Microscopic mechanism for the effect of adding salt on electrospinning by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Wang, Bing-Bing; Wang, Xiao-Dong; Wang, Tian-Hu

2014-09-01

Adding salts into polymer solution has been found to modulate the fiber structure and significantly improve the solution spinnability in electrospinning. However, the mechanisms have not been fully understood. This work adopted molecular dynamics method to investigate the dynamic behavior of poly(ethylene oxide) (PEO)/water droplet with or without dissolved NaCl salt under high-voltage electric field. Our simulation results agreed with the previous experimental reports well. We observed that some daughter droplets detach from the mother droplet due to the ions evaporation and hydration effect, which significantly accelerates the water evaporation and hence improves the solution spinnability. We also observed that some sodium ions are always coordinated with the ether oxygen group in the PEO chain. When these ions are accelerated by the electric field, the PEO chain segments follow the motion of the ions, inevitably stretching the chain and improving the fiber morphology.

Coupled storm-time magnetosphere-ionosphere-thermosphere simulations including microscopic ionospheric turbulence

NASA Astrophysics Data System (ADS)

Merkin, V. G.; Wiltberger, M. J.; Zhang, B.; Liu, J.; Wang, W.; Dimant, Y. S.; Oppenheim, M. M.; Lyon, J.

2017-12-01

During geomagnetic storms the magnetosphere-ionosphere-thermosphere system becomes activated in ways that are unique to disturbed conditions. This leads to emergence of physical feedback loops that provide tighter coupling between the system elements, often operating across disparate spatial and temporal scales. One such process that has recently received renewed interest is the generation of microscopic ionospheric turbulence in the electrojet regions (electrojet turbulence, ET) that results from strong convective electric fields imposed by the solar wind-magnetosphere interaction. ET leads to anomalous electron heating and generation of non-linear Pedersen current - both of which result in significant increases in effective ionospheric conductances. This, in turn, provides strong non-linear feedback on the magnetosphere. Recently, our group has published two studies aiming at a comprehensive analysis of the global effects of this microscopic process on the magnetosphere-ionosphere-thermosphere system. In one study, ET physics was incorporated in the TIEGCM model of the ionosphere-thermosphere. In the other study, ad hoc corrections to the ionospheric conductances based on ET theory were incorporated in the conductance module of the Lyon-Fedder-Mobarry (LFM) global magnetosphere model. In this presentation, we make the final step toward the full coupling of the microscopic ET physics within our global coupled model including LFM, the Rice Convection Model (RCM) and TIEGCM. To this end, ET effects are incorporated in the TIEGCM model and propagate throughout the system via thus modified TIEGCM conductances. The March 17, 2013 geomagnetic storm is used as a testbed for these fully coupled simulations, and the results of the model are compared with various ionospheric and magnetospheric observatories, including DMSP, AMPERE, and Van Allen Probes. Via these comparisons, we investigate, in particular, the ET effects on the global magnetosphere indicators such as the strength of the ionospheric convection, field-aligned current densities and ring current pressure amplitude and distribution.

Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

NASA Astrophysics Data System (ADS)

Bolhuis, Peter

Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

A light field microscope imaging spectrometer based on the microlens array

NASA Astrophysics Data System (ADS)

Yao, Yu-jia; Xu, Feng; Xia, Yin-xiang

2017-10-01

A new light field spectrometry microscope imaging system, which was composed by microscope objective, microlens array and spectrometry system was designed in this paper. 5-D information (4-D light field and 1-D spectrometer) of the sample could be captured by the snapshot system in only one exposure, avoiding the motion blur and aberration caused by the scanning imaging process of the traditional imaging spectrometry. Microscope objective had been used as the former group while microlens array used as the posterior group. The optical design of the system was simulated by Zemax, the parameter matching condition between microscope objective and microlens array was discussed significantly during the simulation process. The result simulated in the image plane was analyzed and discussed.

The Development and Assessment of an Online Microscopic Anatomy Laboratory Course

ERIC Educational Resources Information Center

Barbeau, Michele L.; Johnson, Marjorie; Gibson, Candace; Rogers, Kem A.

2013-01-01

Increasing enrollment in post-secondary institutions across North America, along with an increase in popularity of and demand for distance education is pressuring institutions to offer a greater number and variety of courses online. A fully online laboratory course in microscopic anatomy (histology) which can be taught simultaneously with a…

Designs and concept reliance of a fully automated high-content screening platform.

PubMed

Radu, Constantin; Adrar, Hosna Sana; Alamir, Ab; Hatherley, Ian; Trinh, Trung; Djaballah, Hakim

2012-10-01

High-content screening (HCS) is becoming an accepted platform in academic and industry screening labs and does require slightly different logistics for execution. To automate our stand-alone HCS microscopes, namely, an alpha IN Cell Analyzer 3000 (INCA3000), originally a Praelux unit hooked to a Hudson Plate Crane with a maximum capacity of 50 plates per run, and the IN Cell Analyzer 2000 (INCA2000), in which up to 320 plates could be fed per run using the Thermo Fisher Scientific Orbitor, we opted for a 4 m linear track system harboring both microscopes, plate washer, bulk dispensers, and a high-capacity incubator allowing us to perform both live and fixed cell-based assays while accessing both microscopes on deck. Considerations in design were given to the integration of the alpha INCA3000, a new gripper concept to access the onboard nest, and peripheral locations on deck to ensure a self-reliant system capable of achieving higher throughput. The resulting system, referred to as Hestia, has been fully operational since the new year, has an onboard capacity of 504 plates, and harbors the only fully automated alpha INCA3000 unit in the world.

