Developed Simulation Code Research Articles

Hairygami: Analysis of DNA Nanostructures' Conformational Change Driven by Functionalizable Overhangs.

DNA origami is a widely used method to construct nanostructures by self-assembling designed DNA strands. These structures are often used as "pegboards" for templated assembly of proteins, gold nanoparticles, aptamers, and other molecules, with applications ranging from therapeutics and diagnostics to plasmonics and photonics. Imaging these structures using atomic force microscopy (AFM) or transmission electron microscope (TEM) does not capture their full conformation ensemble as they only show their shape flattened on a surface. However, certain conformations of the nanostructure can position guest molecules into distances unaccounted for in their intended design, thus leading to spurious interactions between guest molecules that are designed to be separated. Here, we use molecular dynamics simulations to capture a conformational ensemble of two-dimensional (2D) DNA origami tiles and show that introducing single-stranded overhangs, which are typically used for functionalization of the origami with guest molecules, induces a curvature of the tile structure in the bulk. We show that the shape deformation is of entropic origin, with implications for the design of robust DNA origami breadboards as well as a potential approach to modulate structure shape by introducing overhangs. We then verify experimentally that the DNA overhangs introduce curvature into the DNA origami tiles under divalent as well as monovalent salt buffer conditions. We further experimentally verify that DNA origami functionalized with attached proteins also experiences such induced curvature. We provide the developed simulation code implementing the enhanced sampling to characterize the conformational space of DNA origami as open source software.

Phonon transport simulation with an extended VOF scheme for nano-structured thin film

Control of phonon transport in solid devices is important for thermoelectric energy conversion and phononic crystal technology, and much attention has been paid to sub-micrometer or nanometer scale structures for that purpose. In order to investigate how various nano-structures affect the phonon transport, we have developed a numerical simulation code based on the Boltzmann transport equation of phonon distribution function in the reciprocal space. To appropriately treat the phonon transport at interface of an arbitrary shape, we newly introduced a volume of fluid like scheme, which was originally developed for multi-phase flow simulation. As a test of the developed simulation code, we investigated two-dimensional thin silicon films with two types of hole shape and two types of hole arrangement. The results essentially agree with recent experiments.

SPH code development for X-pinch plasma simulation

We have developed the first smoothed particle hydrodynamics code for investigating X-pinch plasmas driven by pulsed power generators. To achieve the required code performance, we incorporated and discussed appropriate physics models capable of simulating the X-pinch phenomenon across various domains, encompassing equation of state, plasma transport, and radiation effects. The simulations were conducted in full three dimensions using our newly developed code, and we have compared and evaluated the results with experimental data obtained from the X-pinch device at Seoul National University. As a result, our simulations effectively captured the implosion behavior of X-pinch plasma, faithfully reproducing the four-step evolution process commonly observed in typical X-pinch configurations. Furthermore, it provided comprehensive spatiotemporal data on various plasma parameters, including density, temperature, velocity field, and radiated power. Notably, the electron temperature and density at the hot spot well agree with the experimental measurements, validating the accuracy and reliability of the developed simulation code. Additionally, the radiation data exhibited significantly improved accuracy compared to previous simulation results, confirming the effectiveness of the proposed radiation model, and it provides valuable insights into the X-pinch hot spot formation.

Numerical Modeling and Analysis of Transient and Three-Dimensional Heat Transfer in 3D Printing via Fused-Deposition Modeling (FDM)

Fused-Deposition Modeling (FDM) is a commonly used 3D printing method for rapid prototyping and the fabrication of plastic components. The history of temperature variation during the FDM process plays a crucial role in the degree of bonding between layers. This study presents research on the thermal analysis of the 3D printing process using a developed simulation code. The code employs numerical discretization methods with an implicit scheme and an effective heat transfer coefficient for cooling. The computational model is validated by comparing the results with analytical solutions, demonstrating an agreement of more than 99%. The code is then utilized to perform thermal analyses for the 3D printing process. Interlayer and intralayer reheating effects, sensitivity to printing parameters, and realistic printing patterns are investigated. It is shown that concentric and zigzag paths yield similar peaks at different time intervals. Nodal temperatures can fall below the glass transition temperature (Tg) during the printing process, especially at the outer nodes of the domain and under conditions where the cooling period is longer and the printed volume per unit time is smaller. The article suggests future work to calculate welding time at different conditions and locations for the estimation of the degree of bonding.

