Fourier transform (FFT) routines, which greatly improves the computational efficiency of spatial simulations. We demonstrate the efficiency and accuracy of this fast spectral rate recalculation (FSR) method with two examples: an idealised scenario simulating an SIR-type epidemic outbreak amongst N habitats distributed across a two-dimensional plane; the spread of infection between US cattle farms, illustrating that the FSR method makes continental-scale outbreak forecasting feasible with desktop processing power. The latter model demonstrates which areas of the US are at consistently high risk for cattle-infections, although predictions of epidemic size are highly dependent on assumptions about the tail of the transmission kernel. Copyright © 2015 Elsevier Ltd. All rights reserved.
Discrete vortex method simulations of aerodynamic admittance in bridge aerodynamics
DEFF Research Database (Denmark)
Rasmussen, Johannes Tophøj; Hejlesen, Mads Mølholm; Larsen, Allan
, and to determine aerodynamic forces and the corresponding ﬂutter limit. A simulation of the three-dimensional bridge responseto turbulent wind is carried out by quasi steady theory by modelling the bridge girder as a line like structure [2], applying the aerodynamic load coefﬁcients found from the current version......The meshless and remeshed Discrete Vortex Method (DVM) has been widely used in academia and by the industry to model two-dimensional ﬂow around bluff bodies. The implementation “DVMFLOW” [1] is used by the bridge design company COWI to determine and visualise the ﬂow ﬁeld around bridge sections...
Numerical Simulation of Plasma Antenna with FDTD Method
International Nuclear Information System (INIS)
Chao, Liang; Yue-Min, Xu; Zhi-Jiang, Wang
2008-01-01
We adopt cylindrical-coordinate FDTD algorithm to simulate and analyse a 0.4-m-long column configuration plasma antenna. FDTD method is useful for solving electromagnetic problems, especially when wave characteristics and plasma properties are self-consistently related to each other. Focus on the frequency from 75 MHz to 400 MHz, the input impedance and radiation efficiency of plasma antennas are computed. Numerical results show that, different from copper antenna, the characteristics of plasma antenna vary simultaneously with plasma frequency and collision frequency. The property can be used to construct dynamically reconBgurable antenna. The investigation is meaningful and instructional for the optimization of plasma antenna design
Numerical simulation of plasma antenna with FDTD method
International Nuclear Information System (INIS)
Liang Chao; Xu Yuemin; Wang Zhijiang
2008-01-01
We adopt cylindrical-coordinate FDTD algorithm to simulate and analyse a 0.4-m-long column configuration plasma antenna. FDTD method is useful for solving electromagnetic problems, especially when wave characteristics and plasma properties are self-consistently related to each other. Focus on the frequency from 75 MHz to 400 MHz, the input impedance and radiation efficiency of plasma antennas are computed. Numerical results show that, different from copper antenna, the characteristics of plasma antenna vary simultaneously with plasma frequency and collision frequency. The property can be used to construct dynamically reconfigurable antenna. The investigation is meaningful and instructional for the optimization of plasma antenna design. (authors)
Three-dimensional discrete element method simulation of core disking
Wu, Shunchuan; Wu, Haoyan; Kemeny, John
2018-04-01
The phenomenon of core disking is commonly seen in deep drilling of highly stressed regions in the Earth's crust. Given its close relationship with the in situ stress state, the presence and features of core disking can be used to interpret the stresses when traditional in situ stress measuring techniques are not available. The core disking process was simulated in this paper using the three-dimensional discrete element method software PFC3D (particle flow code). In particular, PFC3D is used to examine the evolution of fracture initiation, propagation and coalescence associated with core disking under various stress states. In this paper, four unresolved problems concerning core disking are investigated with a series of numerical simulations. These simulations also provide some verification of existing results by other researchers: (1) Core disking occurs when the maximum principal stress is about 6.5 times the tensile strength. (2) For most stress situations, core disking occurs from the outer surface, except for the thrust faulting stress regime, where the fractures were found to initiate from the inner part. (3) The anisotropy of the two horizontal principal stresses has an effect on the core disking morphology. (4) The thickness of core disk has a positive relationship with radial stress and a negative relationship with axial stresses.
Simulation of ecological processes using response functions method
International Nuclear Information System (INIS)
Malkina-Pykh, I.G.; Pykh, Yu. A.
1998-01-01
The article describes further development and applications of the already well-known response functions method (MRF). The method is used as a basis for the development of mathematical models of a wide set of ecological processes. The model of radioactive contamination of the ecosystems is chosen as an example. The mathematical model was elaborated for the description of 90 Sr dynamics in the elementary ecosystems of various geographical zones. The model includes the blocks corresponding with the main units of any elementary ecosystem: lower atmosphere, soil, vegetation, surface water. Parameters' evaluation was provided on a wide set of experimental data. A set of computer simulations was done on the model to prove the possibility of the model's use for ecological forecasting
Simulation of bubble motion under gravity by lattice Boltzmann method
International Nuclear Information System (INIS)
Takada, Naoki; Misawa, Masaki; Tomiyama, Akio; Hosokawa, Shigeo
2001-01-01
We describe the numerical simulation results of bubble motion under gravity by the lattice Boltzmann method (LBM), which assumes that a fluid consists of mesoscopic fluid particles repeating collision and translation and a multiphase interface is reproduced in a self-organizing way by repulsive interaction between different kinds of particles. The purposes in this study are to examine the applicability of LBM to the numerical analysis of bubble motions, and to develop a three-dimensional version of the binary fluid model that introduces a free energy function. We included the buoyancy terms due to the density difference in the lattice Boltzmann equations, and simulated single-and two-bubble motions, setting flow conditions according to the Eoetvoes and Morton numbers. The two-dimensional results by LBM agree with those by the Volume of Fluid method based on the Navier-Stokes equations. The three-dimensional model possesses the surface tension satisfying the Laplace's law, and reproduces the motion of single bubble and the two-bubble interaction of their approach and coalescence in circular tube. There results prove that the buoyancy terms and the 3D model proposed here are suitable, and that LBM is useful for the numerical analysis of bubble motion under gravity. (author)
Research methods of simulate digital compensators and autonomous control systems
Directory of Open Access Journals (Sweden)
V. S. Kudryashov
2016-01-01
Full Text Available The peculiarity of the present stage of development of the production is the need to control and regulate a large number of process parameters, the mutual influence on each other that when using single-circuit systems significantly reduces the quality of the transition process, resulting in significant costs of raw materials and energy, reduce the quality of the products. Using a stand-alone digital control system eliminates the correlation of technological parameters, to give the system the desired dynamic and static properties, improve the quality of regulation. However, the complexity of the configuration and implementation of procedures (modeling compensators autonomous systems of this type, associated with the need to perform a significant amount of complex analytic transformation significantly limit the scope of their application. In this regard, the approach based on the decompo sition proposed methods of calculation and simulation (realization, consisting in submitting elements autonomous control part digital control system in a series parallel connection. The above theoretical study carried out in a general way for any dimension systems. The results of computational experiments, obtained during the simulation of the four autonomous control systems, comparative analysis and conclusions on the effectiveness of the use of each of the methods. The results obtained can be used in the development of multi-dimensional process control systems.
Czech Academy of Sciences Publication Activity Database
Havrila, Marek; Zgarbová, M.; Jurečka, P.; Banáš, P.; Krepl, Miroslav; Otyepka, M.; Šponer, Jiří
2015-01-01
Roč. 119, č. 49 (2015), s. 15176-15190 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DIMERIZATION INITIATION SITE * QUANTUM-CHEMICAL COMPUTATIONS Subject RIV: BO - Biophysics Impact factor: 3.187, year: 2015
Review of 40-year MD theses in Medical Oncology
International Nuclear Information System (INIS)
Zeeneldin, A.; Diyaa, A.; Elgammal, M.; Buhoush, W.; Manar Moneer, M.
2014-01-01
Background and objective: It is almost 40 years since the foundation of the Medical Oncology (MO) Department. We aimed to appraise the clinical research to fulfill the Medical Doctorate (MD) degree in MO at the National Cancer Institute, Cairo University (NCI, CU). Methods: This review included 62 MD theses containing 66 studies. They were reviewed regarding aims, type of study, clinical trial phase, design and methodology, statistical tests, results, limitations, consent and IRB approval. Theses were grouped into 3 periods: 1970-1989, 1990-1999 and 2000- 2008. Results: Almost 76% of the studies were interventional and 24% were observational. Informed consent and Institutional Review Board approval were mentioned in 18 and 2 studies, respectively. While all studies mentioned the aims, none, clearly mentioned the research question. Outcomes were mainly efficacy followed by safety. Study design was inadequately considered, especially in 70’s–80’s period (p = 0.038). Median sample size and study duration were almost stable through the three periods (p = 0.441, 0.354, respectively). Most of the studies used both descriptive and analytical statistical methods. In a descending order, researched cancers were lymphoma, breast, leukemia, liver, urinary bladder, lung and colorectal. The commonest stages researched were IV and III. The number of studies focused on assessing biomarkers, biomarkers plus drugs/procedures, drugs and procedures are 20, 20, 16 and 6, respectively. Conclusion: With time, research within MD theses in MO increased quantitatively and qualitatively. Improvements were noticeable in documentation of study design.
2010-08-05
... Airworthiness Directives; McDonnell Douglas Corporation Model MD- 11 and MD-11F Airplanes Equipped With General... Sec. 39.13 by adding the following new AD: 2010-16-03 McDonnell Douglas Corporation: Amendment 39... applies to McDonnell Douglas Corporation Model MD-11 and MD-11F airplanes, certified in any category...
High accuracy mantle convection simulation through modern numerical methods
Kronbichler, Martin
2012-08-21
Numerical simulation of the processes in the Earth\\'s mantle is a key piece in understanding its dynamics, composition, history and interaction with the lithosphere and the Earth\\'s core. However, doing so presents many practical difficulties related to the numerical methods that can accurately represent these processes at relevant scales. This paper presents an overview of the state of the art in algorithms for high-Rayleigh number flows such as those in the Earth\\'s mantle, and discusses their implementation in the Open Source code Aspect (Advanced Solver for Problems in Earth\\'s ConvecTion). Specifically, we show how an interconnected set of methods for adaptive mesh refinement (AMR), higher order spatial and temporal discretizations, advection stabilization and efficient linear solvers can provide high accuracy at a numerical cost unachievable with traditional methods, and how these methods can be designed in a way so that they scale to large numbers of processors on compute clusters. Aspect relies on the numerical software packages deal.II and Trilinos, enabling us to focus on high level code and keeping our implementation compact. We present results from validation tests using widely used benchmarks for our code, as well as scaling results from parallel runs. © 2012 The Authors Geophysical Journal International © 2012 RAS.
MD2190: Q" Stabilization during injection
Schenk, Michael; Li, Kevin Shing Bruce; Malina, Lukas; Metral, Elias; Tomas Garcia, Rogelio; CERN. Geneva. ATS Department
2018-01-01
This MD is a follow-up study of MD1831, where single bunches were stabilized against impedance-driven instabilities at 6.5 TeV in the LHC with Q''. The goals are (i) to explore whether an amplitude detuning free Q'' knob can be implemented at injection energy, and (ii) whether Q'' can provide beam stability at injection, where the beams suffer mostly from electron cloud effects. Ideally, this would relax the use of the Landau octupoles and may help in preserving the beam quality by reducing dynamic aperture limitations originating from the octupoles. The MD has been split into two parts: First, optics corrections were put in place to minimize beta-beating and linear coupling introduced by the knobs. The corrections were achieved by means of orbit bumps and skew quadrupole knobs. Machine safety was then validated with loss maps. While the betatron loss maps were approved, the off-momentum maps showed a priori unexpected losses in several arcs and the MD was stopped at this point for reasons of machine protecti...
MD2725: 16L2 aperture measurement
Mirarchi, Daniele; Rossi, Roberto; CERN. Geneva. ATS Department
2018-01-01
Dumps induced by sudden increase of losses in the half-cell 16L2 have been a serious machine limitation during the 2017 run. The aim of this MD was to perform local aperture measurements in order to assess diﬀerences after the beam screen regeneration, compared to ﬁrst measurements in 2017.
Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash;
2002-01-01
A multidisciplinary, collaborative simulation has been performed on a Grid of geographically distributed PC clusters. The multiscale simulation approach seamlessly combines i) atomistic simulation backed on the molecular dynamics (MD) method and ii) quantum mechanical (QM) calculation based on the density functional theory (DFT), so that accurate but less scalable computations are performed only where they are needed. The multiscale MD/QM simulation code has been Grid-enabled using i) a modular, additive hybridization scheme, ii) multiple QM clustering, and iii) computation/communication overlapping. The Gridified MD/QM simulation code has been used to study environmental effects of water molecules on fracture in silicon. A preliminary run of the code has achieved a parallel efficiency of 94% on 25 PCs distributed over 3 PC clusters in the US and Japan, and a larger test involving 154 processors on 5 distributed PC clusters is in progress.
A survey of modelling methods for high-fidelity wind farm simulations using large eddy simulation
DEFF Research Database (Denmark)
Breton, Simon-Philippe; Sumner, J.; Sørensen, Jens Nørkær
2017-01-01
surveys the most common schemes available to model the rotor, atmospheric conditions and terrain effects within current state-of-the-art LES codes, of which an overview is provided. A summary of the experimental research data available for validation of LES codes within the context of single and multiple......Large eddy simulations (LES) of wind farms have the capability to provide valuable and detailed information about the dynamics of wind turbine wakes. For this reason, their use within the wind energy research community is on the rise, spurring the development of new models and methods. This review...
Temperature dependence of gafchromic MD-55 dosimeter
International Nuclear Information System (INIS)
Klassen, Norman V.; Zwan, Len van der; Cygler, Joanna
1997-01-01
Objective: Gafchromic MD-55 is a fairly new, thin film dosimeter that develops a blue color (λ max = 676 nm) when irradiated with ionizing radiation. The increase in absorbance is nearly proportional to the absorbed dose. MD-55 can be used for high precision dosimetry if care is taken to assure reproducible film orientation in the spectrophotometer as well as temperature control during both irradiation and reading. In order to achieve the maximum sensitivity of this dosimeter the readings of the optical density should be taken at λ max . It was reported for another type of Gafchromic film (DM-1260), that both λ max and ε max decrease with an increase in the temperature of the spectrophotometer. The purpose of this study was to characterize the reading temperature dependence of the new type of Gafchromic film available on the market and to find optimal conditions for using it for high precision dosimetry. Materials and Methods: Irradiations were carried out using 60 Co gamma rays from an Eldorado irradiator. The dosimeters were sandwiched in a lucite phantom with 4.4 mm build-up and irradiated in the center of a 10 cm x 10 cm field at 1 meter from the source. The temperature during irradiations was 22 deg. C. The dose rate was about 0.68 Gy/min. Measurements of optical density were made using a Cary 210 spectrophotometer. A bandpass of 3.5 nm was used. The temperature of the baseplate of the sample holder was regulated to +/-0.05 deg. C and measured by a probe lying on the baseplate. In all cases, values of OD were only recorded after they had come to a constant value, which was reached within 5 minutes of inserting the dosimeter into the sample chamber of the spectrophotometer. Results: The temperature dependence of the OD at 676 nm was measured in 2 studies using 6 dosimeters that had received 0, 1.0, 3.5, 6.2, 14.5 Gy. Readings were taken at 7 temperatures between 18.8 and 28.1 deg. C. By returning to the initial temperature several hours later, it was found
Directory of Open Access Journals (Sweden)
Dilraj Lama
Full Text Available Bcl-XL is a member of Bcl-2 family of proteins involved in the regulation of intrinsic pathway of apoptosis. Its overexpression in many human cancers makes it an important target for anti-cancer drugs. Bcl-XL interacts with the BH3 domain of several pro-apoptotic Bcl-2 partners. This helical bundle protein has a pronounced hydrophobic groove which acts as a binding region for the BH3 domains. Eight independent molecular dynamics simulations of the apo/holo forms of Bcl-XL were carried out to investigate the behavior of solvent-exposed hydrophobic groove. The simulations used either a twin-range cut-off or particle mesh Ewald (PME scheme to treat long-range interactions. Destabilization of the BH3 domain-containing helix H2 was observed in all four twin-range cut-off simulations. Most of the other major helices remained stable. The unwinding of H2 can be related to the ability of Bcl-XL to bind diverse BH3 ligands. The loss of helical character can also be linked to the formation of homo- or hetero-dimers in Bcl-2 proteins. Several experimental studies have suggested that exposure of BH3 domain is a crucial event before they form dimers. Thus unwinding of H2 seems to be functionally very important. The four PME simulations, however, revealed a stable helix H2. It is possible that the H2 unfolding might occur in PME simulations at longer time scales. Hydrophobic residues in the hydrophobic groove are involved in stable interactions among themselves. The solvent accessible surface areas of bulky hydrophobic residues in the groove are significantly buried by the loop LB connecting the helix H2 and subsequent helix. These observations help to understand how the hydrophobic patch in Bcl-XL remains stable in the solvent-exposed state. We suggest that both the destabilization of helix H2 and the conformational heterogeneity of loop LB are important factors for binding of diverse ligands in the hydrophobic groove of Bcl-XL.
A hybrid multiscale kinetic Monte Carlo method for simulation of copper electrodeposition
International Nuclear Information System (INIS)
Zheng Zheming; Stephens, Ryan M.; Braatz, Richard D.; Alkire, Richard C.; Petzold, Linda R.
2008-01-01
A hybrid multiscale kinetic Monte Carlo (HMKMC) method for speeding up the simulation of copper electrodeposition is presented. The fast diffusion events are simulated deterministically with a heterogeneous diffusion model which considers site-blocking effects of additives. Chemical reactions are simulated by an accelerated (tau-leaping) method for discrete stochastic simulation which adaptively selects exact discrete stochastic simulation for the appropriate reaction whenever that is necessary. The HMKMC method is seen to be accurate and highly efficient
A calculation method for RF couplers design based on numerical simulation by microwave studio
International Nuclear Information System (INIS)
Wang Rong; Pei Yuanji; Jin Kai
2006-01-01
A numerical simulation method for coupler design is proposed. It is based on the matching procedure for the 2π/3 structure given by Dr. R.L. Kyhl. Microwave Studio EigenMode Solver is used for such numerical simulation. the simulation for a coupler has been finished with this method and the simulation data are compared with experimental measurements. The results show that this numerical simulation method is feasible for coupler design. (authors)
MD-11 PCA - Research flight team photo
1995-01-01
On Aug. 30, 1995, a the McDonnell Douglas MD-11 transport aircraft landed equipped with a computer-assisted engine control system that has the potential to increase flight safety. In landings at NASA Dryden Flight Research Center, Edwards, California, on August 29 and 30, the aircraft demonstrated software used in the aircraft's flight control computer that essentially landed the MD-11 without a need for the pilot to manipulate the flight controls significantly. In partnership with McDonnell Douglas Aerospace (MDA), with Pratt & Whitney and Honeywell helping to design the software, NASA developed this propulsion-controlled aircraft (PCA) system following a series of incidents in which hydraulic failures resulted in the loss of flight controls. This new system enables a pilot to operate and land the aircraft safely when its normal, hydraulically-activated control surfaces are disabled. This August 29, 1995, photo shows the MD-11 team. Back row, left to right: Tim Dingen, MDA pilot; John Miller, MD-11 Chief pilot (MDA); Wayne Anselmo, MD-11 Flight Test Engineer (MDA); Gordon Fullerton, PCA Project pilot; Bill Burcham, PCA Chief Engineer; Rudey Duran, PCA Controls Engineer (MDA); John Feather, PCA Controls Engineer (MDA); Daryl Townsend, Crew Chief; Henry Hernandez, aircraft mechanic; Bob Baron, PCA Project Manager; Don Hermann, aircraft mechanic; Jerry Cousins, aircraft mechanic; Eric Petersen, PCA Manager (Honeywell); Trindel Maine, PCA Data Engineer; Jeff Kahler, PCA Software Engineer (Honeywell); Steve Goldthorpe, PCA Controls Engineer (MDA). Front row, left to right: Teresa Hass, Senior Project Management Analyst; Hollie Allingham (Aguilera), Senior Project Management Analyst; Taher Zeglum, PCA Data Engineer (MDA); Drew Pappas, PCA Project Manager (MDA); John Burken, PCA Control Engineer.