Designs and Concept-Reliance of a Fully Automated High Content Screening Platform

PubMed Central

Radu, Constantin; Adrar, Hosna Sana; Alamir, Ab; Hatherley, Ian; Trinh, Trung; Djaballah, Hakim

2013-01-01

High content screening (HCS) is becoming an accepted platform in academic and industry screening labs and does require slightly different logistics for execution. To automate our stand alone HCS microscopes, namely an alpha IN Cell Analyzer 3000 (INCA3000) originally a Praelux unit hooked to a Hudson Plate Crane with a maximum capacity of 50 plates per run; and the IN Cell Analyzer 2000 (INCA2000) where up to 320 plates could be fed per run using the Thermo Fisher Scientific Orbitor, we opted for a 4 meter linear track system harboring both microscopes, plate washer, bulk dispensers, and a high capacity incubator allowing us to perform both live and fixed cell based assays while accessing both microscopes on deck. Considerations in design were given to the integration of the alpha INCA3000, a new gripper concept to access the onboard nest, and peripheral locations on deck to ensure a self reliant system capable of achieving higher throughput. The resulting system, referred to as Hestia, has been fully operational since the New Year, has an onboard capacity of 504 plates, and harbors the only fully automated alpha INCA3000 unit in the World. PMID:22797489

Development and evaluation of a calibration and validation procedure for microscopic simulation models.

DOT National Transportation Integrated Search

2004-01-01

Microscopic traffic simulation models have been widely accepted and applied in transportation engineering and planning practice for the past decades because simulation is cost-effective, safe, and fast. To achieve high fidelity and credibility for a ...

Simulation model calibration and validation : phase II : development of implementation handbook and short course.

DOT National Transportation Integrated Search

2006-01-01

A previous study developed a procedure for microscopic simulation model calibration and validation and evaluated the procedure via two relatively simple case studies using three microscopic simulation models. Results showed that default parameters we...

Dynamic heterogeneity in an orientational glass

NASA Astrophysics Data System (ADS)

Caballero, Nirvana B.; Zuriaga, Mariano; Tamarit, Josep Lluís; Serra, Pablo

2017-11-01

The family of compounds CBrnCl4-n has been proven helpful in unraveling microscopic mechanisms responsible for glassy behavior. Some of the family members show translational ordered phases with minimal disorder which appears to reveal glassy features, thus deserving special attention in the search for universal glass anomalies. In this work, we studied CBrCl3 dynamics by performing extensive molecular dynamics simulations. Molecules of this compound perform reorientational discrete jumps, where the atoms exchange equivalent positions among each other revealing a cage-orientational jump motion fully comparable to the cage-rototranslational jump motion in supercooled liquids. Correlation times were calculated from rotational autocorrelation functions showing good agreement with previous reported dielectric results. From mean waiting and persistence times calculated directly from trajectory results, we are able to explain which microscopic mechanisms lead to characteristic times associated with α- and β-relaxation times measured experimentally. We found that two nonequivalent groups of molecules have a longer characteristic time than the other two nonequivalent groups, both of them belonging to the asymmetric unit of the monoclinic (C2/c) lattice.

Dynamic heterogeneity in an orientational glass.

PubMed

Caballero, Nirvana B; Zuriaga, Mariano; Tamarit, Josep Lluís; Serra, Pablo

2017-11-14

The family of compounds CBr n Cl 4-n has been proven helpful in unraveling microscopic mechanisms responsible for glassy behavior. Some of the family members show translational ordered phases with minimal disorder which appears to reveal glassy features, thus deserving special attention in the search for universal glass anomalies. In this work, we studied CBrCl 3 dynamics by performing extensive molecular dynamics simulations. Molecules of this compound perform reorientational discrete jumps, where the atoms exchange equivalent positions among each other revealing a cage-orientational jump motion fully comparable to the cage-rototranslational jump motion in supercooled liquids. Correlation times were calculated from rotational autocorrelation functions showing good agreement with previous reported dielectric results. From mean waiting and persistence times calculated directly from trajectory results, we are able to explain which microscopic mechanisms lead to characteristic times associated with α- and β-relaxation times measured experimentally. We found that two nonequivalent groups of molecules have a longer characteristic time than the other two nonequivalent groups, both of them belonging to the asymmetric unit of the monoclinic (C2/c) lattice.

A hybrid scanning force and light microscope for surface imaging and three-dimensional optical sectioning in differential interference contrast.

PubMed

Stemmer, A

1995-04-01

The design of a scanned-cantilever-type force microscope is presented which is fully integrated into an inverted high-resolution video-enhanced light microscope. This set-up allows us to acquire thin optical sections in differential interference contrast (DIC) or polarization while the force microscope is in place. Such a hybrid microscope provides a unique platform to study how cell surface properties determine, or are affected by, the three-dimensional dynamic organization inside the living cell. The hybrid microscope presented in this paper has proven reliable and versatile for biological applications. It is the only instrument that can image a specimen by force microscopy and high-power DIC without having either to translate the specimen or to remove the force microscope. Adaptation of the design features could greatly enhance the suitability of other force microscopes for biological work.

CUSUM analysis of learning curves for the head-mounted microscope in phonomicrosurgery.

PubMed

Chen, Ting; Vamos, Andrew C; Dailey, Seth H; Jiang, Jack J

2016-10-01

To observe the learning curve of the head-mounted microscope in a phonomicrosurgery simulator using cumulative summation (CUSUM) analysis, which incorporates a magnetic phonomicrosurgery instrument tracking system (MPTS). Retrospective case series. Eight subjects (6 medical students and 2 surgeons inexperienced in phonomicrosurgery) operated on phonomicrosurgical simulation cutting tasks while using the head-mounted microscope for 400 minutes total. Two 20-minute sessions occurred each day for 10 total days, with operation quality (Qs ) and completion time (T) being recorded after each session. Cumulative summation analysis of Qs and T was performed by using subjects' performance data from trials completed using a traditional standing microscope as success criteria. The motion parameters from the head-mounted microscope were significantly better than the standing microscope (P < 0.01), but T was longer than that from the standing microscope (P < 0.01). No subject successfully adapted to the head-mounted microscope, as assessed by CUSUM analysis. Cumulative summation analysis can objectively monitor the learning process associated with a phonomicrosurgical simulator system, ultimately providing a tool to assess learning status. Also, motion parameters determined by our MPTS showed that, although the head-mounted microscope provides better motion control, worse Qs and longer T resulted. This decrease in Qs is likely a result of the relatively unstable visual environment that it provides. Overall, the inexperienced surgeons participating in this study failed to adapt to the head-mounted microscope in our simulated phonomicrosurgery environment. 4 Laryngoscope, 126:2295-2300, 2016. © 2015 The American Laryngological, Rhinological and Otological Society, Inc.