Numerical Study of Hydrocarbon Charge Reduction Methods in HVAC Heat Exchangers

Required refrigerant charge in heat pump systems with propane is analyzed. Two systems are compared: the first a direct heat pump, with fin-and-tube heat exchangers, and the second an indirect system, with plate heat exchangers with an additional brine-to-air heat exchanger. Each system was considered to be able to work reversibly, with 5 kW design cooling capacity in summer and 8 kW design heating capacity in winter. Two separately developed simulation codes were used to calculate the required refrigerant charge and the efficiency of each of the systems. The charge was reduced by the use of microfinned tubes up to 22% in direct system reduced using microfinned tubes compared to the smooth tube. For the indirect system using specially designed plate heat exchangers with the minimum internal volume, their charge was reduced by up to 66% compared to normal plate heat exchangers.

Higher-order Spectral Method for Regular and Irregular Wave Simulations

In this study, a nonlinear wave simulation code is developed using a higher-order spectral (HOS) method. The HOS method is very efficient because it can determine the solution of the boundary value problem using fast Fourier transform (FFT) without matrix operation. Based on the HOS order, the vertical velocity of the free surface boundary was estimated and applied to the nonlinear free surface boundary condition. Time integration was carried out using the fourth order Runge–Kutta method, which is known to be stable for nonlinear free-surface problems. Numerical stability against the aliasing effect was guaranteed by using the zero-padding method. In addition to simulating the initial wave field distribution, a nonlinear adjusted region for wave generation and a damping region for wave absorption were introduced for wave generation simulation. To validate the developed simulation code, the adjusted simulation was carried out and its results were compared to the eighth order Stokes theory. Long-time simulations were carried out on the irregular wave field distribution, and nonlinear wave propagation characteristics were observed from the results of the simulations. Nonlinear adjusted and damping regions were introduced to implement a numerical wave tank that successfully generated nonlinear regular waves. According to the variation in the mean wave steepness, irregular wave simulations were carried out in the numerical wave tank. The simulation results indicated an increase in the nonlinear interaction between the wave components, which was numerically verified as the mean wave steepness. The results of this study demonstrate that the HOS method is an accurate and efficient method for predicting the nonlinear interaction between waves, which increases with wave steepness.

A parametric SPICE model for the simulation of spark gap switches.

The use of SPICE-based software for the simulation of pulsed power systems-even large complex systems-has become commonplace in the pulsed power community. This is in contrast to earlier work in the field that relied on specially developed simulation codes such as Sandia's Screamer or the Navy Research Lab's Bertha, which natively incorporated models for common pulsed power components such as spark gap switches. Unlike these programs, SPICE programs provide a simple and familiar user interface and wide availability. However, SPICE programs do not include realistic models for key pulsed power circuit devices-including the spark gap switch. While simple switch models do exist in SPICE programs, these can only crudely approximate the behavior of a spark gap. This effort focuses on developing an SPICE circuit model for a gas-filled spark gap switch that is physically realistic while being simple enough to permit simulations to run in reasonable times on typical personal computers. Detailed information is provided for implementation in two common versions of SPICE: LTspice and Orcad PSPICE. Adaptation to other SPICE programs is possible with minimal modification. The model is intended as a design tool that uses physical parameters as inputs to connect it directly to the development of useable pulsed power systems. Data collected from the operation of a high-pressure pulsed-charged switch and a complete 12-stage Marx generator have been used to demonstrate the implementation and accuracy of the model over a wide range of parameters.