Adaptive and dynamic meshing methods for numerical simulations
Acikgoz, Nazmiye
-hoc application of the simulated annealing technique, which improves the likelihood of removing poor elements from the grid. Moreover, a local implementation of the simulated annealing is proposed to reduce the computational cost. Many challenging multi-physics and multi-field problems that are unsteady in nature are characterized by moving boundaries and/or interfaces. When the boundary displacements are large, which typically occurs when implicit time marching procedures are used, degenerate elements are easily formed in the grid such that frequent remeshing is required. To deal with this problem, in the second part of this work, we propose a new r-adaptation methodology. The new technique is valid for both simplicial (e.g., triangular, tet) and non-simplicial (e.g., quadrilateral, hex) deforming grids that undergo large imposed displacements at their boundaries. A two- or three-dimensional grid is deformed using a network of linear springs composed of edge springs and a set of virtual springs. The virtual springs are constructed in such a way as to oppose element collapsing. This is accomplished by confining each vertex to its ball through springs that are attached to the vertex and its projection on the ball entities. The resulting linear problem is solved using a preconditioned conjugate gradient method. The new method is compared with the classical spring analogy technique in two- and three-dimensional examples, highlighting the performance improvements achieved by the new method. Meshes are an important part of numerical simulations. Depending on the geometry and flow conditions, the most suitable mesh for each particular problem is different. Meshes are usually generated by either using a suitable software package or solving a PDE. In both cases, engineering intuition plays a significant role in deciding where clusterings should take place. In addition, for unsteady problems, the gradients vary for each time step, which requires frequent remeshing during simulations
Applying Simulation Method in Formulation of Gluten-Free Cookies
Directory of Open Access Journals (Sweden)
Nikitina Marina
2017-01-01
Full Text Available At present time priority direction in the development of new food products its developing of technology products for special purposes. These types of products are gluten-free confectionery products, intended for people with celiac disease. Gluten-free products are in demand among consumers, it needs to expand assortment, and improvement of quality indicators. At this article results of studies on the development of pastry products based on amaranth flour does not contain gluten. Study based on method of simulation recipes gluten-free confectionery functional orientation to optimize their chemical composition. The resulting products will allow to diversify and supplement the necessary nutrients diet for people with gluten intolerance, as well as for those who follow a gluten-free diet.
The Multiscale Material Point Method for Simulating Transient Responses
Chen, Zhen; Su, Yu-Chen; Zhang, Hetao; Jiang, Shan; Sewell, Thomas
2015-06-01
To effectively simulate multiscale transient responses such as impact and penetration without invoking master/slave treatment, the multiscale material point method (Multi-MPM) is being developed in which molecular dynamics at nanoscale and dissipative particle dynamics at mesoscale might be concurrently handled within the framework of the original MPM at microscale (continuum level). The proposed numerical scheme for concurrently linking different scales is described in this paper with simple examples for demonstration. It is shown from the preliminary study that the mapping and re-mapping procedure used in the original MPM could coarse-grain the information at fine scale and that the proposed interfacial scheme could provide a smooth link between different scales. Since the original MPM is an extension from computational fluid dynamics to solid dynamics, the proposed Multi-MPM might also become robust for dealing with multiphase interactions involving failure evolution. This work is supported in part by DTRA and NSFC.
Numerical Simulation of Antennas with Improved Integral Equation Method
International Nuclear Information System (INIS)
Ma Ji; Fang Guang-You; Lu Wei
2015-01-01
Simulating antennas around a conducting object is a challenge task in computational electromagnetism, which is concerned with the behaviour of electromagnetic fields. To analyze this model efficiently, an improved integral equation-fast Fourier transform (IE-FFT) algorithm is presented in this paper. The proposed scheme employs two Cartesian grids with different size and location to enclose the antenna and the other object, respectively. On the one hand, IE-FFT technique is used to store matrix in a sparse form and accelerate the matrix-vector multiplication for each sub-domain independently. On the other hand, the mutual interaction between sub-domains is taken as the additional exciting voltage in each matrix equation. By updating integral equations several times, the whole electromagnetic system can achieve a stable status. Finally, the validity of the presented method is verified through the analysis of typical antennas in the presence of a conducting object. (paper)
Optimized Design of Spacer in Electrodialyzer Using CFD Simulation Method
Jia, Yuxiang; Yan, Chunsheng; Chen, Lijun; Hu, Yangdong
2018-06-01
In this study, the effects of length-width ratio and diversion trench of the spacer on the fluid flow behavior in an electrodialyzer have been investigated through CFD simulation method. The relevant information, including the pressure drop, velocity vector distribution and shear stress distribution, demonstrates the importance of optimized design of the spacer in an electrodialysis process. The results show width of the diversion trench has a great effect on the fluid flow compared with length. Increase of the diversion trench width could strength the fluid flow, but also increase the pressure drop. Secondly, the dead zone of the fluid flow decreases with increase of length-width ratio of the spacer, but the pressure drop increases with the increase of length-width ratio of the spacer. So the appropriate length-width ratio of the space should be moderate.
Study of Flapping Flight Using Discrete Vortex Method Based Simulations
Devranjan, S.; Jalikop, Shreyas V.; Sreenivas, K. R.
2013-12-01
In recent times, research in the area of flapping flight has attracted renewed interest with an endeavor to use this mechanism in Micro Air vehicles (MAVs). For a sustained and high-endurance flight, having larger payload carrying capacity we need to identify a simple and efficient flapping-kinematics. In this paper, we have used flow visualizations and Discrete Vortex Method (DVM) based simulations for the study of flapping flight. Our results highlight that simple flapping kinematics with down-stroke period (tD) shorter than the upstroke period (tU) would produce a sustained lift. We have identified optimal asymmetry ratio (Ar = tD/tU), for which flapping-wings will produce maximum lift and find that introducing optimal wing flexibility will further enhances the lift.
Simulation of galvanic corrosion using boundary element method
International Nuclear Information System (INIS)
Zaifol Samsu; Muhamad Daud; Siti Radiah Mohd Kamaruddin; Nur Ubaidah Saidin; Abdul Aziz Mohamed; Mohd Saari Ripin; Rusni Rejab; Mohd Shariff Sattar
2011-01-01
Boundary element method (BEM) is a numerical technique that used for modeling infinite domain as is the case for galvanic corrosion analysis. The use of boundary element analysis system (BEASY) has allowed cathodic protection (CP) interference to be assessed in terms of the normal current density, which is directly proportional to the corrosion rate. This paper was present the analysis of the galvanic corrosion between Aluminium and Carbon Steel in natural sea water. The result of experimental was validated with computer simulation like BEASY program. Finally, it can conclude that the BEASY software is a very helpful tool for future planning before installing any structure, where it gives the possible CP interference on any nearby unprotected metallic structure. (Author)
An experiment teaching method based on the Optisystem simulation platform
Zhu, Jihua; Xiao, Xuanlu; Luo, Yuan
2017-08-01
The experiment teaching of optical communication system is difficult to achieve because of expensive equipment. The Optisystem is optical communication system design software, being able to provide such a simulation platform. According to the characteristic of the OptiSystem, an approach of experiment teaching is put forward in this paper. It includes three gradual levels, the basics, the deeper looks and the practices. Firstly, the basics introduce a brief overview of the technology, then the deeper looks include demoes and example analyses, lastly the practices are going on through the team seminars and comments. A variety of teaching forms are implemented in class. The fact proves that this method can not only make up the laboratory but also motivate the students' learning interest and improve their practical abilities, cooperation abilities and creative spirits. On the whole, it greatly raises the teaching effect.
A Finite Element Method for Simulation of Compressible Cavitating Flows
Shams, Ehsan; Yang, Fan; Zhang, Yu; Sahni, Onkar; Shephard, Mark; Oberai, Assad
2016-11-01
This work focuses on a novel approach for finite element simulations of multi-phase flows which involve evolving interface with phase change. Modeling problems, such as cavitation, requires addressing multiple challenges, including compressibility of the vapor phase, interface physics caused by mass, momentum and energy fluxes. We have developed a mathematically consistent and robust computational approach to address these problems. We use stabilized finite element methods on unstructured meshes to solve for the compressible Navier-Stokes equations. Arbitrary Lagrangian-Eulerian formulation is used to handle the interface motions. Our method uses a mesh adaptation strategy to preserve the quality of the volumetric mesh, while the interface mesh moves along with the interface. The interface jump conditions are accurately represented using a discontinuous Galerkin method on the conservation laws. Condensation and evaporation rates at the interface are thermodynamically modeled to determine the interface velocity. We will present initial results on bubble cavitation the behavior of an attached cavitation zone in a separated boundary layer. We acknowledge the support from Army Research Office (ARO) under ARO Grant W911NF-14-1-0301.
Steam generator tube rupture simulation using extended finite element method
Energy Technology Data Exchange (ETDEWEB)
Mohanty, Subhasish, E-mail: smohanty@anl.gov; Majumdar, Saurin; Natesan, Ken
2016-08-15
Highlights: • Extended finite element method used for modeling the steam generator tube rupture. • Crack propagation is modeled in an arbitrary solution dependent path. • The FE model is used for estimating the rupture pressure of steam generator tubes. • Crack coalescence modeling is also demonstrated. • The method can be used for crack modeling of tubes under severe accident condition. - Abstract: A steam generator (SG) is an important component of any pressurized water reactor. Steam generator tubes represent a primary pressure boundary whose integrity is vital to the safe operation of the reactor. SG tubes may rupture due to propagation of a crack created by mechanisms such as stress corrosion cracking, fatigue, etc. It is thus important to estimate the rupture pressures of cracked tubes for structural integrity evaluation of SGs. The objective of the present paper is to demonstrate the use of extended finite element method capability of commercially available ABAQUS software, to model SG tubes with preexisting flaws and to estimate their rupture pressures. For the purpose, elastic–plastic finite element models were developed for different SG tubes made from Alloy 600 material. The simulation results were compared with experimental results available from the steam generator tube integrity program (SGTIP) sponsored by the United States Nuclear Regulatory Commission (NRC) and conducted at Argonne National Laboratory (ANL). A reasonable correlation was found between extended finite element model results and experimental results.
Precision of a FDTD method to simulate cold magnetized plasmas
International Nuclear Information System (INIS)
Pavlenko, I.V.; Melnyk, D.A.; Prokaieva, A.O.; Girka, I.O.
2014-01-01
The finite difference time domain (FDTD) method is applied to describe the propagation of the transverse electromagnetic waves through the magnetized plasmas. The numerical dispersion relation is obtained in a cold plasma approximation. The accuracy of the numerical dispersion is calculated as a function of the frequency of the launched wave and time step of the numerical grid. It is shown that the numerical method does not reproduce the analytical results near the plasma resonances for any chosen value of time step if there is not a dissipation mechanism in the system. It means that FDTD method cannot be applied straightforward to simulate the problems where the plasma resonances play a key role (for example, the mode conversion problems). But the accuracy of the numerical scheme can be improved by introducing some artificial damping of the plasma currents. Although part of the wave power is lost in the system in this case but the numerical scheme describes the wave processes in an agreement with analytical predictions.
Steam generator tube rupture simulation using extended finite element method
International Nuclear Information System (INIS)
Mohanty, Subhasish; Majumdar, Saurin; Natesan, Ken
2016-01-01
Highlights: • Extended finite element method used for modeling the steam generator tube rupture. • Crack propagation is modeled in an arbitrary solution dependent path. • The FE model is used for estimating the rupture pressure of steam generator tubes. • Crack coalescence modeling is also demonstrated. • The method can be used for crack modeling of tubes under severe accident condition. - Abstract: A steam generator (SG) is an important component of any pressurized water reactor. Steam generator tubes represent a primary pressure boundary whose integrity is vital to the safe operation of the reactor. SG tubes may rupture due to propagation of a crack created by mechanisms such as stress corrosion cracking, fatigue, etc. It is thus important to estimate the rupture pressures of cracked tubes for structural integrity evaluation of SGs. The objective of the present paper is to demonstrate the use of extended finite element method capability of commercially available ABAQUS software, to model SG tubes with preexisting flaws and to estimate their rupture pressures. For the purpose, elastic–plastic finite element models were developed for different SG tubes made from Alloy 600 material. The simulation results were compared with experimental results available from the steam generator tube integrity program (SGTIP) sponsored by the United States Nuclear Regulatory Commission (NRC) and conducted at Argonne National Laboratory (ANL). A reasonable correlation was found between extended finite element model results and experimental results.
Kwan, Jennifer M; Daye, Dania; Schmidt, Mary Lou; Conlon, Claudia Morrissey; Kim, Hajwa; Gaonkar, Bilwaj; Payne, Aimee S; Riddle, Megan; Madera, Sharline; Adami, Alexander J; Winter, Kate Quinn
2017-07-11
Prior studies have described the career paths of physician-scientist candidates after graduation, but the factors that influence career choices at the candidate stage remain unclear. Additionally, previous work has focused on MD/PhDs, despite many physician-scientists being MDs. This study sought to identify career sector intentions, important factors in career selection, and experienced and predicted obstacles to career success that influence the career choices of MD candidates, MD candidates with research-intense career intentions (MD-RI), and MD/PhD candidates. A 70-question survey was administered to students at 5 academic medical centers with Medical Scientist Training Programs (MSTPs) and Clinical and Translational Science Awards (CTSA) from the NIH. Data were analyzed using bivariate or multivariate analyses. More MD/PhD and MD-RI candidates anticipated or had experienced obstacles related to balancing academic and family responsibilities and to balancing clinical, research, and education responsibilities, whereas more MD candidates indicated experienced and predicted obstacles related to loan repayment. MD/PhD candidates expressed higher interest in basic and translational research compared to MD-RI candidates, who indicated more interest in clinical research. Overall, MD-RI candidates displayed a profile distinct from both MD/PhD and MD candidates. MD/PhD and MD-RI candidates experience obstacles that influence their intentions to pursue academic medical careers from the earliest training stage, obstacles which differ from those of their MD peers. The differences between the aspirations of and challenges facing MD, MD-RI and MD/PhD candidates present opportunities for training programs to target curricula and support services to ensure the career development of successful physician-scientists.
Sun, Yang; Song, Huajing; Zhang, Feng; Yang, Lin; Ye, Zhuo; Mendelev, Mikhail I; Wang, Cai-Zhuang; Ho, Kai-Ming
2018-02-23
The crystal nucleation from liquid in most cases is too rare to be accessed within the limited time scales of the conventional molecular dynamics (MD) simulation. Here, we developed a "persistent embryo" method to facilitate crystal nucleation in MD simulations by preventing small crystal embryos from melting using external spring forces. We applied this method to the pure Ni case for a moderate undercooling where no nucleation can be observed in the conventional MD simulation, and obtained nucleation rate in good agreement with the experimental data. Moreover, the method is applied to simulate an even more sluggish event: the nucleation of the B2 phase in a strong glass-forming Cu-Zr alloy. The nucleation rate was found to be 8 orders of magnitude smaller than Ni at the same undercooling, which well explains the good glass formability of the alloy. Thus, our work opens a new avenue to study solidification under realistic experimental conditions via atomistic computer simulation.
Sun, Yang; Song, Huajing; Zhang, Feng; Yang, Lin; Ye, Zhuo; Mendelev, Mikhail I.; Wang, Cai-Zhuang; Ho, Kai-Ming
2018-02-01
The crystal nucleation from liquid in most cases is too rare to be accessed within the limited time scales of the conventional molecular dynamics (MD) simulation. Here, we developed a "persistent embryo" method to facilitate crystal nucleation in MD simulations by preventing small crystal embryos from melting using external spring forces. We applied this method to the pure Ni case for a moderate undercooling where no nucleation can be observed in the conventional MD simulation, and obtained nucleation rate in good agreement with the experimental data. Moreover, the method is applied to simulate an even more sluggish event: the nucleation of the B 2 phase in a strong glass-forming Cu-Zr alloy. The nucleation rate was found to be 8 orders of magnitude smaller than Ni at the same undercooling, which well explains the good glass formability of the alloy. Thus, our work opens a new avenue to study solidification under realistic experimental conditions via atomistic computer simulation.
International Nuclear Information System (INIS)
Liang, Hongbo; Fan, Man; You, Shijun; Zheng, Wandong; Zhang, Huan; Ye, Tianzhen; Zheng, Xuejing
2017-01-01
Highlights: •Four optical models for parabolic trough solar collectors were compared in detail. •Characteristics of Monte Carlo Method and Finite Volume Method were discussed. •A novel method was presented combining advantages of different models. •The method was suited to optical analysis of collectors with different geometries. •A new kind of cavity receiver was simulated depending on the novel method. -- Abstract: The PTC (parabolic trough solar collector) is widely used for space heating, heat-driven refrigeration, solar power, etc. The concentrated solar radiation is the only energy source for a PTC, thus its optical performance significantly affects the collector efficiency. In this study, four different optical models were constructed, validated and compared in detail. On this basis, a novel coupled method was presented by combining advantages of these models, which was suited to carry out a mass of optical simulations of collectors with different geometrical parameters rapidly and accurately. Based on these simulation results, the optimal configuration of a collector with highest efficiency can be determined. Thus, this method was useful for collector optimization and design. In the four models, MCM (Monte Carlo Method) and FVM (Finite Volume Method) were used to initialize photons distribution, as well as CPEM (Change Photon Energy Method) and MCM were adopted to describe the process of reflecting, transmitting and absorbing. For simulating reflection, transmission and absorption, CPEM was more efficient than MCM, so it was utilized in the coupled method. For photons distribution initialization, FVM saved running time and computation effort, whereas it needed suitable grid configuration. MCM only required a total number of rays for simulation, whereas it needed higher computing cost and its results fluctuated in multiple runs. In the novel coupled method, the grid configuration for FVM was optimized according to the “true values” from MCM of
Simulation and Verificaiton of Flow in Test Methods
DEFF Research Database (Denmark)
Thrane, Lars Nyholm; Szabo, Peter; Geiker, Mette Rica
2005-01-01
Simulations and experimental results of L-box and slump flow test of a self-compacting mortar and a self-compacting concrete are compared. The simulations are based on a single fluid approach and assume an ideal Bingham behavior. It is possible to simulate the experimental results of both tests...
An Importance Sampling Simulation Method for Bayesian Decision Feedback Equalizers
Chen, S.; Hanzo, L.
2000-01-01
An importance sampling (IS) simulation technique is presented for evaluating the lower-bound bit error rate (BER) of the Bayesian decision feedback equalizer (DFE) under the assumption of correct decisions being fed back. A design procedure is developed, which chooses appropriate bias vectors for the simulation density to ensure asymptotic efficiency of the IS simulation.
Numerical simulation for cracks detection using the finite elements method
Directory of Open Access Journals (Sweden)
S Bennoud
2016-09-01
Full Text Available The means of detection must ensure controls either during initial construction, or at the time of exploitation of all parts. The Non destructive testing (NDT gathers the most widespread methods for detecting defects of a part or review the integrity of a structure. In the areas of advanced industry (aeronautics, aerospace, nuclear …, assessing the damage of materials is a key point to control durability and reliability of parts and materials in service. In this context, it is necessary to quantify the damage and identify the different mechanisms responsible for the progress of this damage. It is therefore essential to characterize materials and identify the most sensitive indicators attached to damage to prevent their destruction and use them optimally. In this work, simulation by finite elements method is realized with aim to calculate the electromagnetic energy of interaction: probe and piece (with/without defect. From calculated energy, we deduce the real and imaginary components of the impedance which enables to determine the characteristic parameters of a crack in various metallic parts.