Large-scale Density Structures in Magneto-rotational Disk Turbulence

NASA Astrophysics Data System (ADS)

Youdin, Andrew; Johansen, A.; Klahr, H.

2009-01-01

Turbulence generated by the magneto-rotational instability (MRI) is a strong candidate to drive accretion flows in disks, including sufficiently ionized regions of protoplanetary disks. The MRI is often studied in local shearing boxes, which model a small section of the disk at high resolution. I will present simulations of large, stratified shearing boxes which extend up to 10 gas scale-heights across. These simulations are a useful bridge to fully global disk simulations. We find that MRI turbulence produces large-scale, axisymmetric density perturbations . These structures are part of a zonal flow --- analogous to the banded flow in Jupiter's atmosphere --- which survives in near geostrophic balance for tens of orbits. The launching mechanism is large-scale magnetic tension generated by an inverse cascade. We demonstrate the robustness of these results by careful study of various box sizes, grid resolutions, and microscopic diffusion parameterizations. These gas structures can trap solid material (in the form of large dust or ice particles) with important implications for planet formation. Resolved disk images at mm-wavelengths (e.g. from ALMA) will verify or constrain the existence of these structures.

Microscopic simulation model calibration and validation handbook.

DOT National Transportation Integrated Search

2006-01-01

Microscopic traffic simulation models are widely used in the transportation engineering field. Because of their cost-effectiveness, risk-free nature, and high-speed benefits, areas of use include transportation system design, traffic operations, and ...

Single atom array to form a Rydberg ring

NASA Astrophysics Data System (ADS)

Zhan, Mingsheng; Xu, Peng; He, Xiaodong; Liu, Min; Wang, Jin

2012-02-01

Single atom arrays are ideal quantum systems for studying few-body quantum simulation and quantum computation [1]. Towards realizing a fully controllable array we did a lot of experimental efforts, which include rotating single atoms in a ring optical lattice generated by a spatial light modulator [2], high efficient loading of two atoms into a microscopic optical trap by dynamically reshaping the trap with a spatial light modulator [3], and trapping a single atom in a blue detuned optical bottle beam trap [4]. Recently, we succeeded in trapping up to 6 atoms in a ring optical lattice with one atom in each site. Further laser cooling the array and manipulation of the inner states will provide chance to form Ryberg rings for quantum simulation. [4pt] [1] M. Saffman et al., Rev. Mod. Phys. 82, 2313 (2010)[0pt] [2] X.D. He et al., Opt. Express 17, 21014 (2009)[0pt] [3] X.D. He et al., Opt. Express 18, 13586 (2010)[0pt] [4] P. Xu et al., Opt. Lett. 35, 2164 (2010)

Simulation of transmission electron microscope images of biological specimens.

PubMed

Rullgård, H; Ofverstedt, L-G; Masich, S; Daneholt, B; Oktem, O

2011-09-01

We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrödinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Laboratory observations and simulations of phase reddening

NASA Astrophysics Data System (ADS)

Schröder, S. E.; Grynko, Ye.; Pommerol, A.; Keller, H. U.; Thomas, N.; Roush, T. L.

2014-09-01

The visible reflectance spectrum of many Solar System bodies changes with changing viewing geometry for reasons not fully understood. It is often observed to redden (increasing spectral slope) with increasing solar phase angle, an effect known as phase reddening. Only once, in an observation of the martian surface by the Viking 1 lander, was reddening observed up to a certain phase angle with bluing beyond, making the reflectance ratio as a function of phase angle shaped like an arch. However, in laboratory experiments this arch-shape is frequently encountered. To investigate this, we measured the bidirectional reflectance of particulate samples of several common rock types in the 400-1000 nm wavelength range and performed ray-tracing simulations. We confirm the occurrence of the arch for surfaces that are forward scattering, i.e. are composed of semi-transparent particles and are smooth on the scale of the particles, and for which the reflectance increases from the lower to the higher wavelength in the reflectance ratio. The arch shape is reproduced by the simulations, which assume a smooth surface. However, surface roughness on the scale of the particles, such as the Hapke and van Horn (Hapke, B., van Horn, H. [1963]. J. Geophys. Res. 68, 4545-4570) fairy castles that can spontaneously form when sprinkling a fine powder, leads to monotonic reddening. A further consequence of this form of microscopic roughness (being indistinct without the use of a microscope) is a flattening of the disk function at visible wavelengths, i.e. Lommel-Seeliger-type scattering. The experiments further reveal monotonic reddening for reflectance ratios at near-IR wavelengths. The simulations fail to reproduce this particular reddening, and we suspect that it results from roughness on the surface of the particles. Given that the regolith of atmosphereless Solar System bodies is composed of small particles, our results indicate that the prevalence of monotonic reddening and Lommel-Seeliger-type scattering for these bodies results from microscopic roughness, both in the form of structures built by the particles and roughness on the surface of the particles themselves. It follows from the singular Viking 1 observation that the surface in front of the lander was composed of semi-transparent particles, and was smooth on the scale of the particle size.

Tunable charge donation and spin polarization of metal adsorbates on graphene using an applied electric field

NASA Astrophysics Data System (ADS)

Parq, Jae-Hyeon; Yu, Jaejun; Kwon, Young-Kyun; Kim, Gunn

2010-11-01

Metal atoms on graphene, when ionized, can act as a point-charge impurity to probe a charge response of graphene with the Dirac cone band structure. To understand the microscopic physics of the metal-atom-induced charge and spin polarization in graphene, we present scanning tunneling spectroscopy (STS) simulations based on density-functional theory calculations. We find that a Cs atom on graphene is fully ionized with a significant band-bending feature in the STS whereas the charge and magnetic states of Ba and La atoms on graphene appear to be complicated due to orbital hybridization and Coulomb interaction. By applying external electric field, we observe changes in charge donations and spin magnetic moments of the metal adsorbates on graphene.