Speed-up of simulation of magnetization process for large-scale HTS undulator of X-FEL based on power-law macro-model

The Pure-type HTS undulator is proposed to achieve a high-intensity magnetic field and small size undulator for a compact free-electron laser (FEL). A high precision simulation is required before making the real machine since the sizes and positions are difficult to adjust after the HTSs are magnetized in the cryostat. For this purpose, authors have been developed a numerical simulation code for the magnetization process of HTS undulator of X-FEL based on the power-law macro-model. In this paper, the previously developed simulation code can be speeded up by carefully optimizing the parameters of the power-law macro-model for the 3-HTS magnets model and a large-scale simulation can be performed in an acceptable time by using a multipole expansion for the Biot–Savart law. In addition, for practical applications, the influence of the fluctuation of the magnets thickness and critical current for the electron trajectory are evaluated by using the speed-up simulation code.

Processing of the multigroup cross-sections for MCNP calculations

Stochastic Monte Carlo (MC) neutron transport codes are widely used in various reactorphysics applications, traditionally related to criticality safety analyses, radiation shielding and validation of deterministic transport codes. The main advantage of Monte Carlo codes lies in their ability to model complex and detail geometries without the need of simplifications. Currently, one of the most accurate and developed stochastic MC code for particle transport simulation is MCNP. To achieve the best real world approximations, continuous-energy (CE) cross-section (XS) libraries are often used. These CE libraries consider the rapid changes of XS in the resonance energy range; however, computing-intensive simulations must be performed to utilize this feature. To broaden ourcomputation abilities for industrial application and partially to allow the comparison withdeterministic codes, the CE cross section library of the MCNP code is replaced by the multigroup (MG) cross-section data. This paper is devoted to the cross-section processing scheme involving modified versions of TRANSX and CRSRD codes. Following this approach, the same data may be used in deterministic and stochastic codes. Moreover, using formerly developed and upgraded crosssection processing scheme, new MG libraries may be tailored to the user specific applications. For demonstration of the proposed cross-section processing scheme, the VVER-440 benchmark devoted to fuel assembly and pip-by-pin power distribution was selected. The obtained results are compared with continues energy MCNP calculation and multigroup KENO-VI calculation.

Electrical and thermal analyses of a second generation high temperature superconducting magnet with vanadium III oxide and Kapton polyimide film insulation materials under an over-pulse current

In this study, we developed a novel simulation code to analyze a second-generation high-temperature superconductor (HTS) magnet that was insulated with a polyimide film and vanadium III oxide (V2O3). In particular, V2O3 is one of the metal–insulator transition materials that has resistivity that varies with temperature. For its commercialization for large-scale HTS magnet applications, the HTS magnet that uses V2O3 is expected to achieve both of the desired characteristics, specifically, (a) high electrical and thermal stabilities for the non-insulated coils, and (b) prompt controllability of the insulated coils. First, an equivalent electrical-circuit model is proposed to develop a simulation code for the analysis of electrical and thermal characteristics of polyimide and V2O3. Then, all simulated results were compared with experimental results of a small-scale HTS single pancake coil and discussed to verify the reliability of the developed simulation code.

Development of a mesoscale model for the gas phase fluid dynamics in structured packings based on fundamental experiments and CFD investigations

This paper presents a new mesoscale model simulating the gas phase fluid dynamics and concentration distribution in structured packings, used in absorption and distillation columns. The model describes the structured packing as an arrangement of triangular channel sections and is implemented with an own developed mesoscale simulation code (StructuPack). The velocity field is stored at the cell faces and is driven by pressure, inertial and viscous forces. The coupled continuity and momentum equations are solved with the SIMPLE-algorithm, that is usually applied in CFD solvers. The development of the model is based on fundamental investigations with CFD simulations and experiments, described in the first part of the paper. Particularly, the concentration distribution in a representative geometry of structured packings, a single crisscrossing junction of triangular channels, is analysed. As one result of the fundamental investigations the CFD solver could be validated as a predictive tool with respect to concentration distribution for the laminar regime in structured packings. In the second part, the mesoscale model is described in detail and validated with a scenario of tracer distribution in a packing layer. By means of comparison with CFD simulations of the same scenario it was shown that the mesoscale model has the ability to yield good representations of concentration, pressure and velocity profiles in a structured packing. Thereby the mesoscale computational performance was three orders of magnitudes more efficient with respect to CFD. At the advent of high-performance computing this means that models at intermediate scale are a viable tool to simulate scenarios like maldistribution effects in industrial sized structured packings of distillation and absorption columns.