Application of the maximum entropy method to dynamical fermion simulations
Clowser, Jonathan
This thesis presents results for spectral functions extracted from imaginary-time correlation functions obtained from Monte Carlo simulations using the Maximum Entropy Method (MEM). The advantages this method are (i) no a priori assumptions or parametrisations of the spectral function are needed, (ii) a unique solution exists and (iii) the statistical significance of the resulting image can be quantitatively analysed. The Gross Neveu model in d = 3 spacetime dimensions (GNM3) is a particularly interesting model to study with the MEM because at T = 0 it has a broken phase with a rich spectrum of mesonic bound states and a symmetric phase where there are resonances. Results for the elementary fermion, the Goldstone boson (pion), the sigma, the massive pseudoscalar meson and the symmetric phase resonances are presented. UKQCD Nf = 2 dynamical QCD data is also studied with MEM. Results are compared to those found from the quenched approximation, where the effects of quark loops in the QCD vacuum are neglected, to search for sea-quark effects in the extracted spectral functions. Information has been extract from the difficult axial spatial and scalar as well as the pseudoscalar, vector and axial temporal channels. An estimate for the non-singlet scalar mass in the chiral limit is given which is in agreement with the experimental value of Mao = 985 MeV.
Methods employed to speed up Cathare for simulation uses
International Nuclear Information System (INIS)
Agator, J.M.
1992-01-01
This paper describes the main methods used to speed up the french advanced thermal-hydraulic computer code CATHARE and build a speedy version, called CATHARE-SIMU, adapted to real time calculations and simulation environment. Since CATHARE-SIMU, like CATHARE, uses a numerical scheme based on a fully implicit Newton's iterative method, and therefore with a variable time step, two ways have been explored to reduce the computing time: avoidance of short time steps, and so minimization of the number of iterations per time step, reduction of the computing time needed for an iteration. CATHARE-SIMU uses the same physical laws and correlations as in CATHARE with only some minor simplifications. This was considered the only way to be sure to maintain the level of physical relevance of CATHARE. Finally it is indicated that the validation programme of CATHARE-SIMU includes a set of 33 transient calculations, referring either to CATHARE for two-phase transients, or to measurements on real plants for operational transients
Hybrid Methods for Muon Accelerator Simulations with Ionization Cooling
Energy Technology Data Exchange (ETDEWEB)
Kunz, Josiah [Anderson U.; Snopok, Pavel [Fermilab; Berz, Martin [Michigan State U.; Makino, Kyoko [Michigan State U.
2018-03-28
Muon ionization cooling involves passing particles through solid or liquid absorbers. Careful simulations are required to design muon cooling channels. New features have been developed for inclusion in the transfer map code COSY Infinity to follow the distribution of charged particles through matter. To study the passage of muons through material, the transfer map approach alone is not sufficient. The interplay of beam optics and atomic processes must be studied by a hybrid transfer map--Monte-Carlo approach in which transfer map methods describe the deterministic behavior of the particles, and Monte-Carlo methods are used to provide corrections accounting for the stochastic nature of scattering and straggling of particles. The advantage of the new approach is that the vast majority of the dynamics are represented by fast application of the high-order transfer map of an entire element and accumulated stochastic effects. The gains in speed are expected to simplify the optimization of cooling channels which is usually computationally demanding. Progress on the development of the required algorithms and their application to modeling muon ionization cooling channels is reported.
Jia, Dongjie; Shen, Fei; Wang, Yi; Wu, Ting; Xu, Xuefeng; Zhang, Xinzhong; Han, Zhenhai
2018-05-11
Many efforts have been made to map quantitative trait loci (QTLs) to facilitate practical marker-assisted selection (MAS) in plants. In the present study, we identified four genome-wide major QTLs responsible for apple fruit acidity by MapQTL and BSA-seq analyses using two independent pedigree-based populations. Candidate genes were screened in major QTL regions, and three functional gene markers, including a non-synonymous A/G single nucleotide polymorphism (SNP) in the coding region of MdPP2CH, a 36-bp insertion in the promoter of MdSAUR37, and a previously reported SNP in MdALMTII, were validated to influence the malate content of apple fruits. In addition, MdPP2CH inactivated three vacuolar H + -ATPases (MdVHA-A3, MdVHA-B2 and MdVHA-D2) and one aluminium-activated malate transporter (MdALMTII) via dephosphorylation and negatively influenced fruit malate accumulation. The dephosphotase activity of MdPP2CH was suppressed by MdSAUR37, which implied a higher hierarchy of genetic interaction. Therefore, the MdSAUR37/MdPP2CH/MdALMTII chain cascaded hierarchical epistatic genetic effects to precisely determine apple fruit malate content. An A/G SNP (-1010) on MdMYB44 promoter region from a major QTL (qtl08.1) was closely associated with fruit malate content. The predicted phenotype values (PPVs) were estimated using the tentative genotype values of the gene markers, and the PPVs were significantly correlated with the observed phenotype values. Our findings provide an insight into plant genome-based selection in apples and will aid in conducting research to understand the physiological fundamentals of quantitative genetics. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Baer, T; Bartmann, W; Bracco, C; Carlier, E; Dehning, B; Garrel, N; Goddard, B; Jackson, S; Jimenez, M; Kain, V; Mertens, V; Misiowiec, M; Nordt, A; Papotti, G; Uythoven, J; Wenninger, J; Zerlauth, M; Zamantzas, C; Zimmermann, F
2012-01-01
UFOs ("Unidentified Falling Objects") are expected to be one of the major known performance limitation of the LHC. In this MD, the production mechanism and the dynamics of UFOs at the injection kicker magnets (MKIs) and the tune kicker magnets (MKQs) were studied. This was done by pulsing the MKIs and MKQs on a gap in the partly filled machine. During the MD, in total 58 UFO-type beam loss patterns were observed directly after pulsing the MKIs. None were observed after pulsing the MKQs, which provides important input for possible mitigation strategies. The temporal and spatial distribution of the UFO events could be determined by using a dedicated BLM Study Buffer, the implications for the UFO dynamics are discussed.
Gradient augmented level set method for phase change simulations
Anumolu, Lakshman; Trujillo, Mario F.
2018-01-01
A numerical method for the simulation of two-phase flow with phase change based on the Gradient-Augmented-Level-set (GALS) strategy is presented. Sharp capturing of the vaporization process is enabled by: i) identification of the vapor-liquid interface, Γ (t), at the subgrid level, ii) discontinuous treatment of thermal physical properties (except for μ), and iii) enforcement of mass, momentum, and energy jump conditions, where the gradients of the dependent variables are obtained at Γ (t) and are consistent with their analytical expression, i.e. no local averaging is applied. Treatment of the jump in velocity and pressure at Γ (t) is achieved using the Ghost Fluid Method. The solution of the energy equation employs the sub-grid knowledge of Γ (t) to discretize the temperature Laplacian using second-order one-sided differences, i.e. the numerical stencil completely resides within each respective phase. To carefully evaluate the benefits or disadvantages of the GALS approach, the standard level set method is implemented and compared against the GALS predictions. The results show the expected trend that interface identification and transport are predicted noticeably better with GALS over the standard level set. This benefit carries over to the prediction of the Laplacian and temperature gradients in the neighborhood of the interface, which are directly linked to the calculation of the vaporization rate. However, when combining the calculation of interface transport and reinitialization with two-phase momentum and energy, the benefits of GALS are to some extent neutralized, and the causes for this behavior are identified and analyzed. Overall the additional computational costs associated with GALS are almost the same as those using the standard level set technique.
International Nuclear Information System (INIS)
Morales, J.J.; Nuevo, J.M.; Rull, L.F.
1987-01-01
The new isothermic-isobaric MD(T,p,N) method of Nose and Hoover is applied in Molecular Dynamics simulations to both liquid and solid near the phase transition. We tested for an appropriate value of the isobaric friction coefficient before calculating the correlation length in the liquid and the disclinations per particle in solid on a big system of 2304 particles. The results are compared with those obtained by traditional MD simulation (E,V,N). (author)
Simulation of neutral gas flow in a tokamak divertor using the Direct Simulation Monte Carlo method
International Nuclear Information System (INIS)
Gleason-González, Cristian; Varoutis, Stylianos; Hauer, Volker; Day, Christian
2014-01-01
Highlights: • Subdivertor gas flows calculations in tokamaks by coupling the B2-EIRENE and DSMC method. • The results include pressure, temperature, bulk velocity and particle fluxes in the subdivertor. • Gas recirculation effect towards the plasma chamber through the vertical targets is found. • Comparison between DSMC and the ITERVAC code reveals a very good agreement. - Abstract: This paper presents a new innovative scientific and engineering approach for describing sub-divertor gas flows of fusion devices by coupling the B2-EIRENE (SOLPS) code and the Direct Simulation Monte Carlo (DSMC) method. The present study exemplifies this with a computational investigation of neutral gas flow in the ITER's sub-divertor region. The numerical results include the flow fields and contours of the overall quantities of practical interest such as the pressure, the temperature and the bulk velocity assuming helium as model gas. Moreover, the study unravels the gas recirculation effect located behind the vertical targets, viz. neutral particles flowing towards the plasma chamber. Comparison between calculations performed by the DSMC method and the ITERVAC code reveals a very good agreement along the main sub-divertor ducts
LDRD Final Report: Adaptive Methods for Laser Plasma Simulation
International Nuclear Information System (INIS)
Dorr, M R; Garaizar, F X; Hittinger, J A
2003-01-01
The goal of this project was to investigate the utility of parallel adaptive mesh refinement (AMR) in the simulation of laser plasma interaction (LPI). The scope of work included the development of new numerical methods and parallel implementation strategies. The primary deliverables were (1) parallel adaptive algorithms to solve a system of equations combining plasma fluid and light propagation models, (2) a research code implementing these algorithms, and (3) an analysis of the performance of parallel AMR on LPI problems. The project accomplished these objectives. New algorithms were developed for the solution of a system of equations describing LPI. These algorithms were implemented in a new research code named ALPS (Adaptive Laser Plasma Simulator) that was used to test the effectiveness of the AMR algorithms on the Laboratory's large-scale computer platforms. The details of the algorithm and the results of the numerical tests were documented in an article published in the Journal of Computational Physics [2]. A principal conclusion of this investigation is that AMR is most effective for LPI systems that are ''hydrodynamically large'', i.e., problems requiring the simulation of a large plasma volume relative to the volume occupied by the laser light. Since the plasma-only regions require less resolution than the laser light, AMR enables the use of efficient meshes for such problems. In contrast, AMR is less effective for, say, a single highly filamented beam propagating through a phase plate, since the resulting speckle pattern may be too dense to adequately separate scales with a locally refined mesh. Ultimately, the gain to be expected from the use of AMR is highly problem-dependent. One class of problems investigated in this project involved a pair of laser beams crossing in a plasma flow. Under certain conditions, energy can be transferred from one beam to the other via a resonant interaction with an ion acoustic wave in the crossing region. AMR provides an
International Nuclear Information System (INIS)
Wan Liang; Wang Shaoqing
2010-01-01
The deformation behavior of Cu bicrystals with the symmetric tilt grain boundary (STGB) under pure shear has been studied by atomistic simulation method with the embedded atom method (EAM) interatomic potentials. By using an energy minimization method, it shows that there are two optimized structures of this grain boundary (GB) which correspond to two local energy minima on the potential energy surface of the GB. The structure with lower energy is the stable one while the other is a metastable structure. The pure shear process of the bicrystals at ambient temperature has been studied by molecular dynamics (MD) simulation method. The simulated results indicate that there are three structure transformation modes of this GB depending on the shear direction: (1) pure GB sliding; (2) GB atomic shuffling accompanied by dislocation emission from GB; (3) GB migration coupled GB sliding, namely, GB coupling motion. In addition, an analysis of the structure evolution of the GB shows that, there are two mechanisms for GB coupling motion depending on the shear direction. One is the collective motion of GB atoms and the other is structure transformation realized by uncorrelated atomic shuffling processes. The former mechanism can induce structure transition of GB between the stable one and the metastable one, while the latter introduces faceting of the GB. (authors)
Bayesian statistic methods and theri application in probabilistic simulation models
Directory of Open Access Journals (Sweden)
Sergio Iannazzo
2007-03-01
Full Text Available Bayesian statistic methods are facing a rapidly growing level of interest and acceptance in the field of health economics. The reasons of this success are probably to be found on the theoretical fundaments of the discipline that make these techniques more appealing to decision analysis. To this point should be added the modern IT progress that has developed different flexible and powerful statistical software framework. Among them probably one of the most noticeably is the BUGS language project and its standalone application for MS Windows WinBUGS. Scope of this paper is to introduce the subject and to show some interesting applications of WinBUGS in developing complex economical models based on Markov chains. The advantages of this approach reside on the elegance of the code produced and in its capability to easily develop probabilistic simulations. Moreover an example of the integration of bayesian inference models in a Markov model is shown. This last feature let the analyst conduce statistical analyses on the available sources of evidence and exploit them directly as inputs in the economic model.
Numerical Simulation of Tubular Pumping Systems with Different Regulation Methods
Zhu, Honggeng; Zhang, Rentian; Deng, Dongsheng; Feng, Xusong; Yao, Linbi
2010-06-01
Since the flow in tubular pumping systems is basically along axial direction and passes symmetrically through the impeller, most satisfying the basic hypotheses in the design of impeller and having higher pumping system efficiency in comparison with vertical pumping system, they are being widely applied to low-head pumping engineering. In a pumping station, the fluctuation of water levels in the sump and discharge pool is most common and at most time the pumping system runs under off-design conditions. Hence, the operation of pump has to be flexibly regulated to meet the needs of flow rates, and the selection of regulation method is as important as that of pump to reduce operation cost and achieve economic operation. In this paper, the three dimensional time-averaged Navier-Stokes equations are closed by RNG κ-ɛ turbulent model, and two tubular pumping systems with different regulation methods, equipped with the same pump model but with different designed system structures, are numerically simulated respectively to predict the pumping system performances and analyze the influence of regulation device and help designers make final decision in the selection of design schemes. The computed results indicate that the pumping system with blade-adjusting device needs longer suction box, and the increased hydraulic loss will lower the pumping system efficiency in the order of 1.5%. The pumping system with permanent magnet motor, by means of variable speed regulation, obtains higher system efficiency partly for shorter suction box and partly for different structure design. Nowadays, the varied speed regulation is realized by varied frequency device, the energy consumption of which is about 3˜4% of output power of the motor. Hence, when the efficiency of variable frequency device is considered, the total pumping system efficiency will probably be lower.
Frank, Martin
2015-01-01
Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).
Multiscale simulation of water flow past a C540 fullerene
DEFF Research Database (Denmark)
Walther, Jens Honore; Praprotnik, Matej; Kotsalis, Evangelos M.
2012-01-01
We present a novel, three-dimensional, multiscale algorithm for simulations of water flow past a fullerene. We employ the Schwarz alternating overlapping domain method to couple molecular dynamics (MD) of liquid water around the C540 buckyball with a Lattice–Boltzmann (LB) description for the Nav......We present a novel, three-dimensional, multiscale algorithm for simulations of water flow past a fullerene. We employ the Schwarz alternating overlapping domain method to couple molecular dynamics (MD) of liquid water around the C540 buckyball with a Lattice–Boltzmann (LB) description...
Daru, R.; Venemans, P.
1998-01-01
Visualisation, simulation and communication were always intimately interconnected. Visualisations and simulations impersonate existing or virtual realities. Without those tools it is arduous to communicate mental depictions about virtual objects and events. A communication model is presented to
A study on the plasticity of soda-lime silica glass via molecular dynamics simulations
Urata, Shingo; Sato, Yosuke
2017-11-01
Molecular dynamics (MD) simulations were applied to construct a plasticity model, which enables one to simulate deformations of soda-lime silica glass (SLSG) by using continuum methods. To model the plasticity, stress induced by uniaxial and a variety of biaxial deformations was measured by MD simulations. We found that the surfaces of yield and maximum stresses, which are evaluated from the equivalent stress-strain curves, are reasonably represented by the Mohr-Coulomb ellipsoid. Comparing a finite element model using the constructed plasticity model to a large scale atomistic model on a nanoindentation simulation of SLSG reveals that the empirical method is accurate enough to evaluate the SLSG mechanical responses. Furthermore, the effect of ion-exchange on the SLSG plasticity was examined by using MD simulations. As a result, it was demonstrated that the effects of the initial compressive stress on the yield and maximum stresses are anisotropic contrary to our expectations.
Overview of Computer Simulation Modeling Approaches and Methods
Robert E. Manning; Robert M. Itami; David N. Cole; Randy Gimblett
2005-01-01
The field of simulation modeling has grown greatly with recent advances in computer hardware and software. Much of this work has involved large scientific and industrial applications for which substantial financial resources are available. However, advances in object-oriented programming and simulation methodology, concurrent with dramatic increases in computer...
Simulation as a Method of Teaching Communication for Multinational Corporations.
Stull, James B.; Baird, John W.
Interpersonal simulations may be used as a module in cultural awareness programs to provide realistic environments in which students, supervisors, and managers may practice communication skills that are effective in multicultural environments. To conduct and implement a cross-cultural simulation, facilitators should proceed through four stages:…
DEFF Research Database (Denmark)
Gould, Derek A; Chalmers, Nicholas; Johnson, Sheena J
2012-01-01
Recognition of the many limitations of traditional apprenticeship training is driving new approaches to learning medical procedural skills. Among simulation technologies and methods available today, computer-based systems are topical and bring the benefits of automated, repeatable, and reliable p...... performance assessments. Human factors research is central to simulator model development that is relevant to real-world imaging-guided interventional tasks and to the credentialing programs in which it would be used....
Molecular dynamics simulation of impact test
International Nuclear Information System (INIS)
Akahoshi, Y.; Schmauder, S.; Ludwig, M.
1998-01-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Molecular dynamics simulation of impact test
Energy Technology Data Exchange (ETDEWEB)
Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt
1998-11-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Nuclear power plant training simulator system and method
International Nuclear Information System (INIS)
Ferguson, R.W.; Converse, R.E. Jr.
1975-01-01
A system is described for simulating the real-time dynamic operation of a full scope nuclear powered electrical generating plant for operator training utilizing apparatus that includes a control console with plant component control devices and indicating devices for monitoring plant operation. A general purpose digital computer calculates the dynamic simulation data for operating the indicating devices in accordance with the operation of the control devices. The functions for synchronization and calculation are arranged in a priority structure so as to insure an execution order that provides a maximum overlap of data exchange and simulation calculations. (Official Gazette)
Discrete simulation system based on artificial intelligence methods
Energy Technology Data Exchange (ETDEWEB)
Futo, I; Szeredi, J
1982-01-01
A discrete event simulation system based on the AI language Prolog is presented. The system called t-Prolog extends the traditional possibilities of simulation languages toward automatic problem solving by using backtrack in time and automatic model modification depending on logical deductions. As t-Prolog is an interactive tool, the user has the possibility to interrupt the simulation run to modify the model or to force it to return to a previous state for trying possible alternatives. It admits the construction of goal-oriented or goal-seeking models with variable structure. Models are defined in a restricted version of the first order predicate calculus using Horn clauses. 21 references.
Leiner, Claude; Nemitz, Wolfgang; Schweitzer, Susanne; Kuna, Ladislav; Wenzl, Franz P; Hartmann, Paul; Satzinger, Valentin; Sommer, Christian
2016-03-20
We show that with an appropriate combination of two optical simulation techniques-classical ray-tracing and the finite difference time domain method-an optical device containing multiple diffractive and refractive optical elements can be accurately simulated in an iterative simulation approach. We compare the simulation results with experimental measurements of the device to discuss the applicability and accuracy of our iterative simulation procedure.
Modified enthalpy method for the simulation of melting and ...
Indian Academy of Sciences (India)
These include the implicit time stepping method of Voller & Cross. (1981), explicit enthalpy method of Tacke (1985), centroidal temperature correction method ... In variable viscosity method, viscosity is written as a function of liquid fraction.