JEWEL 2.0.0: directions for use

NASA Astrophysics Data System (ADS)

Zapp, Korinna

2014-02-01

In this publication the first official release of the Jewel 2.0.0 code [The first version Jewel 1 (Zapp et al. in Eur Phys J C 60:617, 2009) could only treat elastic scattering explicitly and the code was never published, The code can be downloaded from the official Jewel homepage http://jewel.hepforge.org] is presented. Jewel is a Monte Carlo event generator simulating QCD jet evolution in heavy-ion collisions. It treats the interplay of QCD radiation and re-scattering in a medium with fully microscopic dynamics in a consistent perturbative framework with minimal assumptions. After a qualitative introduction into the physics of Jewel detailed information about the practical aspects of using the code is given. The code is available from the official Jewel homepage http://jewel.hepforge.org.

Evaluation of traffic signal timing optimization methods using a stochastic and microscopic simulation program.

DOT National Transportation Integrated Search

2003-01-01

This study evaluated existing traffic signal optimization programs including Synchro,TRANSYT-7F, and genetic algorithm optimization using real-world data collected in Virginia. As a first step, a microscopic simulation model, VISSIM, was extensively ...

Attachment of Single Multiwall WS2 Nanotubes and Single WO3-x Nanowhiskers to a Probe

NASA Astrophysics Data System (ADS)

Ashiri, I.; Gartsman, K.; Cohen, S. R.; Tenne, R.

2003-10-01

WS2 nanotubes were the first inorganic fullerene-like (IF) structures to be synthesized. Although the physical properties of IF were not fully studied it seems that the WS2 nanotubes can be suitable for applications in the nanoscale range. An approach toward nanofabrication is simulated in this study. High resolution scanning electron microscope equipped with micromanipulator was used to attach single multiwall WS2 nanotubes and single WO3-x nanowhiskers to a probe, which is an atomic force microscope (AFM) silicon tip in the present case. The imaging capabilities of this nanotube or nanowhisker tip were tested in the AFM. The WO3-x nanowhisker tip was found to be stable, but it has a low lateral resolution (100nm). The WS2 nanotube tips were found to be stable only when its length was smaller than 1 μm. The fabrication technique of WS2 nanotube tip and WO3-x nanowhisker tip was found to be controllable and reliable and it can probably be used to various applications as well as for preparation of single nanotubes samples for measurements, like mechanical or optical probes.

On the way to a microscopic derivation of covariant density functionals in nuclei

NASA Astrophysics Data System (ADS)

Ring, Peter

2018-02-01

Several methods are discussed to derive covariant density functionals from the microscopic input of bare nuclear forces. In a first step there are semi-microscopic functionals, which are fitted to ab-initio calculations of nuclear matter and depend in addition on very few phenomenological parameters. They are able to describe nuclear properties with the same precision as fully phenomenological functionals. In a second step we present first relativistic Brueckner-Hartree-Fock calculations in finite nuclei in order to study properties of such functionals, which cannot be obtained from nuclear matter calculations.

Microscopic diffusion in hydrated encysted eggs of brine shrimp

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mamontov, Eugene

We have studied microscopic diffusion of water in fully hydrated encysted eggs of brine shrimp (Artemia). We utilized quasielastic neutron scattering. Dry eggs of brine shrimp were rehydrated using (1) water without additives, (2) eutectic mixture of water and dimethyl sulfoxide, and (3) a concentrated aqueous solution of lithium chloride. Despite the complexity of the hydrated multicellular organism, measurable microscopic diffusivity of water is rather well defined. Pure hydration water in eggs exhibits freezing temperature depression, whereas hydration water in eggs mixed with dimethyl sulfoxide or lithium chloride does not crystallize at all. The characteristic size of the voids occupiedmore » by water or aqueous solvents in hydrated brine shrimp eggs is between 2 and 10 nm. Those voids are accessible to co-solvents such as dimethyl sulfoxide and lithium chloride. There is no evidence of intracellular water in the hydrated eggs. The lack of intracellular water in the fully hydrated (but still under arrested development) state must be linked to the unique resilience against adverse environmental factors documented not only for the anhydrous, but also hydrated encysted eggs of brine shrimp.« less

Microscopic diffusion in hydrated encysted eggs of brine shrimp

DOE PAGES

Mamontov, Eugene

2017-05-24

We have studied microscopic diffusion of water in fully hydrated encysted eggs of brine shrimp (Artemia). We utilized quasielastic neutron scattering. Dry eggs of brine shrimp were rehydrated using (1) water without additives, (2) eutectic mixture of water and dimethyl sulfoxide, and (3) a concentrated aqueous solution of lithium chloride. Despite the complexity of the hydrated multicellular organism, measurable microscopic diffusivity of water is rather well defined. Pure hydration water in eggs exhibits freezing temperature depression, whereas hydration water in eggs mixed with dimethyl sulfoxide or lithium chloride does not crystallize at all. The characteristic size of the voids occupiedmore » by water or aqueous solvents in hydrated brine shrimp eggs is between 2 and 10 nm. Those voids are accessible to co-solvents such as dimethyl sulfoxide and lithium chloride. There is no evidence of intracellular water in the hydrated eggs. The lack of intracellular water in the fully hydrated (but still under arrested development) state must be linked to the unique resilience against adverse environmental factors documented not only for the anhydrous, but also hydrated encysted eggs of brine shrimp.« less

Fully kinetic simulations of dense plasma focus Z-pinch devices.

PubMed

Schmidt, A; Tang, V; Welch, D

2012-11-16

Dense plasma focus Z-pinch devices are sources of copious high energy electrons and ions, x rays, and neutrons. The mechanisms through which these physically simple devices generate such high-energy beams in a relatively short distance are not fully understood. We now have, for the first time, demonstrated a capability to model these plasmas fully kinetically, allowing us to simulate the pinch process at the particle scale. We present here the results of the initial kinetic simulations, which reproduce experimental neutron yields (~10(7)) and high-energy (MeV) beams for the first time. We compare our fluid, hybrid (kinetic ions and fluid electrons), and fully kinetic simulations. Fluid simulations predict no neutrons and do not allow for nonthermal ions, while hybrid simulations underpredict neutron yield by ~100x and exhibit an ion tail that does not exceed 200 keV. Only fully kinetic simulations predict MeV-energy ions and experimental neutron yields. A frequency analysis in a fully kinetic simulation shows plasma fluctuations near the lower hybrid frequency, possibly implicating lower hybrid drift instability as a contributor to anomalous resistivity in the plasma.