Revisiting the cosmic-ray induced Venusian ionization with the Atmospheric Radiation Interaction Simulator (AtRIS)

Context.Cosmic ray bombardment represents a major source of ionization in planetary atmospheres. The higher the energy of the primary cosmic ray particles, the deeper they can penetrate into the atmosphere. In addition, incident high energy cosmic ray particles induce extensive secondary particle cascades (“air showers”) that can contain up to several billion secondary particles per incoming primary particle. To quantify cosmic ray-induced effects on planetary atmospheres it is therefore important to accurately model the entire secondary particle cascade. This is particularly important in thick planetary atmospheres where the secondary particle cascades can develop extensively before being absorbed by the surface.Aims.Inside the Venusian atmosphere, cosmic rays are the dominant driver for the ionization below an altitude of ~100 km. In this work we revisit the numerical modeling of the galactic and solar cosmic-ray induced atmospheric ionization for cosmic ray ions from Hydrogen (Z= 1) to Nickel (Z= 28) and investigate the influence of strong solar energetic particle events inside the Venusian atmosphere.Methods.The Atmospheric Radiation Interaction Simulator (AtRIS), a newly developed simulation code to model the interaction of the near-(exo)planet particle and radiation field with the (exo)planetary atmosphere, was used to revisit the modeling of the altitude-dependent Venusian atmospheric ionization. Thereby, spherical geometry, the newest version of Geant4 (10.5) as well as the newest Geant4-based hadronic and electromagnetic interaction models were utilized.Results.Based on our new model approach we show that previous studies may have underestimated the galactic cosmic ray-induced atmospheric ion pair production by, amongst others, underestimating the influence of galactic cosmic ray protons above 1 TeV/nuc. Furthermore, we study the influence of 71 exceptionally strong solar particle events that were measured as Ground Level Enhancements at the Earth’s surface, and show a detailed analysis of the impact of such strong events on the Venusian ionization.

Building façade integrated solar thermal collectors for air heating: experimentation, modelling and applications

In this paper the design and the energy performance investigation of a new flat-plate solar thermal air collector prototype is presented. The adoption of cost-effective materials and simple design solutions represent the main novelties of the proposed device when compared to existing commercial collectors. In addition, the prototype is suitably designed to be integrated into the building envelope (façade), which is a key feature for the market uptake of building integrated solar thermal systems. The paper includes the description of the dynamic simulation model, developed for the energy and economic performance analyses of the whole building-prototype system. The simulation model, implemented with a computer code written in MatLab, is able to predict both active (hot air production for building space heating) and passive (winter free heating and summer overheating) effects due to the building integration of the proposed solar collector. By such tool, indoor comfort investigations can also be carried out. The dynamic simulation models of both the building and the collector prototype were successfully validated.In order to show the features of the developed simulation code, a suitable case study was carried out. It refers to an office space, part of a high-rise multi-use building, simulated as located in three different weather zones (Freiburg, Naples and Almeria). The examined solar collector is modelled as vertically integrated into the building façade, and three different orientations (East, South-East and South) were taken into account. Interesting results for the energetic, economic and occupants comfort points of view are obtained. By taking into account an initial cost of the system of about 5 k€, the primary energy savings achieved by the proposed system against the traditional buildings range between 1.9 and 8.0 MWh/y (depending on the selected weather zone and backup system). The shortest payback for all the investigated weather zones is obtained for Naples, which is equal to 6.2 years.

Verification and validation of dynamic response simulation codes for BWR fuel assemblies under seismic loading