Garcia-Tabares Valdivieso, Ana; Salvachua Ferrando, Belen Maria; Skowronski, Piotr Krzysztof; Solfaroli Camillocci, Matteo; Tomas Garcia, Rogelio; Wenninger, Jorg; Coello De Portugal - Martinez Vazquez, Jaime Maria; CERN. Geneva. ATS Department
2016-01-01
The ballistic optics is designed to improve the understanding of optical errors and BPM systematic effects in the critical triplet region. The particularity of that optics is that the triplet is switched off, effectively transforming the triplets on both sides of IR1 and IR5 into drift spaces. Advantage can be taken from that fact to localize better errors in the Q4-Q5-triplet region. During this MD this new optics was tested for the first time at injection with beam 2.
Review of Vortex Methods for Simulation of Vortex Breakdown
National Research Council Canada - National Science Library
Levinski, Oleg
2001-01-01
The aim of this work is to identify current developments in the field of vortex breakdown modelling in order to initiate the development of a numerical model for the simulation of F/A-18 empennage buffet...
High accuracy mantle convection simulation through modern numerical methods
Kronbichler, Martin; Heister, Timo; Bangerth, Wolfgang
2012-01-01
Numerical simulation of the processes in the Earth's mantle is a key piece in understanding its dynamics, composition, history and interaction with the lithosphere and the Earth's core. However, doing so presents many practical difficulties related
New methods for simulation of fractional Brownian motion
International Nuclear Information System (INIS)
Yin, Z.M.
1996-01-01
We present new algorithms for simulation of fractional Brownian motion (fBm) which comprises a set of important random functions widely used in geophysical and physical modeling, fractal image (landscape) simulating, and signal processing. The new algorithms, which are both accurate and efficient, allow us to generate not only a one-dimensional fBm process, but also two- and three-dimensional fBm fields. 23 refs., 3 figs
NUMERICAL METHODS FOR THE SIMULATION OF HIGH INTENSITY HADRON SYNCHROTRONS.
Energy Technology Data Exchange (ETDEWEB)
LUCCIO, A.; D' IMPERIO, N.; MALITSKY, N.
2005-09-12
Numerical algorithms for PIC simulation of beam dynamics in a high intensity synchrotron on a parallel computer are presented. We introduce numerical solvers of the Laplace-Poisson equation in the presence of walls, and algorithms to compute tunes and twiss functions in the presence of space charge forces. The working code for the simulation here presented is SIMBAD, that can be run as stand alone or as part of the UAL (Unified Accelerator Libraries) package.
On Partitioned Simulation of Electrical Circuits using Dynamic Iteration Methods
Ebert, Falk
2008-01-01
Im Rahmen dieser Arbeit wird die partitionierte Simulation elektrischer Schaltkreise untersucht. Hierbei handelt es sich um eine Technik, verschiedene Teile eines Schaltkreises auf unterschiedliche Weise numerisch zu behandeln um eine Simulation für den Gesamtkreis zu erhalten. Dabei wird besonderes Augenmerk auf zwei Dinge gelegt. Zum einen sollen sämtliche analytischen Resultate eine graphentheoretische Interpretation zulassen. Diese Bedingung resultiert daraus, dass Schaltkreisgleichungen ...
Sakamoto, Shinichi; Otsuru, Toru
2014-01-01
This book reviews a variety of methods for wave-based acoustic simulation and recent applications to architectural and environmental acoustic problems. Following an introduction providing an overview of computational simulation of sound environment, the book is in two parts: four chapters on methods and four chapters on applications. The first part explains the fundamentals and advanced techniques for three popular methods, namely, the finite-difference time-domain method, the finite element method, and the boundary element method, as well as alternative time-domain methods. The second part demonstrates various applications to room acoustics simulation, noise propagation simulation, acoustic property simulation for building components, and auralization. This book is a valuable reference that covers the state of the art in computational simulation for architectural and environmental acoustics.
Review of 40-year MD theses in medical oncology.
Zeeneldin, Ahmed; Diyaa, Amira; Moneer, Manar; Elgammal, Mosaad; Buhoush, Wafa
2014-09-01
It is almost 40 years since the foundation of the Medical Oncology (MO) Department. We aimed to appraise the clinical research to fulfill the Medical Doctorate (MD) degree in MO at the National Cancer Institute, Cairo University (NCI, CU). This review included 62 MD theses containing 66 studies. They were reviewed regarding aims, type of study, clinical trial phase, design and methodology, statistical tests, results, limitations, consent and IRB approval. Theses were grouped into 3 periods: 1970-1989, 1990-1999 and 2000-2008. Almost 76% of the studies were interventional and 24% were observational. Informed consent and Institutional Review Board approval were mentioned in 18 and 2 studies, respectively. While all studies mentioned the aims, none, clearly mentioned the research question. Outcomes were mainly efficacy followed by safety. Study design was inadequately considered, especially in 70's-80's period (p=0.038). Median sample size and study duration were almost stable through the three periods (p=0.441, 0.354, respectively). Most of the studies used both descriptive and analytical statistical methods. In a descending order, researched cancers were lymphoma, breast, leukemia, liver, urinary bladder, lung and colorectal. The commonest stages researched were IV and III. The number of studies focused on assessing biomarkers, biomarkers plus drugs/procedures, drugs and procedures are 20, 20, 16 and 6, respectively. With time, research within MD theses in MO increased quantitatively and qualitatively. Improvements were noticeable in documentation of study design. Copyright © 2014. Production and hosting by Elsevier B.V.
Badyal, Dinesh K; Daniel, Sujit R
2016-10-01
To survey the opinion about various curricular components of Doctor of Medicine (MD) pharmacology curriculum in India by stakeholders, including faculty and students. An online survey was done to evaluate the various curricular components of MD pharmacology curriculum being used in India. A total of 393 respondents including faculty, MD students, and other stakeholders completed the survey. The survey was developed using SurveyMonkey platform and link to survey was E-mailed to stakeholders. The results were expressed as percentages. There was a balanced representation of respondents from various designations, teaching experience, regions, and age groups. Most of the respondents (83%) were aware of the MD pharmacology curriculum. However, they reported that it is more inclined to knowledge domain. About half of respondents (53%) said that animal experiments are being used. The most common teaching methods mentioned are seminars (98.5%), journal clubs (95%), and practical exercises by postgraduates (73%), but there is less use of newer methods (25%) in theory and less of clinical pharmacology exercise (39%) in practical classes. The log books are maintained but not assessed regularly. Internal assessment is sparingly used. The MD pharmacology curriculum needs to be made uniform at the national level and updated to include the newer methods in teaching-learning and assessment. There should be sharing of newer methods at a common platform implemented at the national level.
Jakobtorweihen, S.; Zuniga, A. Chaides; Ingram, T.; Gerlach, T.; Keil, F. J.; Smirnova, I.
2014-07-01
Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realistic solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations.
International Nuclear Information System (INIS)
Jakobtorweihen, S.; Ingram, T.; Gerlach, T.; Smirnova, I.; Zuniga, A. Chaides; Keil, F. J.
2014-01-01
Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realistic solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations
QM/MM-MD simulations of conjugated polyelectrolytes
DEFF Research Database (Denmark)
Sjöqvist, Jonas; Linares, Mathieu; Mikkelsen, Kurt Valentin
2014-01-01
A methodological development is reported for the study of luminescence properties of conjugated polyelectrolytes, encompassing systems in which dihedral rotational barriers are easily overcome at room temperature. The components of the model include (i) a molecular mechanics (MM) force field desc...
Simulating Social Networks of Online Communities: Simulation as a Method for Sociability Design
Ang, Chee Siang; Zaphiris, Panayiotis
We propose the use of social simulations to study and support the design of online communities. In this paper, we developed an Agent-Based Model (ABM) to simulate and study the formation of social networks in a Massively Multiplayer Online Role Playing Game (MMORPG) guild community. We first analyzed the activities and the social network (who-interacts-with-whom) of an existing guild community to identify its interaction patterns and characteristics. Then, based on the empirical results, we derived and formalized the interaction rules, which were implemented in our simulation. Using the simulation, we reproduced the observed social network of the guild community as a means of validation. The simulation was then used to examine how various parameters of the community (e.g. the level of activity, the number of neighbors of each agent, etc) could potentially influence the characteristic of the social networks.
The Simulation and Analysis of the Closed Die Hot Forging Process by A Computer Simulation Method
Directory of Open Access Journals (Sweden)
Dipakkumar Gohil
2012-06-01
Full Text Available The objective of this research work is to study the variation of various parameters such as stress, strain, temperature, force, etc. during the closed die hot forging process. A computer simulation modeling approach has been adopted to transform the theoretical aspects in to a computer algorithm which would be used to simulate and analyze the closed die hot forging process. For the purpose of process study, the entire deformation process has been divided in to finite number of steps appropriately and then the output values have been computed at each deformation step. The results of simulation have been graphically represented and suitable corrective measures are also recommended, if the simulation results do not agree with the theoretical values. This computer simulation approach would significantly improve the productivity and reduce the energy consumption of the overall process for the components which are manufactured by the closed die forging process and contribute towards the efforts in reducing the global warming.
High viscosity fluid simulation using particle-based method
Chang, Yuanzhang; Bao, Kai; Zhu, Jian; Wu, Enhua
2011-01-01
the boundary, ghost particles are employed to enforce the solid boundary condition. Compared with Finite Element Methods with complicated and time-consuming remeshing operations, our method is much more straightforward to implement. Moreover, our method doesn
Reddy, M Rami; Erion, Mark D
2009-12-01
Molecular dynamics (MD) simulations in conjunction with thermodynamic perturbation approach was used to calculate relative solvation free energies of five pairs of small molecules, namely; (1) methanol to ethane, (2) acetone to acetamide, (3) phenol to benzene, (4) 1,1,1 trichloroethane to ethane, and (5) phenylalanine to isoleucine. Two studies were performed to evaluate the dependence of the convergence of these calculations on MD simulation length and starting configuration. In the first study, each transformation started from the same well-equilibrated configuration and the simulation length was varied from 230 to 2,540 ps. The results indicated that for transformations involving small structural changes, a simulation length of 860 ps is sufficient to obtain satisfactory convergence. In contrast, transformations involving relatively large structural changes, such as phenylalanine to isoleucine, require a significantly longer simulation length (>2,540 ps) to obtain satisfactory convergence. In the second study, the transformation was completed starting from three different configurations and using in each case 860 ps of MD simulation. The results from this study suggest that performing one long simulation may be better than averaging results from three different simulations using a shorter simulation length and three different starting configurations.
Method for numerical simulation of two-term exponentially correlated colored noise
International Nuclear Information System (INIS)
Yilmaz, B.; Ayik, S.; Abe, Y.; Gokalp, A.; Yilmaz, O.
2006-01-01
A method for numerical simulation of two-term exponentially correlated colored noise is proposed. The method is an extension of traditional method for one-term exponentially correlated colored noise. The validity of the algorithm is tested by comparing numerical simulations with analytical results in two physical applications
The null-event method in computer simulation
International Nuclear Information System (INIS)
Lin, S.L.
1978-01-01
The simulation of collisions of ions moving under the influence of an external field through a neutral gas to non-zero temperatures is discussed as an example of computer models of processes in which a probe particle undergoes a series of interactions with an ensemble of other particles, such that the frequency and outcome of the events depends on internal properties of the second particles. The introduction of null events removes the need for much complicated algebra, leads to a more efficient simulation and reduces the likelihood of logical error. (Auth.)
Adaptive Multiscale Finite Element Method for Subsurface Flow Simulation
Van Esch, J.M.
2010-01-01
Natural geological formations generally show multiscale structural and functional heterogeneity evolving over many orders of magnitude in space and time. In subsurface hydrological simulations the geological model focuses on the structural hierarchy of physical sub units and the flow model addresses
Crop canopy BRDF simulation and analysis using Monte Carlo method
Huang, J.; Wu, B.; Tian, Y.; Zeng, Y.
2006-01-01
This author designs the random process between photons and crop canopy. A Monte Carlo model has been developed to simulate the Bi-directional Reflectance Distribution Function (BRDF) of crop canopy. Comparing Monte Carlo model to MCRM model, this paper analyzes the variations of different LAD and
Predicting Flory-Huggins χ from Simulations
Zhang, Wenlin; Gomez, Enrique D.; Milner, Scott T.
2017-07-01
We introduce a method, based on a novel thermodynamic integration scheme, to extract the Flory-Huggins χ parameter as small as 10-3k T for polymer blends from molecular dynamics (MD) simulations. We obtain χ for the archetypical coarse-grained model of nonpolar polymer blends: flexible bead-spring chains with different Lennard-Jones interactions between A and B monomers. Using these χ values and a lattice version of self-consistent field theory (SCFT), we predict the shape of planar interfaces for phase-separated binary blends. Our SCFT results agree with MD simulations, validating both the predicted χ values and our thermodynamic integration method. Combined with atomistic simulations, our method can be applied to predict χ for new polymers from their chemical structures.
A Ten-Step Design Method for Simulation Games in Logistics Management
Fumarola, M.; Van Staalduinen, J.P.; Verbraeck, A.
2011-01-01
Simulation games have often been found useful as a method of inquiry to gain insight in complex system behavior and as aids for design, engineering simulation and visualization, and education. Designing simulation games are the result of creative thinking and planning, but often not the result of a
Shallow boron dopant on silicon An MD study
International Nuclear Information System (INIS)
Perez-Martin, A. Mari Carmen; Jimenez-Rodriguez, Jose J.; Jimenez-Saez, Jose Carlos
2004-01-01
Low energy boron bombardment of silicon has been simulated at room temperature by molecular dynamics (MD). Tersoff potential T3 was used in the simulation smoothly linked up with the universal potential. The boron-silicon (B-Si) interaction was simulated according to Tersoff potential for SiC but modified to account for the B-Si interaction. The algorithm can distinguish a B from a Si neighbour. Si-c, with (2 x 1) surface reconstruction, was bombarded with boron at 200 and 500 eV. These energies were initially chosen as good representative values of the low energy range. Reliable results require of a reasonable good statistic so that 1000-impact points were chosen uniformly distributed over a representative area of a 2 x 1 surface. The distribution of mean projected range for B is given. All kinds of point defect were looked for in a Si damaged target after bombardment. Energetically stable substitutional and interstitial configurations are presented and the relative appearances of the different types of interstitials, for both Si and B, are given. It is also determined the mean length of the distance to the first neighbours of defects
The Simulation of the Recharging Method Based on Solar Radiation for an Implantable Biosensor.
Li, Yun; Song, Yong; Kong, Xianyue; Li, Maoyuan; Zhao, Yufei; Hao, Qun; Gao, Tianxin
2016-09-10
A method of recharging implantable biosensors based on solar radiation is proposed. Firstly, the models of the proposed method are developed. Secondly, the recharging processes based on solar radiation are simulated using Monte Carlo (MC) method and the energy distributions of sunlight within the different layers of human skin have been achieved and discussed. Finally, the simulation results are verified experimentally, which indicates that the proposed method will contribute to achieve a low-cost, convenient and safe method for recharging implantable biosensors.
Truncated Newton-Raphson Methods for Quasicontinuum Simulations
National Research Council Canada - National Science Library
Liang, Yu; Kanapady, Ramdev; Chung, Peter W
2006-01-01
.... In this research, we report the effectiveness of the truncated Newton-Raphson method and quasi-Newton method with low-rank Hessian update strategy that are evaluated against the full Newton-Raphson...
Numerical simulation of GEW equation using RBF collocation method
Directory of Open Access Journals (Sweden)
Hamid Panahipour
2012-08-01
Full Text Available The generalized equal width (GEW equation is solved numerically by a meshless method based on a global collocation with standard types of radial basis functions (RBFs. Test problems including propagation of single solitons, interaction of two and three solitons, development of the Maxwellian initial condition pulses, wave undulation and wave generation are used to indicate the efficiency and accuracy of the method. Comparisons are made between the results of the proposed method and some other published numerical methods.
External individual monitoring: experiments and simulations using Monte Carlo Method
International Nuclear Information System (INIS)
Guimaraes, Carla da Costa
2005-01-01
In this work, we have evaluated the possibility of applying the Monte Carlo simulation technique in photon dosimetry of external individual monitoring. The GEANT4 toolkit was employed to simulate experiments with radiation monitors containing TLD-100 and CaF 2 :NaCl thermoluminescent detectors. As a first step, X ray spectra were generated impinging electrons on a tungsten target. Then, the produced photon beam was filtered in a beryllium window and additional filters to obtain the radiation with desired qualities. This procedure, used to simulate radiation fields produced by a X ray tube, was validated by comparing characteristics such as half value layer, which was also experimentally measured, mean photon energy and the spectral resolution of simulated spectra with that of reference spectra established by international standards. In the construction of thermoluminescent dosimeter, two approaches for improvements have. been introduced. The first one was the inclusion of 6% of air in the composition of the CaF 2 :NaCl detector due to the difference between measured and calculated values of its density. Also, comparison between simulated and experimental results showed that the self-attenuation of emitted light in the readout process of the fluorite dosimeter must be taken into account. Then, in the second approach, the light attenuation coefficient of CaF 2 :NaCl compound estimated by simulation to be 2,20(25) mm -1 was introduced. Conversion coefficients C p from air kerma to personal dose equivalent were calculated using a slab water phantom with polymethyl-metacrilate (PMMA) walls, for reference narrow and wide X ray spectrum series [ISO 4037-1], and also for the wide spectra implanted and used in routine at Laboratorio de Dosimetria. Simulations of backscattered radiations by PMMA slab water phantom and slab phantom of ICRU tissue-equivalent material produced very similar results. Therefore, the PMMA slab water phantom that can be easily constructed with low
MD-11 PCA - First Landing at Edwards
1995-01-01
This McDonnell Douglas MD-11 approaches the first landing ever of a transport aircraft under engine power only on Aug. 29, 1995, at NASA's Dryden Flight Research Center, Edwards, California. The milestone flight, flown by NASA research pilot and former astronaut Gordon Fullerton, was part of a NASA project to develop a computer-assisted engine control system that enables a pilot to land a plane safely when it normal control surfaces are disabled. The Propulsion-Controlled Aircraft (PCA) system uses standard autopilot controls already present in the cockpit, together with the new programming in the aircraft's flight control computers. The PCA concept is simple--for pitch control, the program increases thrust to climb and reduces thrust to descend. To turn right, the autopilot increases the left engine thrust while decreasing the right engine thrust. The initial Propulsion-Controlled Aircraft studies by NASA were carried out at Dryden with a modified twin-engine F-15 research aircraft.
MD-11 PCA - Research flight team egress
1995-01-01
This McDonnell Douglas MD-11 has parked on the flightline at NASA's Dryden Flight Research Center, Edwards, California, following its completion of the first and second landings ever performed by a transport aircraft under engine power only (on Aug. 29, 1995). The milestone flight, with NASA research pilot and former astronaut Gordon Fullerton at the controls, was part of a NASA project to develop a computer-assisted engine control system that enables a pilot to land a plane safely when its normal control surfaces are disabled. Coming down the steps from the aircraft are Gordon Fullerton (in front), followed by Bill Burcham, Propulsion Controlled Aircraft (PCA) project engineer at Dryden; NASA Dryden controls engineer John Burken; John Feather of McDonnell Douglas; and Drew Pappas, McDonnell Douglas' project manager for PCA.
Fast Multilevel Panel Method for Wind Turbine Rotor Flow Simulations
van Garrel, Arne; Venner, Cornelis H.; Hoeijmakers, Hendrik Willem Marie
2017-01-01
A fast multilevel integral transform method has been developed that enables the rapid analysis of unsteady inviscid flows around wind turbines rotors. A low order panel method is used and the new multi-level multi-integration cluster (MLMIC) method reduces the computational complexity for
Simulation methods for multiperiodic and aperiodic nanostructured dielectric waveguides
DEFF Research Database (Denmark)
Paulsen, Moritz; Neustock, Lars Thorben; Jahns, Sabrina
2017-01-01
on Rudin–Shapiro, Fibonacci, and Thue–Morse binary sequences. The near-field and far-field properties are computed employing the finite-element method (FEM), the finite-difference time-domain (FDTD) method as well as a rigorous coupled wave algorithm (RCWA). The results show that all three methods...