The history and development of the helium ion microscope.

PubMed

Economou, Nicholas P; Notte, John A; Thompson, William B

2012-01-01

The helium ion microscope has recently emerged as a commercially available instrument. However, its roots go back more than 60 years to the development of the field ion microscope in Berlin, first reported in 1951. Over the intervening years, numerous researchers have pursued the development of a gas field ionization source with the goal of producing a suitable source for an ion microscope. This proved to be an elusive goal until early in this century when a number of discoveries led to a successful source, and shortly thereafter, an instrument fully able to exploit its advantages. Many individuals and many technical advances have come together to make this new class of microscope. The long history of this quest is reviewed along with the recent advances that led to the achievement of this milestone. A brief summary of the current status of the technology and its applications are given. © Wiley Periodicals, Inc.

Oxide driven strength evolution of silicon surfaces

DOE PAGES

Grutzik, Scott J.; Milosevic, Erik; Boyce, Brad L.; ...

2015-11-19

Previous experiments have shown a link between oxidation and strength changes in single crystal silicon nanostructures but provided no clues as to the mechanisms leading to this relationship. Using atomic force microscope-based fracture strength experiments, molecular dynamics modeling, and measurement of oxide development with angle resolved x-ray spectroscopy we study the evolution of strength of silicon (111) surfaces as they oxidize and with fully developed oxide layers. We find that strength drops with partial oxidation but recovers when a fully developed oxide is formed and that surfaces intentionally oxidized from the start maintain their high initial strengths. MD simulations showmore » that strength decreases with the height of atomic layer steps on the surface. These results are corroborated by a completely separate line of testing using micro-scale, polysilicon devices, and the slack chain method in which strength recovers over a long period of exposure to the atmosphere. Lastly, combining our results with insights from prior experiments we conclude that previously described strength decrease is a result of oxidation induced roughening of an initially flat silicon (1 1 1) surface and that this effect is transient, a result consistent with the observation that surfaces flatten upon full oxidation.« less

Characterization of Nanopipettes.

PubMed

Perry, David; Momotenko, Dmitry; Lazenby, Robert A; Kang, Minkyung; Unwin, Patrick R

2016-05-17

Nanopipettes are widely used in electrochemical and analytical techniques as tools for sizing, sequencing, sensing, delivery, and imaging. For all of these applications, the response of a nanopipette is strongly affected by its geometry and surface chemistry. As the size of nanopipettes becomes smaller, precise geometric characterization is increasingly important, especially if nanopipette probes are to be used for quantitative studies and analysis. This contribution highlights the combination of data from voltage-scanning ion conductivity experiments, transmission electron microscopy and finite element method simulations to fully characterize nanopipette geometry and surface charge characteristics, with an accuracy not achievable using existing approaches. Indeed, it is shown that presently used methods for characterization can lead to highly erroneous information on nanopipettes. The new approach to characterization further facilitates high-level quantification of the behavior of nanopipettes in electrochemical systems, as demonstrated herein for a scanning ion conductance microscope setup.

Nuclear quantum effect with pure anharmonicity and the anomalous thermal expansion of silicon.

PubMed

Kim, D S; Hellman, O; Herriman, J; Smith, H L; Lin, J Y Y; Shulumba, N; Niedziela, J L; Li, C W; Abernathy, D L; Fultz, B

2018-02-27

Despite the widespread use of silicon in modern technology, its peculiar thermal expansion is not well understood. Adapting harmonic phonons to the specific volume at temperature, the quasiharmonic approximation, has become accepted for simulating the thermal expansion, but has given ambiguous interpretations for microscopic mechanisms. To test atomistic mechanisms, we performed inelastic neutron scattering experiments from 100 K to 1,500 K on a single crystal of silicon to measure the changes in phonon frequencies. Our state-of-the-art ab initio calculations, which fully account for phonon anharmonicity and nuclear quantum effects, reproduced the measured shifts of individual phonons with temperature, whereas quasiharmonic shifts were mostly of the wrong sign. Surprisingly, the accepted quasiharmonic model was found to predict the thermal expansion owing to a large cancellation of contributions from individual phonons.

A computational continuum model of poroelastic beds

PubMed Central

Zampogna, G. A.

2017-01-01

Despite the ubiquity of fluid flows interacting with porous and elastic materials, we lack a validated non-empirical macroscale method for characterizing the flow over and through a poroelastic medium. We propose a computational tool to describe such configurations by deriving and validating a continuum model for the poroelastic bed and its interface with the above free fluid. We show that, using stress continuity condition and slip velocity condition at the interface, the effective model captures the effects of small changes in the microstructure anisotropy correctly and predicts the overall behaviour in a physically consistent and controllable manner. Moreover, we show that the performance of the effective model is accurate by validating with fully microscopic resolved simulations. The proposed computational tool can be used in investigations in a wide range of fields, including mechanical engineering, bio-engineering and geophysics. PMID:28413355

Features of microscopic pedestrian movement in a panic situation based on cellular automata model

NASA Astrophysics Data System (ADS)

Ibrahim, Najihah; Hassan, Fadratul Hafinaz

2017-10-01

Pedestrian movement is the one of the subset for the crowd management under simulation objective. During panic situation, pedestrian usually will create a microscopic movement that lead towards the self-organization. During self-organizing, the behavioral and physical factors had caused the mass effect on the pedestrian movement. The basic CA model will create a movement path for each pedestrian over a time step. However, due to the factors immerge, the CA model needs some enhancement that will establish a real simulation state. Hence, this concept paper will discuss on the enhanced features of CA model for microscopic pedestrian movement during panic situation for a better pedestrian simulation.

Combining cellular automata and Lattice Boltzmann method to model multiscale avascular tumor growth coupled with nutrient diffusion and immune competition.