The purpose of this study is to verify and validate two independently developed simulation codes for investigating dynamic response behaviors of fuel assemblies in a boiling water reactor (BWR) under seismic loading. The core of BWR consists of several hundreds of fuel assemblies. They are supported with both top guide and fuel support and are surrounded by coolant water. It is important to grasp their dynamic response behaviors under seismic loading for securing the structural integrity of the fuel assembly itself as well as for assessing control rod scrammability. For this evaluation of dynamic response behaviors, reliable simulation codes are required. In this study, we employ two different numerical simulation methods of acoustic fluid-structure interaction (AFSI) developed by the present authors independently. The one is a three-dimensional parallel finite element method for AFSI problems with solid elements based on a partitioned coupling approach, while the other is a finite element method of beam elements for fuel assemblies combining added mass matrix, which represents coupled inertia effects caused by coolant water. Both methods are implemented and applied to a problem of 368 fuel assemblies for verification and validation. The problem was set up based on the demonstration test performed by Nuclear Power Engineering Corporation in 1986. Both simulation results agreed well with each other, and the simulated results also agreed well with the experimental ones. In addition, we have discussed seismic response behaviors of fuel assemblies, which were not shown in the demonstration test. Finally, we conclude that the both developed simulation codes based on the proposed methods are powerful tools to grasp the behavior of huge number of fuel assemblies of BWR under seismic loading and to improve the seismic safety design of BWR core.

Numerical analysis of pulsed magnetic field diffusion dynamics in gold cone target

Strong magnetic fields from a few hundred to a thousand tesla have been produced in a laboratory by using high-intensity laser beams. This strong magnetic field in a laboratory becomes a powerful tool to perform experiments in the fields such as laboratory astrophysics and nuclear fusion research. The diffusion dynamics of a pulsed magnetic field in a target is a key phenomenon for experiments with the laser-produced magnetic field. Here, we have developed a two-dimensional (2D) electromagnetic dynamics simulation code with consideration of inductive heating to simulate spatiotemporally resolved 2D profiles of the applied magnetic field in a target. The application of an external kilo-tesla-level magnetic field to a gold-cone-attached target is a promising scheme for the enhancement of heating efficiency of the fast-ignition inertial confinement fusion scheme. Our simulation revealed that the magnetic field heats the gold cone due to the inductive heating and penetrates the gold cone during its pulse duration. The developed simulation code is generally useful for designing and analyzing experiments using a strong magnetic field.

Large-Scale Nonlinear Device-Level Power Electronic Circuit Simulation on Massively Parallel Graphics Processing Architectures

Device-level power electronic circuit simulation is so cumbersome that engineers are forced to make model simplification or reduce circuit size to obtain a reasonable execution time for repeated simulation runs. This paper proposes a massive-thread parallel simulation of large-scale power electronic circuits employing device-level modeling on the graphics processors (GPUs) to obtain higher data throughput and lower execution times. Parallel massive-thread modules are proposed for the nonlinear physics-based insulated gate bipolar transistor and power diode components. The nonlinear solution algorithm comprised of Newton–Raphson iterations and partial LU decomposition is fully parallelized on the GPU. Furthermore, the commonly used behavioral model with reduced computational complexity is also employed to represent the switches. The developed simulation codes are used to run large-scale test cases of the modular multilevel converter (MMC) system. The accuracy and efficiency of the GPU-based parallel simulation are compared with sequential CPU-based codes and the SaberRD program to show the advantages of the parallelized simulation; execution time speedups of 15 times and 70 times are reported for the MMC system using the nonlinear physics-based modeling and behavior-based modeling, respectively.

Response of LiF: Mg, Cu, P TL Detector Simulated with Geant4

The Geant4 simulation code was developed to study the Hp(10) energy response of the LiF:Mg,Cu,P (TLD-100H). Initial study chose the simulation conditions similar to the work reported by Obryk et al. in year 2011, in which a TLD-100H chip without filter was used. The work went further to simulate the Hp(10) results obtained experimentally at SSDL Malaysia. The experiment used a TLD-100H chip embedded in a TLD card and the card was enclosed in a badge complete with PTFE filter. Irradiation with eleven photon energies in the range of 24-1250 keV was applied. The simulation code therefore took into accounts the details of the badge (the materials type and the dimensions of the chip, the card, the badge and the filters) and the set-up of the experiment (the source distance and the energies). In comparison with Obryk’s work, the simulation code yielded the mean deviation of 0.59%. For the experimental work, the simulated Hp(10) curves obtained were quite similar and comparable and a mean deviation of 13.96% was obtained. As both 0.59% and 13.96% deviations are within the acceptable limit of ±25%, it was concluded that a satisfactory level of accuracy has been achieved by the developed simulation code and the selection materials and physics processes that have been adapted in the code were correct. Sources of uncertainty that has contributed to this deviation are discussed.