Simulating elastic light scattering using high performance computing methods
Hoekstra, A.G.; Sloot, P.M.A.; Verbraeck, A.; Kerckhoffs, E.J.H.
1993-01-01
The Coupled Dipole method, as originally formulated byPurcell and Pennypacker, is a very powerful method tosimulate the Elastic Light Scattering from arbitraryparticles. This method, which is a particle simulationmodel for Computational Electromagnetics, has one majordrawback: if the size of the
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
Absolute efficiency calibration of HPGe detector by simulation method
International Nuclear Information System (INIS)
Narayani, K.; Pant, Amar D.; Verma, Amit K.; Bhosale, N.A.; Anilkumar, S.
2018-01-01
High resolution gamma ray spectrometry by HPGe detectors is a powerful radio analytical technique for estimation of activity of various radionuclides. In the present work absolute efficiency calibration of the HPGe detector was carried out using Monte Carlo simulation technique and results are compared with those obtained by experiment using standard radionuclides of 152 Eu and 133 Ba. The coincidence summing correction factors for the measurement of these nuclides were also calculated
Quantum mechanical simulation methods for studying biological systems
International Nuclear Information System (INIS)
Bicout, D.; Field, M.
1996-01-01
Most known biological mechanisms can be explained using fundamental laws of physics and chemistry and a full understanding of biological processes requires a multidisciplinary approach in which all the tools of biology, chemistry and physics are employed. An area of research becoming increasingly important is the theoretical study of biological macromolecules where numerical experimentation plays a double role of establishing a link between theoretical models and predictions and allowing a quantitative comparison between experiments and models. This workshop brought researchers working on different aspects of the development and application of quantum mechanical simulation together, assessed the state-of-the-art in the field and highlighted directions for future research. Fourteen lectures (theoretical courses and specialized seminars) deal with following themes: 1) quantum mechanical calculations of large systems, 2) ab initio molecular dynamics where the calculation of the wavefunction and hence the energy and forces on the atoms for a system at a single nuclear configuration are combined with classical molecular dynamics algorithms in order to perform simulations which use a quantum mechanical potential energy surface, 3) quantum dynamical simulations, electron and proton transfer processes in proteins and in solutions and finally, 4) free seminars that helped to enlarge the scope of the workshop. (N.T.)
Shen, Lin; Yang, Weitao
2018-03-13
Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of
Methods and Experimental Protocols to Design a Simulated Bio-Mimetic Quadruped Robot
Directory of Open Access Journals (Sweden)
Hadi El Daou
2013-05-01
Full Text Available Abstract This paper presents a bio-mimetic approach to design and simulate a tortoise-like virtual robot. This study takes a multidisciplinary approach: from in vivo and in vitro experiments on animals, data are collected and used to design, control and simulate a bio-mimetic virtual robot using MD ADAMS platform. From the in vitro experiments, the geometrical and inertial properties of body limbs are measured, and a model of tortoise kinematics is derived. From the in vivo experiments the contact forces between each limb and the ground are measured. The contributions of hind and forelimbs in the generation of propelling and braking forces are studied. The motion of the joints between limb segments are recorded and used to solve the inverse kinematics problem. A virtual model of a tortoise-like robot is built; it is a linkage of 15 rigid bodies articulated by 22 degrees of freedom. This model is referred to as TATOR II. It has the inertial and geometrical properties measured during the in vitro experiments. TATOR II motion is achieved using a Proportional-Derivative controller copying the joint angle trajectories calculated from the in vivo experiments.
Pengaruh Brand Ambassador Terhadap Minat Beli Konsumen MD Clinic By Lazeta
Directory of Open Access Journals (Sweden)
Nurvita Septya Ningrum
2016-10-01
Full Text Available This research at MD Clinic by Lazeta which is in the beauty services that offer health care and facial, under of PT. Medina Global Care. MD Cilinic by Lazeta use the brand ambassador of introducing their products. The selection of brand ambassador motivated by positive image brought by the celebrities. Brand ambassadors chosen by the company as a symbol or a marker to represent the wishes and needs of prospective customers. MD Clinic by Lazeta choose Syahnaz as a brand ambassador for their products which is expected to to represent the product of MD Clinic by Lazeta, so the message can be understood by the consumer, who eventually would to lead the purchase intention. The purpose of this research was to investigate the influence of brand ambassadors on consumer purchase intention MD Clinic by Lazeta, Study on Business Administration Students year in 2103 Telkom University. Researchers used quantitative research methods. This research is population research, because all population is being respondent in this research. Populations of this research are 137 respondents. Collecting data in this research is conducted by using questionnaire distributed to all respondents, which all Students on Business Administration Telkom University who knows the MD Clinic by Lazeta. Data were analyzed using simple regression analysis and descriptive analysis.The results showed that the Brand Ambassador impact of consumer purchase intention on MD Clinic by Lazeta at the Students on Business Administration Telkom University years in 2013. Based on the calculation of the coefficient of determination (R2 can be seen the influence of brand ambassador variable (X on purchase intention (Y is 42.9%. While the remaining 57.1% is influenced by other factors which not examined in this research such as, pricing, marketing strategy and others.
Moustafa, Sabry Gad Al-Hak Mohammad
Molecular simulation (MS) methods (e.g. Monte Carlo (MC) and molecular dynamics (MD)) provide a reliable tool (especially at extreme conditions) to measure solid properties. However, measuring them accurately and efficiently (smallest uncertainty for a given time) using MS can be a big challenge especially with ab initio-type models. In addition, comparing with experimental results through extrapolating properties from finite size to the thermodynamic limit can be a critical obstacle. We first estimate the free energy (FE) of crystalline system of simple discontinuous potential, hard-spheres (HS), at its melting condition. Several approaches are explored to determine the most efficient route. The comparison study shows a considerable improvement in efficiency over the standard MS methods that are known for solid phases. In addition, we were able to accurately extrapolate to the thermodynamic limit using relatively small system sizes. Although the method is applied to HS model, it is readily extended to more complex hard-body potentials, such as hard tetrahedra. The harmonic approximation of the potential energy surface is usually an accurate model (especially at low temperature and large density) to describe many realistic solid phases. In addition, since the analysis is done numerically the method is relatively cheap. Here, we apply lattice dynamics (LD) techniques to get the FE of clathrate hydrates structures. Rigid-bonds model is assumed to describe water molecules; this, however, requires additional orientation degree-of-freedom in order to specify each molecule. However, we were able to efficiently avoid using those degrees of freedom through a mathematical transformation that only uses the atomic coordinates of water molecules. In addition, the proton-disorder nature of hydrate water networks adds extra complexity to the problem, especially when extrapolating to the thermodynamic limit is needed. The finite-size effects of the proton disorder contribution is
DEFF Research Database (Denmark)
Völcker, Carsten; Jørgensen, John Bagterp; Thomsen, Per Grove
2010-01-01
The implicit Euler method, normally refered to as the fully implicit (FIM) method, and the implicit pressure explicit saturation (IMPES) method are the traditional choices for temporal discretization in reservoir simulation. The FIM method offers unconditionally stability in the sense of discrete......-Kutta methods, ESDIRK, Newton-Raphson, convergence control, error control, stepsize selection....
Mock ECHO: A Simulation-Based Medical Education Method.
Fowler, Rebecca C; Katzman, Joanna G; Comerci, George D; Shelley, Brian M; Duhigg, Daniel; Olivas, Cynthia; Arnold, Thomas; Kalishman, Summers; Monnette, Rebecca; Arora, Sanjeev
2018-04-16
This study was designed to develop a deeper understanding of the learning and social processes that take place during the simulation-based medical education for practicing providers as part of the Project ECHO® model, known as Mock ECHO training. The ECHO model is utilized to expand access to care of common and complex diseases by supporting the education of primary care providers with an interprofessional team of specialists via videoconferencing networks. Mock ECHO trainings are conducted through a train the trainer model targeted at leaders replicating the ECHO model at their organizations. Trainers conduct simulated teleECHO clinics while participants gain skills to improve communication and self-efficacy. Three focus groups, conducted between May 2015 and January 2016 with a total of 26 participants, were deductively analyzed to identify common themes related to simulation-based medical education and interdisciplinary education. Principal themes generated from the analysis included (a) the role of empathy in community development, (b) the value of training tools as guides for learning, (c) Mock ECHO design components to optimize learning, (d) the role of interdisciplinary education to build community and improve care delivery, (e) improving care integration through collaboration, and (f) development of soft skills to facilitate learning. Mock ECHO trainings offer clinicians the freedom to learn in a noncritical environment while emphasizing real-time multidirectional feedback and encouraging knowledge and skill transfer. The success of the ECHO model depends on training interprofessional healthcare providers in behaviors needed to lead a teleECHO clinic and to collaborate in the educational process. While building a community of practice, Mock ECHO provides a safe opportunity for a diverse group of clinician experts to practice learned skills and receive feedback from coparticipants and facilitators.
Computerized method for X-ray angular distribution simulation in radiological systems
International Nuclear Information System (INIS)
Marques, Marcio A.; Oliveira, Henrique J.Q. de; Frere, Annie F.; Schiabel, Homero; Marques, Paulo M.A.
1996-01-01
A method to simulate the changes in X-ray angular distribution (the Heel effect) for radiologic imaging systems is presented. This simulation method is described as to predict images for any exposure technique considering that the distribution is the cause of the intensity variation along the radiation field
Contribution of the ultrasonic simulation to the testing methods qualification process
International Nuclear Information System (INIS)
Le Ber, L.; Calmon, P.; Abittan, E.
2001-01-01
The CEA and EDF have started a study concerning the simulation interest in the qualification of nuclear components control by ultrasonic methods. In this framework, the simulation tools of the CEA, as CIVA, have been tested on real control. The method and the results obtained on some examples are presented. (A.L.B.)
2D Quantum Simulation of MOSFET Using the Non Equilibrium Green's Function Method
Svizhenko, Alexel; Anantram, M. P.; Govindan, T. R.; Yan, Jerry (Technical Monitor)
2000-01-01
The objectives this viewgraph presentation summarizes include: (1) the development of a quantum mechanical simulator for ultra short channel MOSFET simulation, including theory, physical approximations, and computer code; (2) explore physics that is not accessible by semiclassical methods; (3) benchmarking of semiclassical and classical methods; and (4) study other two-dimensional devices and molecular structure, from discretized Hamiltonian to tight-binding Hamiltonian.
Digital system verification a combined formal methods and simulation framework
Li, Lun
2010-01-01
Integrated circuit capacity follows Moore's law, and chips are commonly produced at the time of this writing with over 70 million gates per device. Ensuring correct functional behavior of such large designs before fabrication poses an extremely challenging problem. Formal verification validates the correctness of the implementation of a design with respect to its specification through mathematical proof techniques. Formal techniques have been emerging as commercialized EDA tools in the past decade. Simulation remains a predominantly used tool to validate a design in industry. After more than 5
Achieving better cooling of turbine blades using numerical simulation methods
Inozemtsev, A. A.; Tikhonov, A. S.; Sendyurev, C. I.; Samokhvalov, N. Yu.
2013-02-01
A new design of the first-stage nozzle vane for the turbine of a prospective gas-turbine engine is considered. The blade's thermal state is numerically simulated in conjugate statement using the ANSYS CFX 13.0 software package. Critical locations in the blade design are determined from the distribution of heat fluxes, and measures aimed at achieving more efficient cooling are analyzed. Essentially lower (by 50-100°C) maximal temperature of metal has been achieved owing to the results of the performed work.
Simulation Methods in the Contact with Impact of Rigid Bodies
Directory of Open Access Journals (Sweden)
Cristina Basarabă-Opritescu
2007-10-01
Full Text Available The analysis of impacts of elastic bodies is topical and it has many applications, practical and theoretical, too. The elastic character of collision is put in evidence, especially by the velocities of some parts of a particular body, named “ring”. In the presented paper, the situation of elastic collisions is put in evidence by the simulation with the help of the program ANSYS and it refers to the particular case of the ring, with the mechanical characteristics, given in the paper
Modelling and simulation of diffusive processes methods and applications
Basu, SK
2014-01-01
This book addresses the key issues in the modeling and simulation of diffusive processes from a wide spectrum of different applications across a broad range of disciplines. Features: discusses diffusion and molecular transport in living cells and suspended sediment in open channels; examines the modeling of peristaltic transport of nanofluids, and isotachophoretic separation of ionic samples in microfluidics; reviews thermal characterization of non-homogeneous media and scale-dependent porous dispersion resulting from velocity fluctuations; describes the modeling of nitrogen fate and transport
Multinuclear NMR of CaSiO(3) glass: simulation from first-principles.
Pedone, Alfonso; Charpentier, Thibault; Menziani, Maria Cristina
2010-06-21
An integrated computational method which couples classical molecular dynamics simulations with density functional theory calculations is used to simulate the solid-state NMR spectra of amorphous CaSiO(3). Two CaSiO(3) glass models are obtained by shell-model molecular dynamics simulations, successively relaxed at the GGA-PBE level of theory. The calculation of the NMR parameters (chemical shielding and quadrupolar parameters), which are then used to simulate solid-state 1D and 2D-NMR spectra of silicon-29, oxygen-17 and calcium-43, is achieved by the gauge including projector augmented-wave (GIPAW) and the projector augmented-wave (PAW) methods. It is shown that the limitations due to the finite size of the MD models can be overcome using a Kernel Estimation Density (KDE) approach to simulate the spectra since it better accounts for the disorder effects on the NMR parameter distribution. KDE allows reconstructing a smoothed NMR parameter distribution from the MD/GIPAW data. Simulated NMR spectra calculated with the present approach are found to be in excellent agreement with the experimental data. This further validates the CaSiO(3) structural model obtained by MD simulations allowing the inference of relationships between structural data and NMR response. The methods used to simulate 1D and 2D-NMR spectra from MD GIPAW data have been integrated in a package (called fpNMR) freely available on request.
2016-06-12
Particle Size in Discrete Element Method to Particle Gas Method (DEM_PGM) Coupling in Underbody Blast Simulations Venkatesh Babu, Kumar Kulkarni, Sanjay...buried in soil viz., (1) coupled discrete element & particle gas methods (DEM-PGM) and (2) Arbitrary Lagrangian-Eulerian (ALE), are investigated. The...DEM_PGM and identify the limitations/strengths compared to the ALE method. Discrete Element Method (DEM) can model individual particle directly, and
International Nuclear Information System (INIS)
Satake, Shin-ichi; Kunugi, Tomoaki
2006-01-01
Scientific computational methods have advanced remarkably with the progress of nuclear development. They have played the role of weft connecting each realm of nuclear engineering and then an introductory course of advanced scientific computational methods and their applications to nuclear technologies were prepared in serial form. This is the third issue showing the introduction of continuum simulation methods and their applications. Spectral methods and multi-interface calculation methods in fluid dynamics are reviewed. (T. Tanaka)
Jia, Shouqing; La, Dongsheng; Ma, Xuelian
2018-04-01
The finite difference time domain (FDTD) algorithm and Green function algorithm are implemented into the numerical simulation of electromagnetic waves in Schwarzschild space-time. FDTD method in curved space-time is developed by filling the flat space-time with an equivalent medium. Green function in curved space-time is obtained by solving transport equations. Simulation results validate both the FDTD code and Green function code. The methods developed in this paper offer a tool to solve electromagnetic scattering problems.
Simulation Methods for Multiperiodic and Aperiodic Nanostructured Dielectric Waveguides
DEFF Research Database (Denmark)
Paulsen, Moritz; Neustock, Lars Thorben; Jahns, Sabrina
on Rudin-Shapiro, Fibonacci, and Thue-Morse binary sequences. The near-field and far-field properties are calculated employing the finite-element method (FEM), the finite- difference time-domain (FDTD) method as well as a rigorous coupled wave algorithm (RCWA). References [1] S. V. Boriskina, A. Gopinath...
Nonequilibrium relaxation method – An alternative simulation strategy
Indian Academy of Sciences (India)
This equilibrium method traces over the standard theory of the thermal ... The purpose of this article is to give a concise review of the idea of the NER method .... using the NER functions from mixed initial configuration, that is, half of the system.
Simulation of crystalline pattern formation by the MPFC method
Directory of Open Access Journals (Sweden)
Starodumov Ilya
2017-01-01
Full Text Available The Phase Field Crystal model in hyperbolic formulation (modified PFC or MPFC, is investigated as one of the most promising techniques for modeling the formation of crystal patterns. MPFC is a convenient and fundamentally based description linking nano-and meso-scale processes in the evolution of crystal structures. The presented model is a powerful tool for mathematical modeling of the various operations in manufacturing. Among them is the definition of process conditions for the production of metal castings with predetermined properties, the prediction of defects in the crystal structure during casting, the evaluation of quality of special coatings, and others. Our paper presents the structure diagram which was calculated for the one-mode MPFC model and compared to the results of numerical simulation for the fast phase transitions. The diagram is verified by the numerical simulation and also strongly correlates to the previously calculated diagrams. The computations have been performed using software based on the effective parallel computational algorithm.
Numerical simulation methods of fires in nuclear power plants
International Nuclear Information System (INIS)
Keski-Rahkonen, O.; Bjoerkman, J.; Heikkilae, L.
1992-01-01
Fire is a significant hazard to the safety of nuclear power plants (NPP). Fire may be serious accident as such, but even small fire at a critical point in a NPP may cause an accident much more serious than fire itself. According to risk assessments a fire may be an initial cause or a contributing factor in a large part of reactor accidents. At the Fire Technology and the the Nuclear Engineering Laboratory of the Technical Research Centre of Finland (VTT) fire safety research for NPPs has been carried out in a large extent since 1985. During years 1988-92 a project Advanced Numerical Modelling in Nuclear Power Plants (PALOME) was carried out. In the project the level of numerical modelling for fire research in Finland was improved by acquiring, preparing for use and developing numerical fire simulation programs. Large scale test data of the German experimental program (PHDR Sicherheitsprogramm in Kernforschungscentral Karlsruhe) has been as reference. The large scale tests were simulated by numerical codes and results were compared to calculations carried out by others. Scientific interaction with outstanding foreign laboratories and scientists has been an important part of the project. This report describes the work of PALOME-project carried out at the Fire Technology Laboratory only. A report on the work at the Nuclear Engineering Laboratory will be published separatively. (au)
The PDF method for Lagrangian two-phase flow simulations
International Nuclear Information System (INIS)
Minier, J.P.; Pozorski, J.
1996-04-01
A recent turbulence model put forward by Pope (1991) in the context of PDF modelling has been used. In this approach, the one-point joint velocity-dissipation pdf equation is solved by simulating the instantaneous behaviour of a large number of Lagrangian fluid particles. Closure of the evolution equations of these Lagrangian particles is based on stochastic models and more specifically on diffusion processes. Such models are of direct use for two-phase flow modelling where the so-called fluid seen by discrete inclusions has to be modelled. Full Lagrangian simulations have been performed for shear-flows. It is emphasized that this approach gives far more information than traditional turbulence closures (such as the K-ε model) and therefore can be very useful for situations involving complex physics. It is also believed that the present model represents the first step towards a complete Lagrangian-Lagrangian model for dispersed two-phase flow problems. (authors). 21 refs., 6 figs
A Method for Functional Task Alignment Analysis of an Arthrocentesis Simulator.