PubMed

Alemani, Davide; Pappalardo, Francesco; Pennisi, Marzio; Motta, Santo; Brusic, Vladimir

2012-02-28

In the last decades the Lattice Boltzmann method (LB) has been successfully used to simulate a variety of processes. The LB model describes the microscopic processes occurring at the cellular level and the macroscopic processes occurring at the continuum level with a unique function, the probability distribution function. Recently, it has been tried to couple deterministic approaches with probabilistic cellular automata (probabilistic CA) methods with the aim to model temporal evolution of tumor growths and three dimensional spatial evolution, obtaining hybrid methodologies. Despite the good results attained by CA-PDE methods, there is one important issue which has not been completely solved: the intrinsic stochastic nature of the interactions at the interface between cellular (microscopic) and continuum (macroscopic) level. CA methods are able to cope with the stochastic phenomena because of their probabilistic nature, while PDE methods are fully deterministic. Even if the coupling is mathematically correct, there could be important statistical effects that could be missed by the PDE approach. For such a reason, to be able to develop and manage a model that takes into account all these three level of complexity (cellular, molecular and continuum), we believe that PDE should be replaced with a statistic and stochastic model based on the numerical discretization of the Boltzmann equation: The Lattice Boltzmann (LB) method. In this work we introduce a new hybrid method to simulate tumor growth and immune system, by applying Cellular Automata Lattice Boltzmann (CA-LB) approach. Copyright © 2011 Elsevier B.V. All rights reserved.

Coarse-grained stochastic processes and kinetic Monte Carlo simulators for the diffusion of interacting particles

NASA Astrophysics Data System (ADS)

Katsoulakis, Markos A.; Vlachos, Dionisios G.

2003-11-01

We derive a hierarchy of successively coarse-grained stochastic processes and associated coarse-grained Monte Carlo (CGMC) algorithms directly from the microscopic processes as approximations in larger length scales for the case of diffusion of interacting particles on a lattice. This hierarchy of models spans length scales between microscopic and mesoscopic, satisfies a detailed balance, and gives self-consistent fluctuation mechanisms whose noise is asymptotically identical to the microscopic MC. Rigorous, detailed asymptotics justify and clarify these connections. Gradient continuous time microscopic MC and CGMC simulations are compared under far from equilibrium conditions to illustrate the validity of our theory and delineate the errors obtained by rigorous asymptotics. Information theory estimates are employed for the first time to provide rigorous error estimates between the solutions of microscopic MC and CGMC, describing the loss of information during the coarse-graining process. Simulations under periodic boundary conditions are used to verify the information theory error estimates. It is shown that coarse-graining in space leads also to coarse-graining in time by q2, where q is the level of coarse-graining, and overcomes in part the hydrodynamic slowdown. Operation counting and CGMC simulations demonstrate significant CPU savings in continuous time MC simulations that vary from q3 for short potentials to q4 for long potentials. Finally, connections of the new coarse-grained stochastic processes to stochastic mesoscopic and Cahn-Hilliard-Cook models are made.

Microscopic model of road capacity for highway systems in port based metropolitan areas.

DOT National Transportation Integrated Search

2011-03-01

In this report, we present our approach to use microscopic modeling to assess : highway traffic mobility during lane blockage situation. A test microscopic model using : ARENA software is developed. In this model, we specifically aim to simulate the ...

Five years of experience teaching pathology to dental students using the WebMicroscope

PubMed Central

2011-01-01

Background We describe development and evaluation of the user-friendly web based virtual microscopy - WebMicroscope for teaching and learning dental students basic and oral pathology. Traditional students microscopes were replaced by computer workstations. Methods The transition of the basic and oral pathology courses from light to virtual microscopy has been completed gradually over a five-year period. A pilot study was conducted in academic year 2005/2006 to estimate the feasibility of integrating virtual microscopy into a traditional light microscopy-based pathology course. The entire training set of glass slides was subsequently converted to virtual slides and placed on the WebMicroscope server. Giving access to fully digitized slides on the web with a browser and a viewer plug-in, the computer has become a perfect companion of the student. Results The study material consists now of over 400 fully digitized slides which covering 15 entities in basic and systemic pathology and 15 entities in oral pathology. Digitized slides are linked with still macro- and microscopic images, organized with clinical information into virtual cases and supplemented with text files, syllabus, PowerPoint presentations and animations on the web, serving additionally as material for individual studies. After their examinations, the students rated the use of the software, quality of the images, the ease of handling the images, and the effective use of virtual slides during the laboratory practicals. Responses were evaluated on a standardized scale. Because of the positive opinions and support from the students, the satisfaction surveys had shown a progressive improvement over the past 5 years. The WebMicroscope as a didactic tool for laboratory practicals was rated over 8 on a 1-10 scale for basic and systemic pathology and 9/10 for oral pathology especially as various students’ suggestions were implemented. Overall, the quality of the images was rated as very good. Conclusions An overwhelming majority of our students regarded a possibility of using virtual slides at their convenience as highly desirable. Our students and faculty consider the use of the virtual microscope for the study of basic as well as oral pathology as a significant improvement over the light microscope. PMID:21489183

Enabling Microscopic Simulators to Perform System Level Tasks: A System-Identification Based, Closure-on-Demand Toolkit for Multiscale Simulation Stability/Bifurcation Analysis, Optimization and Control

DTIC Science & Technology

2006-10-01

The objective was to construct a bridge between existing and future microscopic simulation codes ( kMC , MD, MC, BD, LB etc.) and traditional, continuum...kinetic Monte Carlo, kMC , equilibrium MC, Lattice-Boltzmann, LB, Brownian Dynamics, BD, or general agent-based, AB) simulators. It also, fortuitously...cond-mat/0310460 at arXiv.org. 27. Coarse Projective kMC Integration: Forward/Reverse Initial and Boundary Value Problems", R. Rico-Martinez, C. W

Virtual Microscopic Simulation (VMS) to Promote Students' Conceptual Change: A Case Study of Heat Transfer