Simulation of femtosecond laser absorption by metallic targets and their thermal evolution

AbstractThe interaction of femtosecond laser with initially cold solid metallic targets (Al, Au, Cu, Mo, Ni) was investigated in a wide range of laser intensity with focus on the laser energy absorption efficiency. Our developed simulation code (FEMTO-2D) is based on two-temperature model in two-dimensional configuration, where the temperature-dependent optical and thermodynamic properties of the target material were considered. The role of the collisional processes in the ultrashort pulse laser–matter interaction has been carefully analyzed throughout the process of material transition from the cold solid state into the dense plasma state during the pulse. We have compared the simulation predictions of the laser pulse absorption with temperature-dependent reflectivity and optical penetration depth to the case of constant optical parameters. By considering the effect of the temporal and spatial (radial) distribution of the laser intensity on the light absorption efficiency, we obtained a good agreement between the simulated results and available experimental data. The appropriate model for temperature-dependent optical parameters defining the laser absorption efficiency will allow more accurate simulation of the target thermal response in the applications where it is critical, such as prediction of the material damage threshold, laser ablation threshold, and the ablation profile.

Microstructural and magnetic properties of thin obliquely deposited films: A simulation approach

The relation between microstructural and magnetic properties of thin obliquely deposited films has been studied by means of numerical techniques. Using our developed simulation code based on ballistic deposition model and Fourier space approach, we have investigated dependences of magnetometric tensor components and magnetic anisotropy parameters on the deposition angle of the films. A modified Netzelmann approach has been employed to study structural and magnetic parameters of an isolated column in the samples with tilted columnar microstructure. Reliability and validity of used numerical methods is confirmed by a good agreement of the calculation results with each other, as well as with our experimental data obtained by the ferromagnetic resonance measurements of obliquely deposited thin Ni80Fe20 films. The combination of these numerical methods can be used to design a magnetic film with a desirable value of uniaxial magnetic anisotropy and to extract the obliquely deposited film structure from only magnetic measurements.

Analysis of the influence of 111In on 90Y-bremsstrahlung SPECT based on Monte Carlo simulation.

90Y-ibritumomab tiuxetan (Zevalin) which is used for the treatment of malignant lymphomas can be used for SPECT imaging based on bremsstrahlung from 90Y beta particles. However, gamma rays emitted by 111In, which is administered to evaluate the indication for the treatment, contaminate the 90Y bremsstrahlung images. Our objective is to investigate the influence of 111In on the 90Y SPECT images using Monte Carlo simulation. We used an in-house developed simulation code for the Monte Carlo simulation of electrons and photons (MCEP). Two hot spheres with diameters of 40mm were put in an elliptical phantom. Both spheres ("sphere 1" and "sphere 2") were filled with 90Y and 111In mixed solutions. The activities of 90Y in sphere 1 and sphere 2 were 241 and 394kBq/mL, respectively, and the ones of 111In were 8.14 and 13.3kBq/mL, respectively. The background activity of 90Y was 38.6kBq/mL, whereas that of 111In was 1.30kBq/mL; moreover, the acquisition time was 30min. Two energy windows were used: one is 90-190keV included the 111In photopeak; the other is 90-160keV. To evaluate the quality of the SPECT images, the contrast recovery coefficient (CRC) and the constant noise ratio (CNR) of the SPECT images were derived. For the energy window between 90 and 160keV, the 111In count was 74% of the total. In that case, the CRC values were 30.1 and 30.7% for "sphere 1" and "sphere 2", respectively, whereas the CNR values were 6.8 and 12.1, respectively. For the energy window between 90 and 190keV, the 111In count reached 85% of the total count. The CRC and CNR values were 38.6 and 40.0% and 10.6 and 19.4, respectively. Our simulation study revealed that the cross talk between 111In and 90Y in SPECT imaging is rather serious. Even for the energy window excluding the 111In photopeak, the count ratio of 90Y was less than 30% of the total. However, the influence of 111In on 90Y-SPECT imaging cannot be ignored, and the count ratio because of 111In is important to estimate the density of 90Y.