Adams, Reid A; Gilbert, Gregory E; Buckley, Lisa A; Nino Fong, Rodolfo; Fuentealba, I Carmen; Little, Erika L
2018-05-16
During simulation-based education, simulators are subjected to procedures composed of a variety of tasks and processes. Simulators should functionally represent a patient in response to the physical action of these tasks. The aim of this work was to describe a method for determining whether a simulator does or does not have sufficient functional task alignment (FTA) to be used in a simulation. Potential performance checklist items were gathered from published arthrocentesis guidelines and aggregated into a performance checklist using Lawshe's method. An expert panel used this performance checklist and an FTA analysis questionnaire to evaluate a simulator's ability to respond to the physical actions required by the performance checklist. Thirteen items, from a pool of 39, were included on the performance checklist. Experts had mixed reviews of the simulator's FTA and its suitability for use in simulation. Unexpectedly, some positive FTA was found for several tasks where the simulator lacked functionality. By developing a detailed list of specific tasks required to complete a clinical procedure, and surveying experts on the simulator's response to those actions, educators can gain insight into the simulator's clinical accuracy and suitability. Unexpected of positive FTA ratings of function deficits suggest that further revision of the survey method is required.
Cutting Method of the CAD model of the Nuclear facility for Dismantling Simulation
Energy Technology Data Exchange (ETDEWEB)
Kim, Ikjune; Choi, ByungSeon; Hyun, Dongjun; Jeong, KwanSeong; Kim, GeunHo; Lee, Jonghwan [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)
2015-05-15
Current methods for process simulation cannot simulate the cutting operation flexibly. As is, to simulate a cutting operation, user needs to prepare the result models of cutting operation based on pre-define cutting path, depth and thickness with respect to a dismantle scenario in advance. And those preparations should be built again as scenario changes. To be, user can change parameters and scenarios dynamically within a simulation configuration process so that the user saves time and efforts to simulate cutting operations. This study presents the methodology of cutting operation which can be applied to all the procedure in the simulation of dismantling of nuclear facilities. We developed the cutting simulation module for cutting operation in the dismantling of the nuclear facilities based on proposed cutting methodology. We defined the requirement of model cutting methodology based on the requirement of the dismantling of nuclear facilities. And we implemented cutting simulation module based on API of the commercial CAD system.
Comparative Study on Two Melting Simulation Methods: Melting Curve of Gold
International Nuclear Information System (INIS)
Liu Zhong-Li; Li Rui; Sun Jun-Sheng; Zhang Xiu-Lu; Cai Ling-Cang
2016-01-01
Melting simulation methods are of crucial importance to determining melting temperature of materials efficiently. A high-efficiency melting simulation method saves much simulation time and computational resources. To compare the efficiency of our newly developed shock melting (SM) method with that of the well-established two-phase (TP) method, we calculate the high-pressure melting curve of Au using the two methods based on the optimally selected interatomic potentials. Although we only use 640 atoms to determine the melting temperature of Au in the SM method, the resulting melting curve accords very well with the results from the TP method using much more atoms. Thus, this shows that a much smaller system size in SM method can still achieve a fully converged melting curve compared with the TP method, implying the robustness and efficiency of the SM method. (paper)
Multigrid methods for fully implicit oil reservoir simulation
Energy Technology Data Exchange (ETDEWEB)
Molenaar, J.
1995-12-31
In this paper, the authors consider the simultaneous flow of oil and water in reservoir rock. This displacement process is modeled by two basic equations the material balance or continuity equations, and the equation of motion (Darcy`s law). For the numerical solution of this system of nonlinear partial differential equations, there are two approaches: the fully implicit or simultaneous solution method, and the sequential solution method. In this paper, the authors consider the possibility of applying multigrid methods for the iterative solution of the systems of nonlinear equations.
Industrial development of a simulation method for ore recovery evaluation
International Nuclear Information System (INIS)
Deraisme; De Fouquet; Fraisse
1983-01-01
The purpose of downstream geostatistics is to provide to engineers, responsible for mining project studies, with a method for predicting the ore reserve recovery coming from different mining methods and for choosing the best one according to economic criteria. In the case of the BEN LOMOND uranium deposit, the metal recovery at the production stage depends on the geometry of mineralized lenses. For the first step of this study the usual technique for constructing a numerical model of deposit has been used. But this does not reproduce the geological structures very precisely. The recovered reserves have been computed for three more or less selective mining methods. This has been done inputing the outlines of stopes on a digitalizer. In the case of a cut and fill method an automatic algorithm for the optimization under constraints has been developed [fr
Phase portrait methods for verifying fluid dynamic simulations
Energy Technology Data Exchange (ETDEWEB)
Stewart, H.B.
1989-01-01
As computing resources become more powerful and accessible, engineers more frequently face the difficult and challenging engineering problem of accurately simulating nonlinear dynamic phenomena. Although mathematical models are usually available, in the form of initial value problems for differential equations, the behavior of the solutions of nonlinear models is often poorly understood. A notable example is fluid dynamics: while the Navier-Stokes equations are believed to correctly describe turbulent flow, no exact mathematical solution of these equations in the turbulent regime is known. Differential equations can of course be solved numerically, but how are we to assess numerical solutions of complex phenomena without some understanding of the mathematical problem and its solutions to guide us
Crystal twinning of human MD-2 recognizing endotoxin cores of lipopolysaccharide
International Nuclear Information System (INIS)
Ohto, Umeharu; Satow, Yoshinori
2008-01-01
Twinned crystals of humaan MD-2 are transformed into single crystals with cryoprotectant optimization. Twinning of crystals causes overlapping of two or more reciprocal lattice points, and hence structure amplitudes for a single crystalline domain are hardly obtained from X-ray diffraction intensities. MD-2 protein forms a stable complex with Toll-like receptor 4 and recognizes bacterial lipopolysaccharide (LPS). Excessive immune responses activated by LPS cause septic shocks. Saccharide-trimmed human MD-2 crystallizes in the tetragonal form with apparent Laue symmetry of 4/mmm, and diffraction intensities from these crystals indicate crystal twinning. The crystal consists of two different domains, A and B. The c A axis of domain A coincides with the c B axis of domain B with a smaller lattice, and the a A axis corresponds to the (a B + b B ) axis. This twinning severely imposes difficulty in structure determination. Through optimization of cryoprotectant, domain A was thoroughly transformed into domain B. The crystal containing only domain B is in space group P4 1 2 1 2 with one MD-2 molecule in the asymmetric unit. The structure of this form of MD-2 as well as its complex with antiendotoxic lipid IVa was successfully determined using the multiple isomorphous replacement method
Energy Technology Data Exchange (ETDEWEB)
NONE
2000-02-01
Commercialization feasibility of the SWD method has been tested and studied. This method uses a bit as the vibration source while a drilling is excavated, to collect information of geological structures and the like in front of the bit. In this study, the reflected and direct waves propagating from the drill bit while the N11-MD-3 drilling was excavated at the Busadake area were extracted and analyzed by the receivers installed on the surface of the earth, to estimate the default shapes which determine the geothermal structures. Analysis of the direct waves has statistically determined that the defaults are inclined at 81.5 degrees, based on the reasonable assumption. No reflection of the waves by the default plane was observed. However, it was observed that the waves were reflected by the stratum planes, when drilling was excavated to 1,006 and 1,008 m, and the results were used to map the reflecting planes. No reflecting planes with a default in-between was obtained, because of, e.g., limited depth sections and large stratum inclination. As a result, no default shape could be estimated. It is however confirmed that the SWD method produces reflected waves by bit signals even in a geothermal area, suggesting applicability of the method to default detection. (NEDO)
Coupling methods for parallel running RELAPSim codes in nuclear power plant simulation
Energy Technology Data Exchange (ETDEWEB)
Li, Yankai; Lin, Meng, E-mail: linmeng@sjtu.edu.cn; Yang, Yanhua
2016-02-15
When the plant is modeled detailedly for high precision, it is hard to achieve real-time calculation for one single RELAP5 in a large-scale simulation. To improve the speed and ensure the precision of simulation at the same time, coupling methods for parallel running RELAPSim codes were proposed in this study. Explicit coupling method via coupling boundaries was realized based on a data-exchange and procedure-control environment. Compromise of synchronization frequency was well considered to improve the precision of simulation and guarantee the real-time simulation at the same time. The coupling methods were assessed using both single-phase flow models and two-phase flow models and good agreements were obtained between the splitting–coupling models and the integrated model. The mitigation of SGTR was performed as an integral application of the coupling models. A large-scope NPP simulator was developed adopting six splitting–coupling models of RELAPSim and other simulation codes. The coupling models could improve the speed of simulation significantly and make it possible for real-time calculation. In this paper, the coupling of the models in the engineering simulator is taken as an example to expound the coupling methods, i.e., coupling between parallel running RELAPSim codes, and coupling between RELAPSim code and other types of simulation codes. However, the coupling methods are also referable in other simulator, for example, a simulator employing ATHLETE instead of RELAP5, other logic code instead of SIMULINK. It is believed the coupling method is commonly used for NPP simulator regardless of the specific codes chosen in this paper.
LHC β*-reach MD: aperture measurements at small β*
Fuster Martinez, Nuria; Redaelli, Stefano; CERN. Geneva. ATS Department
2017-01-01
During this MD, performed on the 25th of July 2017, we measured the LHC aperture at top energy for β*=30 cm using the Transverse Damper (ADT) blow-up method. These measurements are part of the standard commissioning of an optics and have been performed in order to provide early on inputs for a possible change of β* later in 2017, as envisaged previously to fully profit from the additional margins introduced by the rematched phase advance between dump kickers and the TCTs (Target Collimator Tertiary). In addition to the aperture measurements, two other commissioning important tests were performed: loss maps for the nominal TCTs settings and an asynchronous dump validation with tighter TCT gaps.
Multiscale molecular dynamics using the matched interface and boundary method
International Nuclear Information System (INIS)
Geng Weihua; Wei, G.W.
2011-01-01
The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.
DEFF Research Database (Denmark)
Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P
2008-01-01
. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...
International Nuclear Information System (INIS)
Sekimura, Naoto; Okita, Taira
2006-01-01
Scientific computational methods have advanced remarkably with the progress of nuclear development. They have played the role of weft connecting each realm of nuclear engineering and then an introductory course of advanced scientific computational methods and their applications to nuclear technologies were prepared in serial form. This is the fourth issue showing the overview of scientific computational methods with the introduction of continuum simulation methods and their applications. Simulation methods on physical radiation effects on materials are reviewed based on the process such as binary collision approximation, molecular dynamics, kinematic Monte Carlo method, reaction rate method and dislocation dynamics. (T. Tanaka)
Application of Conjugate Gradient methods to tidal simulation
Barragy, E.; Carey, G.F.; Walters, R.A.
1993-01-01
A harmonic decomposition technique is applied to the shallow water equations to yield a complex, nonsymmetric, nonlinear, Helmholtz type problem for the sea surface and an accompanying complex, nonlinear diagonal problem for the velocities. The equation for the sea surface is linearized using successive approximation and then discretized with linear, triangular finite elements. The study focuses on applying iterative methods to solve the resulting complex linear systems. The comparative evaluation includes both standard iterative methods for the real subsystems and complex versions of the well known Bi-Conjugate Gradient and Bi-Conjugate Gradient Squared methods. Several Incomplete LU type preconditioners are discussed, and the effects of node ordering, rejection strategy, domain geometry and Coriolis parameter (affecting asymmetry) are investigated. Implementation details for the complex case are discussed. Performance studies are presented and comparisons made with a frontal solver. ?? 1993.
Hybrid statistics-simulations based method for atom-counting from ADF STEM images
Energy Technology Data Exchange (ETDEWEB)
De wael, Annelies, E-mail: annelies.dewael@uantwerpen.be [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); De Backer, Annick [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Jones, Lewys; Nellist, Peter D. [Department of Materials, University of Oxford, Parks Road, OX1 3PH Oxford (United Kingdom); Van Aert, Sandra, E-mail: sandra.vanaert@uantwerpen.be [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium)
2017-06-15
A hybrid statistics-simulations based method for atom-counting from annular dark field scanning transmission electron microscopy (ADF STEM) images of monotype crystalline nanostructures is presented. Different atom-counting methods already exist for model-like systems. However, the increasing relevance of radiation damage in the study of nanostructures demands a method that allows atom-counting from low dose images with a low signal-to-noise ratio. Therefore, the hybrid method directly includes prior knowledge from image simulations into the existing statistics-based method for atom-counting, and accounts in this manner for possible discrepancies between actual and simulated experimental conditions. It is shown by means of simulations and experiments that this hybrid method outperforms the statistics-based method, especially for low electron doses and small nanoparticles. The analysis of a simulated low dose image of a small nanoparticle suggests that this method allows for far more reliable quantitative analysis of beam-sensitive materials. - Highlights: • A hybrid method for atom-counting from ADF STEM images is introduced. • Image simulations are incorporated into a statistical framework in a reliable manner. • Limits of the existing methods for atom-counting are far exceeded. • Reliable counting results from an experimental low dose image are obtained. • Progress towards reliable quantitative analysis of beam-sensitive materials is made.
Biasing transition rate method based on direct MC simulation for probabilistic safety assessment
Institute of Scientific and Technical Information of China (English)
Xiao-Lei Pan; Jia-Qun Wang; Run Yuan; Fang Wang; Han-Qing Lin; Li-Qin Hu; Jin Wang
2017-01-01
Direct Monte Carlo (MC) simulation is a powerful probabilistic safety assessment method for accounting dynamics of the system.But it is not efficient at simulating rare events.A biasing transition rate method based on direct MC simulation is proposed to solve the problem in this paper.This method biases transition rates of the components by adding virtual components to them in series to increase the occurrence probability of the rare event,hence the decrease in the variance of MC estimator.Several cases are used to benchmark this method.The results show that the method is effective at modeling system failure and is more efficient at collecting evidence of rare events than the direct MC simulation.The performance is greatly improved by the biasing transition rate method.
Simulation of electrically driven jet using Chebyshev collocation method
Institute of Scientific and Technical Information of China (English)
无
2011-01-01
The model of electrically driven jet is governed by a series of quasi 1D dimensionless partial differential equations(PDEs).Following the method of lines,the Chebyshev collocation method is employed to discretize the PDEs and obtain a system of differential-algebraic equations(DAEs).By differentiating constrains in DAEs twice,the system is transformed into a set of ordinary differential equations(ODEs) with invariants.Then the implicit differential equations solver "ddaskr" is used to solve the ODEs and ...
FDTD method using for electrodynamic simulation of resonator accelerating structures
International Nuclear Information System (INIS)
Vorogushin, M.F.; Svistunov, Yu.A.; Chetverikov, I.O.; Malyshev, V.N.; Malyukhov, M.V.
2000-01-01
The finite difference method in the time area (FDTD) makes it possible to model both stationary and nonstationary processes, originating by the beam and field interaction. Possibilities of the method by modeling the fields in the resonant accelerating structures are demonstrated. The possibility of considering the transition processes is important besides the solution of the problem on determination of frequencies and distribution in the space of the resonators oscillations proper types. The program presented makes it possible to obtain practical results for modeling accelerating structures on personal computers [ru
Pasaribu, Hendra; Sitanggang, Delima; Rizki Damanik, Rudolfo; Rudianto Sitompul, Alex Chandra
2018-04-01
File transfer by using a smartphone has some security issues like data theft by irresponsible parties. To improve the quality of data security systems on smartphones, in this research the integration of AES 256 bit algorithm by using MD5 hashing is proposed. The use of MD5 aims to increase the key strength of the encryption and decryption process of document files. The test results show that the proposed method can increase the key strength of the encryption and decryption process in the document file. Encryption and decryption time by using AES and MD5 combination is faster than using AES only on *.txt file type and reverse results for *.docx, *.xlsx, *.pptx and *.pdf file files.
Orbit Feedback Operation with RCBX (MD 1209)
Wenninger, Jorg; Nisbet, David; Ponce, Laurette; Louro Alves, Diogo Miguel; CERN. Geneva. ATS Department
2017-01-01
The LHC Orbit Feedback (OFB) is able to drive any orbit corrector circuit (COD) to steer the LHC orbit. But during the first feedback tests in 2010, all attempts to use the common triplet orbit correctors (MCBX) failed because the QPS system installed to protect those magnets triggered power aborts as soon as the OFB steered the beam with those CODs. The reason was most likely the violation of the RCBX circuit acceleration limits. For this reason the MCBX orbit correctors were never driven by the OFB in regular operation. Although the performance of the OFB is generally excellent, the quality of the beam steering around IRs could be improved if the OFB could correct the orbit with the MCBX to counteract locally triplet quadrupole movements. The aim of this MD was to make a new attempt to use the MCBX in the OFB. The test was successful at injection (no circuit trip) and failed during the ramp (QPS power abort). The PC voltages and QPS Ures signals revealed the presence of voltage spikes with a period of 10~s...
Numerical simulation methods for phase-transitional flow
Pecenko, A.
2010-01-01
The object of the present dissertation is a numerical study of multiphase flow of one fluid component. In particular, the research described in this thesis focuses on the development of numerical methods that are based on a diffuse-interface model (DIM). With this approach, the modeling problem
Clearance gap flow: Simulations by discontinuous Galerkin method and experiments
Czech Academy of Sciences Publication Activity Database
Hála, Jindřich; Luxa, Martin; Bublík, O.; Prausová, H.; Vimmr, J.
2016-01-01
Roč. 92, May (2016), 02073-02073 ISSN 2100-014X. [EFM14 – Experimental Fluid Mechanics 2014. Český Krumlov, 18.11.2014-21.11.2014] Institutional support: RVO:61388998 Keywords : compressible fluid flow * narrow channel flow * discontinuous Galerkin finite element method Subject RIV: BK - Fluid Dynamics
TreePM Method for Two-Dimensional Cosmological Simulations ...
Indian Academy of Sciences (India)
R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22
We discuss the integration of the equations of motion that we use in the 2d TreePM code in section 7. .... spaced values of r in order to keep interpolation errors in control. .... hence we cannot use the usual leap-frog method. We recast the ...
A Simulator to Enhance Teaching and Learning of Mining Methods ...
African Journals Online (AJOL)
Audio visual education that incorporates devices and materials which involve sight, sound, or both has become a sine qua non in recent times in the teaching and learning process. An automated physical model of mining methods aided with video instructions was designed and constructed by harnessing locally available ...
Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4
Mishra, S. B.; Nanda, B. R. K.
2017-05-01
Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.
A new method to estimate heat source parameters in gas metal arc welding simulation process
International Nuclear Information System (INIS)
Jia, Xiaolei; Xu, Jie; Liu, Zhaoheng; Huang, Shaojie; Fan, Yu; Sun, Zhi
2014-01-01
Highlights: •A new method for accurate simulation of heat source parameters was presented. •The partial least-squares regression analysis was recommended in the method. •The welding experiment results verified accuracy of the proposed method. -- Abstract: Heat source parameters were usually recommended by experience in welding simulation process, which induced error in simulation results (e.g. temperature distribution and residual stress). In this paper, a new method was developed to accurately estimate heat source parameters in welding simulation. In order to reduce the simulation complexity, a sensitivity analysis of heat source parameters was carried out. The relationships between heat source parameters and welding pool characteristics (fusion width (W), penetration depth (D) and peak temperature (T p )) were obtained with both the multiple regression analysis (MRA) and the partial least-squares regression analysis (PLSRA). Different regression models were employed in each regression method. Comparisons of both methods were performed. A welding experiment was carried out to verify the method. The results showed that both the MRA and the PLSRA were feasible and accurate for prediction of heat source parameters in welding simulation. However, the PLSRA was recommended for its advantages of requiring less simulation data
Partial Variance of Increments Method in Solar Wind Observations and Plasma Simulations
Greco, A.; Matthaeus, W. H.; Perri, S.; Osman, K. T.; Servidio, S.; Wan, M.; Dmitruk, P.
2018-02-01
The method called "PVI" (Partial Variance of Increments) has been increasingly used in analysis of spacecraft and numerical simulation data since its inception in 2008. The purpose of the method is to study the kinematics and formation of coherent structures in space plasmas, a topic that has gained considerable attention, leading the development of identification methods, observations, and associated theoretical research based on numerical simulations. This review paper will summarize key features of the method and provide a synopsis of the main results obtained by various groups using the method. This will enable new users or those considering methods of this type to find details and background collected in one place.
Timko, Jeff; Kuyucak, Serdar
2012-11-28
Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.