ERIC Educational Resources Information Center

Wibowo, Firmanul Catur; Suhandi, Andi; Nahadi; Samsudin, Achmad; Darman, Dina Rahmi; Suherli, Zulmiswal; Hasani, Aceng; Leksono, Sroso Mukti; Hendrayana, Aan; Suherman; Hidayat, Soleh; Hamdani, Dede; Costu, Bayram

2017-01-01

Most students cannot understand the concepts of science concepts. The abstract concepts that require visualization help students to promote to the understanding about the concept. The aim of this study was to develop Virtual Microscopic Simulation (VMS) in terms of encouraging conceptual change and to promote its effectiveness connected to…

Scanning electron microscope fine tuning using four-bar piezoelectric actuated mechanism

NASA Astrophysics Data System (ADS)

Hatamleh, Khaled S.; Khasawneh, Qais A.; Al-Ghasem, Adnan; Jaradat, Mohammad A.; Sawaqed, Laith; Al-Shabi, Mohammad

2018-01-01

Scanning Electron Microscopes are extensively used for accurate micro/nano images exploring. Several strategies have been proposed to fine tune those microscopes in the past few years. This work presents a new fine tuning strategy of a scanning electron microscope sample table using four bar piezoelectric actuated mechanisms. The introduced paper presents an algorithm to find all possible inverse kinematics solutions of the proposed mechanism. In addition, another algorithm is presented to search for the optimal inverse kinematic solution. Both algorithms are used simultaneously by means of a simulation study to fine tune a scanning electron microscope sample table through a pre-specified circular or linear path of motion. Results of the study shows that, proposed algorithms were able to minimize the power required to drive the piezoelectric actuated mechanism by a ratio of 97.5% for all simulated paths of motion when compared to general non-optimized solution.

Soft control of scanning probe microscope with high flexibility.

PubMed

Liu, Zhenghui; Guo, Yuzheng; Zhang, Zhaohui; Zhu, Xing

2007-01-01

Most commercial scanning probe microscopes have multiple embedded digital microprocessors and utilize complex software for system control, which is not easily obtained or modified by researchers wishing to perform novel and special applications. In this paper, we present a simple and flexible control solution that just depends on software running on a single-processor personal computer with real-time Linux operating system to carry out all the control tasks including negative feedback, tip moving, data processing and user interface. In this way, we fully exploit the potential of a personal computer in calculating and programming, enabling us to manipulate the scanning probe as required without any special digital control circuits and related technical know-how. This solution has been successfully applied to a homemade ultrahigh vacuum scanning tunneling microscope and a multiprobe scanning tunneling microscope.

Evaluating Red Reflex and Surgeon Preference Between Nearly-Collimated and Focused Beam Microscope Illumination Systems.

PubMed

Cionni, Robert J; Pei, Ron; Dimalanta, Ramon; Lubeck, David

2015-08-01

To evaluate the intensity and stability of the red reflex produced by ophthalmic surgical microscopes with nearly-collimated versus focused illumination systems and to assess surgeon preference in a simulated surgical setting. This two-part evaluation consisted of postproduction surgical video analysis of red reflex intensity and a microscope use and preference survey completed by 13 experienced cataract surgeons. Survey responses were based on bench testing and experience in a simulated surgical setting. A microscope with nearly-collimated beam illumination and two focused beam microscopes were assessed. Red reflex intensity and stability were greater with the nearly-collimated microscope illumination system. In the bench testing survey, surgeons reported that the red reflex was maintained over significantly greater distances away from pupillary center, and depth of focus was numerically greater with nearly-collimated illumination relative to focused illumination. Most participating surgeons (≥64%) reported a preference for the microscope with nearly-collimated illumination with regard to red reflex stability, depth of focus, visualization, surgical working distance, and perceived patient comfort. The microscope with nearly-collimated illumination produced a more intense and significantly more stable red reflex and was preferred overall by more surgeons. This is the first report of an attempt to quantify red reflex intensity and stability and to evaluate surgically-relevant parameters between microscope systems. The data and methods presented here may provide a basis for future studies attempting to quantify differences between surgical microscopes that may affect surgeon preference and microscope use in ophthalmic surgery.

Steady-state shear flows via nonequilibrium molecular dynamics and smooth-particle applied mechanics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Posch, H.A.; Hoover, W.G.; Kum, O.

1995-08-01

We simulate both microscopic and macroscopic shear flows in two space dimensions using nonequilibrium molecular dynamics and smooth-particle applied mechanics. The time-reversible {ital microscopic} equations of motion are isomorphic to the smooth-particle description of inviscid {ital macroscopic} continuum mechanics. The corresponding microscopic particle interactions are relatively weak and long ranged. Though conventional Green-Kubo theory suggests instability or divergence in two-dimensional flows, we successfully define and measure a finite shear viscosity coefficient by simulating stationary plane Couette flow. The special nature of the weak long-ranged smooth-particle functions corresponds to an unusual kind of microscopic transport. This microscopic analog is mainly kinetic,more » even at high density. For the soft Lucy potential which we use in the present work, nearly all the system energy is potential, but the resulting shear viscosity is nearly all kinetic. We show that the measured shear viscosities can be understood, in terms of a simple weak-scattering model, and that this understanding is useful in assessing the usefulness of continuum simulations using the smooth-particle method. We apply that method to the Rayleigh-Benard problem of thermally driven convection in a gravitational field.« less

Transition temperature and fracture mode of as-castand austempered ductile iron.

PubMed

Rajnovic, D; Eric, O; Sidjanin, L

2008-12-01

The ductile to brittle transition temperature is a very important criterion that is used for selection of materials in some applications, especially in low-temperature conditions. For that reason, in this paper transition temperature of as-cast and austempered copper and copper-nickel alloyed ductile iron (DI) in the temperature interval from -196 to +150 degrees C have been investigated. The microstructures of DIs and ADIs were examined by light microscope, whereas the fractured surfaces were observed by scanning electron microscope. The ADI materials have higher impact energies compared with DIs in an as-cast condition. In addition, the transition curves for ADIs are shifted towards lower temperatures. The fracture mode of Dls is influenced by a dominantly pearlitic matrix, exhibiting mostly brittle fracture through all temperatures of testing. By contrast, with decrease of temperature, the fracture mode for ADI materials changes gradually from fully ductile to fully brittle.