77 FR 5201 - Drawbridge Operation Regulation; Bear Creek, Dundalk, MD
2012-02-02
...-AA09 Drawbridge Operation Regulation; Bear Creek, Dundalk, MD AGENCY: Coast Guard, DHS. ACTION: Notice... operation of the Baltimore County highway bridge at Wise Avenue across Bear Creek, mile 3.4, between Dundalk... Avenue across Bear Creek, mile 3.4 between Dundalk and Sparrows Point, MD. This change would require the...
Bednarek, Mateusz Jakub; Lechner, Anton; CERN. Geneva. ATS Department
2016-01-01
The detailed program proposed for the LHC Machine Development concerning a quench induced by fast losses on the MQY.4L6 quadrupole is presented. The merit of the MD, the necessary modifications of the machine protection systems are presented together with a preliminary analysis of the MD results.
Chosen-Prefix Collisions for MD5 and Applications
M.M.J. Stevens (Marc); A.K. Lenstra (Arjen); B. de Weger (Benne)
2012-01-01
textabstractWe present a novel, automated way to find differential paths for MD5. Its main application is in the construction of \\emph{chosen-prefix collisions}. We have shown how, at an approximate expected cost of $2^{39}$ calls to the MD5 compression function, for any two chosen
Waiting time distribution in M/D/1 queueing systems
DEFF Research Database (Denmark)
Iversen, Villy Bæk; Staalhagen, Lars
1999-01-01
The well-known formula for the waiting time distribution of M/D/1 queueing systems is numerically unsuitable when the load is close to 1.0 and/or the results for a large waiting time are required. An algorithm for any load and waiting time is presented, based on the state probabilities of M/D/1...
Stockner, Thomas; Mullen, Anna; MacMillan, Fraser
2015-10-01
ABC transporters are primary active transporters found in all kingdoms of life. Human multidrug resistance transporter ABCB1, or P-glycoprotein, has an extremely broad substrate spectrum and confers resistance against chemotherapy drug treatment in cancer cells. The bacterial ABC transporter MsbA is a lipid A flippase and a homolog to the human ABCB1 transporter, with which it partially shares its substrate spectrum. Crystal structures of MsbA and ABCB1 have been solved in multiple conformations, providing a glimpse into the possible conformational changes the transporter could be going through during the transport cycle. Crystal structures are inherently static, while a dynamic picture of the transporter in motion is needed for a complete understanding of transporter function. Molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy can provide structural information on ABC transporters, but the strength of these two methods lies in the potential to characterise the dynamic regime of these transporters. Information from the two methods is quite complementary. MD simulations provide an all atom dynamic picture of the time evolution of the molecular system, though with a narrow time window. EPR spectroscopy can probe structural, environmental and dynamic properties of the transporter in several time regimes, but only through the attachment sites of an exogenous spin label. In this review the synergistic effects that can be achieved by combining the two methods are highlighted, and a brief methodological background is also presented. © 2015 Authors; published by Portland Press Limited.
Methods for Factor Screening in Computer Simulation Experiments
1979-03-01
of the dat-a In a-space, impacto the variable selection problem s ign if Lrast ly. S-arch-type variable selection methods include the all-po"sible...i.iv 41.1 ti * n wt- -iu’pt-v c C it st’vt’re mu It ico11 inear it v is pro-crtnt Lind. , ii;.qt4pai tlv * Iti’lt- c- j c. tic j icivnt, art, verv
An assessment of communication skills of the MD/MS students of institute of medicine in Nepal
Directory of Open Access Journals (Sweden)
Jagdish Prasad Agrawal
2013-09-01
Full Text Available Introduction The main objective of this study was to assess the level of interpersonal communication skills of MD/MS resident doctors and to provide recommendations for the future. Methods Descriptive, cross sectional, qualitative and quantitative research design was used. 7- point Likert scale (0 to 6 MAAS-Global scoring instrument was used. The subjects of the research were the MD/MS residents from various departments of Maharajgunj Medical Campus (MMC of Institute of Medicine, Maharajgunj, Kathmandu. Out of 162 MD/MS residents, only 30 (18.5% MD/MS residents were selected for the sample size for the study from 1st, 2nd and 3rd year. One MD/MS resident was required four video recording to conduct four interviews with patients coming to the outpatient department. Results There was high degree of positive correlation between Information sharing and Management (r=0.746 whereas weak negative correlation on clarification and diagnosis (r=-0.011. Inter-rater correlation was established before hand and was satisfactory (p < 0.05. Conclusions This base line study of MD/MS residents shows that over all MD/MS residents are deficient in almost all the components of interpersonal communication skills. A communication skills training course in postgraduate medical education could improve the existing communication skills of the doctors in Nepal.
Empirical method for simulation of water tables by digital computers
International Nuclear Information System (INIS)
Carnahan, C.L.; Fenske, P.R.
1975-09-01
An empirical method is described for computing a matrix of water-table elevations from a matrix of topographic elevations and a set of observed water-elevation control points which may be distributed randomly over the area of interest. The method is applicable to regions, such as the Great Basin, where the water table can be assumed to conform to a subdued image of overlying topography. A first approximation to the water table is computed by smoothing a matrix of topographic elevations and adjusting each node of the smoothed matrix according to a linear regression between observed water elevations and smoothed topographic elevations. Each observed control point is assumed to exert a radially decreasing influence on the first approximation surface. The first approximation is then adjusted further to conform to observed water-table elevations near control points. Outside the domain of control, the first approximation is assumed to represent the most probable configuration of the water table. The method has been applied to the Nevada Test Site and the Hot Creek Valley areas in Nevada
Simulation Methods and Validation Criteria for Modeling Cardiac Ventricular Electrophysiology.
Directory of Open Access Journals (Sweden)
Shankarjee Krishnamoorthi
Full Text Available We describe a sequence of methods to produce a partial differential equation model of the electrical activation of the ventricles. In our framework, we incorporate the anatomy and cardiac microstructure obtained from magnetic resonance imaging and diffusion tensor imaging of a New Zealand White rabbit, the Purkinje structure and the Purkinje-muscle junctions, and an electrophysiologically accurate model of the ventricular myocytes and tissue, which includes transmural and apex-to-base gradients of action potential characteristics. We solve the electrophysiology governing equations using the finite element method and compute both a 6-lead precordial electrocardiogram (ECG and the activation wavefronts over time. We are particularly concerned with the validation of the various methods used in our model and, in this regard, propose a series of validation criteria that we consider essential. These include producing a physiologically accurate ECG, a correct ventricular activation sequence, and the inducibility of ventricular fibrillation. Among other components, we conclude that a Purkinje geometry with a high density of Purkinje muscle junctions covering the right and left ventricular endocardial surfaces as well as transmural and apex-to-base gradients in action potential characteristics are necessary to produce ECGs and time activation plots that agree with physiological observations.
Simulation Methods and Validation Criteria for Modeling Cardiac Ventricular Electrophysiology.
Krishnamoorthi, Shankarjee; Perotti, Luigi E; Borgstrom, Nils P; Ajijola, Olujimi A; Frid, Anna; Ponnaluri, Aditya V; Weiss, James N; Qu, Zhilin; Klug, William S; Ennis, Daniel B; Garfinkel, Alan
2014-01-01
We describe a sequence of methods to produce a partial differential equation model of the electrical activation of the ventricles. In our framework, we incorporate the anatomy and cardiac microstructure obtained from magnetic resonance imaging and diffusion tensor imaging of a New Zealand White rabbit, the Purkinje structure and the Purkinje-muscle junctions, and an electrophysiologically accurate model of the ventricular myocytes and tissue, which includes transmural and apex-to-base gradients of action potential characteristics. We solve the electrophysiology governing equations using the finite element method and compute both a 6-lead precordial electrocardiogram (ECG) and the activation wavefronts over time. We are particularly concerned with the validation of the various methods used in our model and, in this regard, propose a series of validation criteria that we consider essential. These include producing a physiologically accurate ECG, a correct ventricular activation sequence, and the inducibility of ventricular fibrillation. Among other components, we conclude that a Purkinje geometry with a high density of Purkinje muscle junctions covering the right and left ventricular endocardial surfaces as well as transmural and apex-to-base gradients in action potential characteristics are necessary to produce ECGs and time activation plots that agree with physiological observations.
Computer codes and methods for simulating accelerator driven systems
International Nuclear Information System (INIS)
Sartori, E.; Byung Chan Na
2003-01-01
A large set of computer codes and associated data libraries have been developed by nuclear research and industry over the past half century. A large number of them are in the public domain and can be obtained under agreed conditions from different Information Centres. The areas covered comprise: basic nuclear data and models, reactor spectra and cell calculations, static and dynamic reactor analysis, criticality, radiation shielding, dosimetry and material damage, fuel behaviour, safety and hazard analysis, heat conduction and fluid flow in reactor systems, spent fuel and waste management (handling, transportation, and storage), economics of fuel cycles, impact on the environment of nuclear activities etc. These codes and models have been developed mostly for critical systems used for research or power generation and other technological applications. Many of them have not been designed for accelerator driven systems (ADS), but with competent use, they can be used for studying such systems or can form the basis for adapting existing methods to the specific needs of ADS's. The present paper describes the types of methods, codes and associated data available and their role in the applications. It provides Web addresses for facilitating searches for such tools. Some indications are given on the effect of non appropriate or 'blind' use of existing tools to ADS. Reference is made to available experimental data that can be used for validating the methods use. Finally, some international activities linked to the different computational aspects are described briefly. (author)
Methods and Simulations of Muon Tomography and Reconstruction
Schreiner, Henry Fredrick, III
This dissertation investigates imaging with cosmic ray muons using scintillator-based portable particle detectors, and covers a variety of the elements required for the detectors to operate and take data, from the detector internal communications and software algorithms to a measurement to allow accurate predictions of the attenuation of physical targets. A discussion of the tracking process for the three layer helical design developed at UT Austin is presented, with details of the data acquisition system, and the highly efficient data format. Upgrades to this system provide a stable system for taking images in harsh or inaccessible environments, such as in a remote jungle in Belize. A Geant4 Monte Carlo simulation was used to develop our understanding of the efficiency of the system, as well as to make predictions for a variety of different targets. The projection process is discussed, with a high-speed algorithm for sweeping a plane through data in near real time, to be used in applications requiring a search through space for target discovery. Several other projections and a foundation of high fidelity 3D reconstructions are covered. A variable binning scheme for rapidly varying statistics over portions of an image plane is also presented and used. A discrepancy in our predictions and the observed attenuation through smaller targets is shown, and it is resolved with a new measurement of low energy spectrum, using a specially designed enclosure to make a series of measurements underwater. This provides a better basis for understanding the images of small amounts of materials, such as for thin cover materials.
Read margin analysis of crossbar arrays using the cell-variability-aware simulation method
Sun, Wookyung; Choi, Sujin; Shin, Hyungsoon
2018-02-01
This paper proposes a new concept of read margin analysis of crossbar arrays using cell-variability-aware simulation. The size of the crossbar array should be considered to predict the read margin characteristic of the crossbar array because the read margin depends on the number of word lines and bit lines. However, an excessively high-CPU time is required to simulate large arrays using a commercial circuit simulator. A variability-aware MATLAB simulator that considers independent variability sources is developed to analyze the characteristics of the read margin according to the array size. The developed MATLAB simulator provides an effective method for reducing the simulation time while maintaining the accuracy of the read margin estimation in the crossbar array. The simulation is also highly efficient in analyzing the characteristic of the crossbar memory array considering the statistical variations in the cell characteristics.
A simulation of portable PET with a new geometric image reconstruction method
Energy Technology Data Exchange (ETDEWEB)
Kawatsu, Shoji [Department of Radiology, Kyoritu General Hospital, 4-33 Go-bancho, Atsuta-ku, Nagoya-shi, Aichi 456 8611 (Japan): Department of Brain Science and Molecular Imaging, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, 36-3, Gengo Moriaka-cho, Obu-shi, Aichi 474 8522 (Japan)]. E-mail: b6rgw@fantasy.plala.or.jp; Ushiroya, Noboru [Department of General Education, Wakayama National College of Technology, 77 Noshima, Nada-cho, Gobo-shi, Wakayama 644 0023 (Japan)
2006-12-20
A new method is proposed for three-dimensional positron emission tomography image reconstruction. The method uses the elementary geometric property of line of response whereby two lines of response, which originate from radioactive isotopes in the same position, lie within a few millimeters distance of each other. The method differs from the filtered back projection method and the iterative reconstruction method. The method is applied to a simulation of portable positron emission tomography.
Nakano, Masaru; Kubota, Fumiko; Inamori, Yutaka; Mitsuyuki, Keiji
Manufacturing system designers should concentrate on designing and planning manufacturing systems instead of spending their efforts on creating the simulation models to verify the design. This paper proposes a method and its tool to navigate the designers through the engineering process and generate the simulation model automatically from the design results. The design agent also supports collaborative design projects among different companies or divisions with distributed engineering and distributed simulation techniques. The idea was implemented and applied to a factory planning process.
International Nuclear Information System (INIS)
BEEBE - WANG, J.; LUCCIO, A.U.; D IMPERIO, N.; MACHIDA, S.
2002-01-01
Space charge in high intensity beams is an important issue in accelerator physics. Due to the complicity of the problems, the most effective way of investigating its effect is by computer simulations. In the resent years, many space charge simulation methods have been developed and incorporated in various 2D or 3D multi-particle-tracking codes. It has becoming necessary to benchmark these methods against each other, and against experimental results. As a part of global effort, we present our initial comparison of the space charge methods incorporated in simulation codes ORBIT++, ORBIT and SIMPSONS. In this paper, the methods included in these codes are overviewed. The simulation results are presented and compared. Finally, from this study, the advantages and disadvantages of each method are discussed
Energy Technology Data Exchange (ETDEWEB)
BEEBE - WANG,J.; LUCCIO,A.U.; D IMPERIO,N.; MACHIDA,S.
2002-06-03
Space charge in high intensity beams is an important issue in accelerator physics. Due to the complicity of the problems, the most effective way of investigating its effect is by computer simulations. In the resent years, many space charge simulation methods have been developed and incorporated in various 2D or 3D multi-particle-tracking codes. It has becoming necessary to benchmark these methods against each other, and against experimental results. As a part of global effort, we present our initial comparison of the space charge methods incorporated in simulation codes ORBIT++, ORBIT and SIMPSONS. In this paper, the methods included in these codes are overviewed. The simulation results are presented and compared. Finally, from this study, the advantages and disadvantages of each method are discussed.
The Monte Carlo Simulation Method for System Reliability and Risk Analysis
Zio, Enrico
2013-01-01
Monte Carlo simulation is one of the best tools for performing realistic analysis of complex systems as it allows most of the limiting assumptions on system behavior to be relaxed. The Monte Carlo Simulation Method for System Reliability and Risk Analysis comprehensively illustrates the Monte Carlo simulation method and its application to reliability and system engineering. Readers are given a sound understanding of the fundamentals of Monte Carlo sampling and simulation and its application for realistic system modeling. Whilst many of the topics rely on a high-level understanding of calculus, probability and statistics, simple academic examples will be provided in support to the explanation of the theoretical foundations to facilitate comprehension of the subject matter. Case studies will be introduced to provide the practical value of the most advanced techniques. This detailed approach makes The Monte Carlo Simulation Method for System Reliability and Risk Analysis a key reference for senior undergra...
3D simulation of friction stir welding based on movable cellular automaton method
Eremina, Galina M.
2017-12-01
The paper is devoted to a 3D computer simulation of the peculiarities of material flow taking place in friction stir welding (FSW). The simulation was performed by the movable cellular automaton (MCA) method, which is a representative of particle methods in mechanics. Commonly, the flow of material in FSW is simulated based on computational fluid mechanics, assuming the material as continuum and ignoring its structure. The MCA method considers a material as an ensemble of bonded particles. The rupture of interparticle bonds and the formation of new bonds enable simulations of crack nucleation and healing as well as mas mixing and microwelding. The simulation results showed that using pins of simple shape (cylinder, cone, and pyramid) without a shoulder results in small displacements of plasticized material in workpiece thickness directions. Nevertheless, the optimal ratio of longitudinal velocity to rotational speed makes it possible to transport the welded material around the pin several times and to produce a joint of good quality.
Development and simulation of various methods for neutron activation analysis
International Nuclear Information System (INIS)
Otgooloi, B.
1993-01-01
Simple methods for neutron activation analysis have been developed. The results on the studies of installation for determination of fluorine in fluorite ores directly on the lorry by fast neutron activation analysis have been shown. Nitrogen in organic materials was shown by N 14 and N 15 activation. The description of the new equipment 'FLUORITE' for fluorate factory have been shortly given. Pu and Be isotope in organic materials, including in wheat, was measured. 25 figs, 19 tabs. (Author, Translated by J.U)
A virtual source method for Monte Carlo simulation of Gamma Knife Model C
Energy Technology Data Exchange (ETDEWEB)
Kim, Tae Hoon; Kim, Yong Kyun [Hanyang University, Seoul (Korea, Republic of); Chung, Hyun Tai [Seoul National University College of Medicine, Seoul (Korea, Republic of)
2016-05-15
The Monte Carlo simulation method has been used for dosimetry of radiation treatment. Monte Carlo simulation is the method that determines paths and dosimetry of particles using random number. Recently, owing to the ability of fast processing of the computers, it is possible to treat a patient more precisely. However, it is necessary to increase the simulation time to improve the efficiency of accuracy uncertainty. When generating the particles from the cobalt source in a simulation, there are many particles cut off. So it takes time to simulate more accurately. For the efficiency, we generated the virtual source that has the phase space distribution which acquired a single gamma knife channel. We performed the simulation using the virtual sources on the 201 channel and compared the measurement with the simulation using virtual sources and real sources. A virtual source file was generated to reduce the simulation time of a Gamma Knife Model C. Simulations with a virtual source executed about 50 times faster than the original source code and there was no statistically significant difference in simulated results.
A virtual source method for Monte Carlo simulation of Gamma Knife Model C
International Nuclear Information System (INIS)
Kim, Tae Hoon; Kim, Yong Kyun; Chung, Hyun Tai
2016-01-01
The Monte Carlo simulation method has been used for dosimetry of radiation treatment. Monte Carlo simulation is the method that determines paths and dosimetry of particles using random number. Recently, owing to the ability of fast processing of the computers, it is possible to treat a patient more precisely. However, it is necessary to increase the simulation time to improve the efficiency of accuracy uncertainty. When generating the particles from the cobalt source in a simulation, there are many particles cut off. So it takes time to simulate more accurately. For the efficiency, we generated the virtual source that has the phase space distribution which acquired a single gamma knife channel. We performed the simulation using the virtual sources on the 201 channel and compared the measurement with the simulation using virtual sources and real sources. A virtual source file was generated to reduce the simulation time of a Gamma Knife Model C. Simulations with a virtual source executed about 50 times faster than the original source code and there was no statistically significant difference in simulated results
Spectral Element Method for the Simulation of Unsteady Compressible Flows
Diosady, Laslo Tibor; Murman, Scott M.
2013-01-01
This work uses a discontinuous-Galerkin spectral-element method (DGSEM) to solve the compressible Navier-Stokes equations [1{3]. The inviscid ux is computed using the approximate Riemann solver of Roe [4]. The viscous fluxes are computed using the second form of Bassi and Rebay (BR2) [5] in a manner consistent with the spectral-element approximation. The method of lines with the classical 4th-order explicit Runge-Kutta scheme is used for time integration. Results for polynomial orders up to p = 15 (16th order) are presented. The code is parallelized using the Message Passing Interface (MPI). The computations presented in this work are performed using the Sandy Bridge nodes of the NASA Pleiades supercomputer at NASA Ames Research Center. Each Sandy Bridge node consists of 2 eight-core Intel Xeon E5-2670 processors with a clock speed of 2.6Ghz and 2GB per core memory. On a Sandy Bridge node the Tau Benchmark [6] runs in a time of 7.6s.
An adaptative finite element method for turbulent flow simulations
International Nuclear Information System (INIS)
Arnoux-Guisse, F.; Bonnin, O.; Leal de Sousa, L.; Nicolas, G.
1995-05-01
After outlining the space and time discretization methods used in the N3S thermal hydraulic code developed at EDF/NHL, we describe the possibilities of the peripheral version, the Adaptative Mesh, which comprises two separate parts: the error indicator computation and the development of a module subdividing elements usable by the solid dynamics code ASTER and the electromagnetism code TRIFOU also developed by R and DD. The error indicators implemented in N3S are described. They consist of a projection indicator quantifying the space error in laminar or turbulent flow calculations and a Navier-Stokes residue indicator calculated on each element. The method for subdivision of triangles into four sub-triangles and tetrahedra into eight sub-tetrahedra is then presented with its advantages and drawbacks. It is illustrated by examples showing the efficiency of the module. The last concerns the 2 D case of flow behind a backward-facing step. (authors). 9 refs., 5 figs., 1 tab
Heterogeneous Rock Simulation Using DIP-Micromechanics-Statistical Methods
Directory of Open Access Journals (Sweden)
H. Molladavoodi
2018-01-01
Full Text Available Rock as a natural material is heterogeneous. Rock material consists of minerals, crystals, cement, grains, and microcracks. Each component of rock has a different mechanical behavior under applied loading condition. Therefore, rock component distribution has an important effect on rock mechanical behavior, especially in the postpeak region. In this paper, the rock sample was studied by digital image processing (DIP, micromechanics, and statistical methods. Using image processing, volume fractions of the rock minerals composing the rock sample were evaluated precisely. The mechanical properties of the rock matrix were determined based on upscaling micromechanics. In order to consider the rock heterogeneities effect on mechanical behavior, the heterogeneity index was calculated in a framework of statistical method. A Weibull distribution function was fitted to the Young modulus distribution of minerals. Finally, statistical and Mohr–Coulomb strain-softening models were used simultaneously as a constitutive model in DEM code. The acoustic emission, strain energy release, and the effect of rock heterogeneities on the postpeak behavior process were investigated. The numerical results are in good agreement with experimental data.
Simulation As a Method To Support Complex Organizational Transformations in Healthcare
Rothengatter, D.C.F.; Katsma, Christiaan; van Hillegersberg, Jos
2010-01-01
In this paper we study the application of simulation as a method to support information system and process design in complex organizational transitions. We apply a combined use of a collaborative workshop approach with the use of a detailed and accurate graphical simulation model in a hospital that
Discrete event simulation of crop operations in sweet pepper in support of work method innovation
Ooster, van 't Bert; Aantjes, Wiger; Melamed, Z.
2017-01-01
Greenhouse Work Simulation, GWorkS, is a model that simulates crop operations in greenhouses for the purpose of analysing work methods. GWorkS is a discrete event model that approaches reality as a discrete stochastic dynamic system. GWorkS was developed and validated using cut-rose as a case
An analytical method to simulate the H I 21-cm visibility signal for intensity mapping experiments
Sarkar, Anjan Kumar; Bharadwaj, Somnath; Marthi, Visweshwar Ram
2018-01-01
Simulations play a vital role in testing and validating H I 21-cm power spectrum estimation techniques. Conventional methods use techniques like N-body simulations to simulate the sky signal which is then passed through a model of the instrument. This makes it necessary to simulate the H I distribution in a large cosmological volume, and incorporate both the light-cone effect and the telescope's chromatic response. The computational requirements may be particularly large if one wishes to simulate many realizations of the signal. In this paper, we present an analytical method to simulate the H I visibility signal. This is particularly efficient if one wishes to simulate a large number of realizations of the signal. Our method is based on theoretical predictions of the visibility correlation which incorporate both the light-cone effect and the telescope's chromatic response. We have demonstrated this method by applying it to simulate the H I visibility signal for the upcoming Ooty Wide Field Array Phase I.
Simulation-based investigation of the paired-gear method in cod-end selectivity studies
DEFF Research Database (Denmark)
Herrmann, Bent; Frandsen, Rikke; Holst, René
2007-01-01
In this paper, the paired-gear and covered cod-end methods for estimating the selectivity of trawl cod-ends are compared. A modified version of the cod-end selectivity simulator PRESEMO is used to simulate the data that would be collected from a paired-gear experiment where the test cod-end also ...
Energy Technology Data Exchange (ETDEWEB)
Berthiau, G
1995-10-01
The circuit design problem consists in determining acceptable parameter values (resistors, capacitors, transistors geometries ...) which allow the circuit to meet various user given operational criteria (DC consumption, AC bandwidth, transient times ...). This task is equivalent to a multidimensional and/or multi objective optimization problem: n-variables functions have to be minimized in an hyper-rectangular domain ; equality constraints can be eventually specified. A similar problem consists in fitting component models. In this way, the optimization variables are the model parameters and one aims at minimizing a cost function built on the error between the model response and the data measured on the component. The chosen optimization method for this kind of problem is the simulated annealing method. This method, provided by the combinatorial optimization domain, has been adapted and compared with other global optimization methods for the continuous variables problems. An efficient strategy of variables discretization and a set of complementary stopping criteria have been proposed. The different parameters of the method have been adjusted with analytical functions of which minima are known, classically used in the literature. Our simulated annealing algorithm has been coupled with an open electrical simulator SPICE-PAC of which the modular structure allows the chaining of simulations required by the circuit optimization process. We proposed, for high-dimensional problems, a partitioning technique which ensures proportionality between CPU-time and variables number. To compare our method with others, we have adapted three other methods coming from combinatorial optimization domain - the threshold method, a genetic algorithm and the Tabu search method - The tests have been performed on the same set of test functions and the results allow a first comparison between these methods applied to continuous optimization variables. (Abstract Truncated)
Hybrid vortex simulations of wind turbines using a three-dimensional viscous-inviscid panel method
DEFF Research Database (Denmark)
Ramos García, Néstor; Hejlesen, Mads Mølholm; Sørensen, Jens Nørkær
2017-01-01
adirect calculation, whereas the contribution from the large downstream wake is calculated using a mesh-based method. Thehybrid method is first validated in detail against the well-known MEXICO experiment, using the direct filament method asa comparison. The second part of the validation includes a study......A hybrid filament-mesh vortex method is proposed and validated to predict the aerodynamic performance of wind turbinerotors and to simulate the resulting wake. Its novelty consists of using a hybrid method to accurately simulate the wakedownstream of the wind turbine while reducing...
Some recent developments of the immersed interface method for flow simulation
Xu, Sheng
2017-11-01
The immersed interface method is a general methodology for solving PDEs subject to interfaces. In this talk, I will give an overview of some recent developments of the method toward the enhancement of its robustness for flow simulation. In particular, I will present with numerical results how to capture boundary conditions on immersed rigid objects, how to adopt interface triangulation in the method, and how to parallelize the method for flow with moving objects. With these developments, the immersed interface method can achieve accurate and efficient simulation of a flow involving multiple moving complex objects. Thanks to NSF for the support of this work under Grant NSF DMS 1320317.
Research of Monte Carlo method used in simulation of different maintenance processes
International Nuclear Information System (INIS)
Zhao Siqiao; Liu Jingquan
2011-01-01
The paper introduces two kinds of Monte Carlo methods used in equipment life process simulation under the least maintenance: condition: method of producing the interval of lifetime, method of time scale conversion. The paper also analyzes the characteristics and the using scope of the two methods. By using the conception of service age reduction factor, the model of equipment's life process under incomplete maintenance condition is established, and also the life process simulation method applicable to this situation is invented. (authors)
Deviation from equilibrium conditions in molecular dynamic simulations of homogeneous nucleation.
Halonen, Roope; Zapadinsky, Evgeni; Vehkamäki, Hanna
2018-04-28
We present a comparison between Monte Carlo (MC) results for homogeneous vapour-liquid nucleation of Lennard-Jones clusters and previously published values from molecular dynamics (MD) simulations. Both the MC and MD methods sample real cluster configuration distributions. In the MD simulations, the extent of the temperature fluctuation is usually controlled with an artificial thermostat rather than with more realistic carrier gas. In this study, not only a primarily velocity scaling thermostat is considered, but also Nosé-Hoover, Berendsen, and stochastic Langevin thermostat methods are covered. The nucleation rates based on a kinetic scheme and the canonical MC calculation serve as a point of reference since they by definition describe an equilibrated system. The studied temperature range is from T = 0.3 to 0.65 ϵ/k. The kinetic scheme reproduces well the isothermal nucleation rates obtained by Wedekind et al. [J. Chem. Phys. 127, 064501 (2007)] using MD simulations with carrier gas. The nucleation rates obtained by artificially thermostatted MD simulations are consistently lower than the reference nucleation rates based on MC calculations. The discrepancy increases up to several orders of magnitude when the density of the nucleating vapour decreases. At low temperatures, the difference to the MC-based reference nucleation rates in some cases exceeds the maximal nonisothermal effect predicted by classical theory of Feder et al. [Adv. Phys. 15, 111 (1966)].
Energy Technology Data Exchange (ETDEWEB)
Morillon, B.
1996-12-31
With most of the traditional and contemporary techniques, it is still impossible to solve the transport equation if one takes into account a fully detailed geometry and if one studies precisely the interactions between particles and matters. Only the Monte Carlo method offers such a possibility. However with significant attenuation, the natural simulation remains inefficient: it becomes necessary to use biasing techniques where the solution of the adjoint transport equation is essential. The Monte Carlo code Tripoli has been using such techniques successfully for a long time with different approximate adjoint solutions: these methods require from the user to find out some parameters. If this parameters are not optimal or nearly optimal, the biases simulations may bring about small figures of merit. This paper presents a description of the most important biasing techniques of the Monte Carlo code Tripoli ; then we show how to calculate the importance function for general geometry with multigroup cases. We present a completely automatic biasing technique where the parameters of the biased simulation are deduced from the solution of the adjoint transport equation calculated by collision probabilities. In this study we shall estimate the importance function through collision probabilities method and we shall evaluate its possibilities thanks to a Monte Carlo calculation. We compare different biased simulations with the importance function calculated by collision probabilities for one-group and multigroup problems. We have run simulations with new biasing method for one-group transport problems with isotropic shocks and for multigroup problems with anisotropic shocks. The results show that for the one-group and homogeneous geometry transport problems the method is quite optimal without splitting and russian roulette technique but for the multigroup and heterogeneous X-Y geometry ones the figures of merit are higher if we add splitting and russian roulette technique.
Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations
DEFF Research Database (Denmark)
Larsen, Anders Støttrup; Rantanen, Jukka; Johansson, Kristoffer E
2017-01-01
Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach...... to the dehydration of ampicillin trihydrate. The crystallographic unit cell of the trihydrate is used to construct the simulation cell containing 216 ampicillin and 648 water molecules. This system is dehydrated by removing water molecules during a 2200 ps simulation, and depending on the computational dehydration....... The structural changes could be followed in real time, and in addition, an intermediate amorphous phase was identified. The computationally identified dehydrated structure (anhydrate) was slightly different from the experimentally known anhydrate structure suggesting that the simulated computational structure...
The adaptation method in the Monte Carlo simulation for computed tomography
Energy Technology Data Exchange (ETDEWEB)
Lee, Hyoung Gun; Yoon, Chang Yeon; Lee, Won Ho [Dept. of Bio-convergence Engineering, Korea University, Seoul (Korea, Republic of); Cho, Seung Ryong [Dept. of Nuclear and Quantum Engineering, Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of); Park, Sung Ho [Dept. of Neurosurgery, Ulsan University Hospital, Ulsan (Korea, Republic of)
2015-06-15
The patient dose incurred from diagnostic procedures during advanced radiotherapy has become an important issue. Many researchers in medical physics are using computational simulations to calculate complex parameters in experiments. However, extended computation times make it difficult for personal computers to run the conventional Monte Carlo method to simulate radiological images with high-flux photons such as images produced by computed tomography (CT). To minimize the computation time without degrading imaging quality, we applied a deterministic adaptation to the Monte Carlo calculation and verified its effectiveness by simulating CT image reconstruction for an image evaluation phantom (Catphan; Phantom Laboratory, New York NY, USA) and a human-like voxel phantom (KTMAN-2) (Los Alamos National Laboratory, Los Alamos, NM, USA). For the deterministic adaptation, the relationship between iteration numbers and the simulations was estimated and the option to simulate scattered radiation was evaluated. The processing times of simulations using the adaptive method were at least 500 times faster than those using a conventional statistical process. In addition, compared with the conventional statistical method, the adaptive method provided images that were more similar to the experimental images, which proved that the adaptive method was highly effective for a simulation that requires a large number of iterations-assuming no radiation scattering in the vicinity of detectors minimized artifacts in the reconstructed image.
METHODS OF SIMULATION ON THE MAP OF ETHNOGEOGRAPHICAL KNOWLEDGE
Directory of Open Access Journals (Sweden)
A. M. Saraeva
2017-01-01
Full Text Available The article deals with the features of the spatial representation of the location of objects and phenomena on the Earth. One of the types of “cartographic representation” is modeling on the contour map. The advantages of the method are revealed. The application of modeling techniques that allows one to include ethnogeographic data in the content of the characteristics of the territory and reflect them on the contour map. The basis of ethnogeographic modeling is the identification and creation of elements of the material and spiritual culture of peoples by means of conventional signs. Comparison of these elements, their superimposition with respect to each other, as well as their comparison with geographic maps allow us to determine the interrelations and the dependence of the phenomenon. Modeling on contour maps is the basic method of learning in geography. On the one hand, it creates a cartographic image of the studied territory, and on the other hand it facilitates the creation of “visual supports” on the map.Modeling on contour maps, at the beginning students put the basic geographical names, which will serve as the basic knowledge. Then, by purposefully analyzing and comparing the thematic maps of the atlas or textbook, the students reflect specific ethno-geographical knowledge on contour maps. As a result, contour maps acquire “their own face”, and do not become a simple copy of maps of an atlas or textbook.Also, the features of the effect of this technique on the formation of spatial representations about the studied object have been analyzed. Thanks to the cartographic model, one can maintain a constant cognitive interest in the material studied. Modeling on the contour map will allow one to present the structure of the links between the elements of the ethnogeographical material. The basis of ethnogeographic modeling on the contour map is the identification and mapping of elements of the material and spiritual culture of
Real-time tumor ablation simulation based on the dynamic mode decomposition method
Bourantas, George C.; Ghommem, Mehdi; Kagadis, George C.; Katsanos, Konstantinos H.; Loukopoulos, Vassilios C.; Burganos, Vasilis N.; Nikiforidis, George C.
2014-01-01
Purpose: The dynamic mode decomposition (DMD) method is used to provide a reliable forecasting of tumor ablation treatment simulation in real time, which is quite needed in medical practice. To achieve this, an extended Pennes bioheat model must
Estimation of functional failure probability of passive systems based on subset simulation method
International Nuclear Information System (INIS)
Wang Dongqing; Wang Baosheng; Zhang Jianmin; Jiang Jing
2012-01-01
In order to solve the problem of multi-dimensional epistemic uncertainties and small functional failure probability of passive systems, an innovative reliability analysis algorithm called subset simulation based on Markov chain Monte Carlo was presented. The method is found on the idea that a small failure probability can be expressed as a product of larger conditional failure probabilities by introducing a proper choice of intermediate failure events. Markov chain Monte Carlo simulation was implemented to efficiently generate conditional samples for estimating the conditional failure probabilities. Taking the AP1000 passive residual heat removal system, for example, the uncertainties related to the model of a passive system and the numerical values of its input parameters were considered in this paper. And then the probability of functional failure was estimated with subset simulation method. The numerical results demonstrate that subset simulation method has the high computing efficiency and excellent computing accuracy compared with traditional probability analysis methods. (authors)
Reliability Assessment of Active Distribution System Using Monte Carlo Simulation Method
Directory of Open Access Journals (Sweden)
Shaoyun Ge
2014-01-01
Full Text Available In this paper we have treated the reliability assessment problem of low and high DG penetration level of active distribution system using the Monte Carlo simulation method. The problem is formulated as a two-case program, the program of low penetration simulation and the program of high penetration simulation. The load shedding strategy and the simulation process were introduced in detail during each FMEA process. Results indicate that the integration of DG can improve the reliability of the system if the system was operated actively.
Analysis of time integration methods for the compressible two-fluid model for pipe flow simulations
B. Sanderse (Benjamin); I. Eskerud Smith (Ivar); M.H.W. Hendrix (Maurice)
2017-01-01
textabstractIn this paper we analyse different time integration methods for the two-fluid model and propose the BDF2 method as the preferred choice to simulate transient compressible multiphase flow in pipelines. Compared to the prevailing Backward Euler method, the BDF2 scheme has a significantly
Salati, Amin; Mokhtari, Esmail; Panjepour, Masoud; Aryanpour, Gholamreza
2013-04-01
The temperature at which polymorphic phase transformation occurs in nanocrystalline (NC) materials is different from that of coarse-grained specimens. This anomaly has been related to the role of grain boundary component in these materials and can be predicted by a dilated crystal model. In this study, based on this model, a modified equation of state (MEOS) method (instead of equation of state, EOS, method) is used to calculate the total Gibbs free energy of each phase (β-Zr or α-Zr) in NC Zr. Thereupon, the change in the total Gibbs free energy for β-Zr to α-Zr phase transformation (ΔGβ→α) via the grain size is calculated by this method. Similar to polymorphic transformation in other NC materials (Fe, Nb, Co, TiO2, Al2O3 and ZnS), it is found that the estimated transformation temperature in NC Zr (β→α) is reduced with decreasing grain size. Finally, a molecular dynamics (MD) simulation is employed to confirm the theoretical results.
To improve training methods in an engine room simulator-based training
Lin, Chingshin
2016-01-01
The simulator based training are used widely in both industry and school education to reduce the accidents nowadays. This study aims to suggest the improved training methods to increase the effectiveness of engine room simulator training. The effectiveness of training in engine room will be performance indicators and the self-evaluation by participants. In the first phase of observation, the aim is to find out the possible shortcomings of current training methods based on train...
Study of the quantitative analysis approach of maintenance by the Monte Carlo simulation method
International Nuclear Information System (INIS)
Shimizu, Takashi
2007-01-01
This study is examination of the quantitative valuation by Monte Carlo simulation method of maintenance activities of a nuclear power plant. Therefore, the concept of the quantitative valuation of maintenance that examination was advanced in the Japan Society of Maintenology and International Institute of Universality (IUU) was arranged. Basis examination for quantitative valuation of maintenance was carried out at simple feed water system, by Monte Carlo simulation method. (author)
Ngada, Narcisse
2015-06-15
The complexity and cost of building and running high-power electrical systems make the use of simulations unavoidable. The simulations available today provide great understanding about how systems really operate. This paper helps the reader to gain an insight into simulation in the field of power converters for particle accelerators. Starting with the definition and basic principles of simulation, two simulation types, as well as their leading tools, are presented: analog and numerical simulations. Some practical applications of each simulation type are also considered. The final conclusion then summarizes the main important items to keep in mind before opting for a simulation tool or before performing a simulation.
Evaluation of a proposed optimization method for discrete-event simulation models
Directory of Open Access Journals (Sweden)
Alexandre Ferreira de Pinho
2012-12-01
Full Text Available Optimization methods combined with computer-based simulation have been utilized in a wide range of manufacturing applications. However, in terms of current technology, these methods exhibit low performance levels which are only able to manipulate a single decision variable at a time. Thus, the objective of this article is to evaluate a proposed optimization method for discrete-event simulation models based on genetic algorithms which exhibits more efficiency in relation to computational time when compared to software packages on the market. It should be emphasized that the variable's response quality will not be altered; that is, the proposed method will maintain the solutions' effectiveness. Thus, the study draws a comparison between the proposed method and that of a simulation instrument already available on the market and has been examined in academic literature. Conclusions are presented, confirming the proposed optimization method's efficiency.