Social judgment theory based model on opinion formation, polarization and evolution

NASA Astrophysics Data System (ADS)

Chau, H. F.; Wong, C. Y.; Chow, F. K.; Fung, Chi-Hang Fred

2014-12-01

The dynamical origin of opinion polarization in the real world is an interesting topic that physical scientists may help to understand. To properly model the dynamics, the theory must be fully compatible with findings by social psychologists on microscopic opinion change. Here we introduce a generic model of opinion formation with homogeneous agents based on the well-known social judgment theory in social psychology by extending a similar model proposed by Jager and Amblard. The agents’ opinions will eventually cluster around extreme and/or moderate opinions forming three phases in a two-dimensional parameter space that describes the microscopic opinion response of the agents. The dynamics of this model can be qualitatively understood by mean-field analysis. More importantly, first-order phase transition in opinion distribution is observed by evolving the system under a slow change in the system parameters, showing that punctuated equilibria in public opinion can occur even in a fully connected social network.

Stochastic modelling of microstructure formation in solidification processes

NASA Astrophysics Data System (ADS)

Nastac, Laurentiu; Stefanescu, Doru M.

1997-07-01

To relax many of the assumptions used in continuum approaches, a general stochastic model has been developed. The stochastic model can be used not only for an accurate description of the fraction of solid evolution, and therefore accurate cooling curves, but also for simulation of microstructure formation in castings. The advantage of using the stochastic approach is to give a time- and space-dependent description of solidification processes. Time- and space-dependent processes can also be described by partial differential equations. Unlike a differential formulation which, in most cases, has to be transformed into a difference equation and solved numerically, the stochastic approach is essentially a direct numerical algorithm. The stochastic model is comprehensive, since the competition between various phases is considered. Furthermore, grain impingement is directly included through the structure of the model. In the present research, all grain morphologies are simulated with this procedure. The relevance of the stochastic approach is that the simulated microstructures can be directly compared with microstructures obtained from experiments. The computer becomes a `dynamic metallographic microscope'. A comparison between deterministic and stochastic approaches has been performed. An important objective of this research was to answer the following general questions: (1) `Would fully deterministic approaches continue to be useful in solidification modelling?' and (2) `Would stochastic algorithms be capable of entirely replacing purely deterministic models?'

Motorization of a surgical microscope for intra-operative navigation and intuitive control.

PubMed

Finke, M; Schweikard, A

2010-09-01

During surgical procedures, various medical systems, e.g. microscope or C-arm, are used. Their precise and repeatable manual positioning can be very cumbersome and interrupts the surgeon's work flow. Robotized systems can assist the surgeon but they require suitable kinematics and control. However, positioning must be fast, flexible and intuitive. We describe a fully motorized surgical microscope. Hardware components as well as implemented applications are specified. The kinematic equations are described and a novel control concept is proposed. Our microscope combines fast manual handling with accurate, automatic positioning. Intuitive control is provided by a small remote control mounted to one of the surgical instruments. Positioning accuracy and repeatability are < 1 mm and vibrations caused by automatic movements fade away in about 1 s. The robotic system assists the surgeon, so that he can position the microscope precisely and repeatedly without interrupting the clinical workflow. The combination of manual und automatic control guarantees fast and flexible positioning during surgical procedures. Copyright 2010 John Wiley & Sons, Ltd.

4D blood flow mapping using SPIM-microPIV in the developing zebrafish heart

NASA Astrophysics Data System (ADS)

Zickus, Vytautas; Taylor, Jonathan M.

2018-02-01

Fluid-structure interaction in the developing heart is an active area of research in developmental biology. However, investigation of heart dynamics is mostly limited to computational uid dynamics simulations using heart wall structure information only, or single plane blood ow information - so there is a need for 3D + time resolved data to fully understand cardiac function. We present an imaging platform combining selective plane illumination microscopy (SPIM) with micro particle image velocimetry (μPIV) to enable 3D-resolved flow mapping in a microscopic environment, free from many of the sources of error and bias present in traditional epi uorescence-based μPIV systems. By using our new system in conjunction with optical heart beat synchronization, we demonstrate the ability obtain non-invasive 3D + time resolved blood flow measurements in the heart of a living zebrafish embryo.

The Microstructure of Lunar Micrometeorite Impact Craters

NASA Technical Reports Server (NTRS)

Noble, S. K.; Keller, L. P.; Christoffersen, R.; Rahman, Z.

2016-01-01

The peak of the mass flux of impactors striking the lunar surface is made up of objects approximately 200 micrometers in diameter that erode rocks, comminute regolith grains, and produce agglutinates. The effects of these micro-scale impacts are still not fully understood. Much effort has focused on evaluating the physical and optical effects of micrometeorite impacts on lunar and meteoritic material using pulsed lasers to simulate the energy deposited into a substrate in a typical hypervelocity impact. Here we characterize the physical and chemical changes that accompany natural micrometeorite impacts into lunar rocks with long surface exposure to the space environment (12075 and 76015). Transmission electron microscope (TEM) observations were obtained from cross-sections of approximately 10-20 micrometers diameter craters that revealed important micro-structural details of micrometeorite impact processes, including the creation of npFe (sup 0) in the melt, and extensive deformation around the impact site.

Optimizing the performance of dual-axis confocal microscopes via Monte-Carlo scattering simulations and diffraction theory.

PubMed

Chen, Ye; Liu, Jonathan T C

2013-06-01

Dual-axis confocal (DAC) microscopy has been found to exhibit superior rejection of out-of-focus and multiply scattered background light compared to conventional single-axis confocal microscopy. DAC microscopes rely on the use of separated illumination and collection beam paths that focus and intersect at a single focal volume (voxel) within tissue. While it is generally recognized that the resolution and contrast of a DAC microscope depends on both the crossing angle of the DAC beams, 2θ, and the focusing numerical aperture of the individual beams, α, a detailed study to investigate these dependencies has not been performed. Contrast and resolution are considered as two main criteria to assess the performance of a point-scanned DAC microscope (DAC-PS) and a line-scanned DAC microscope (DAC-LS) as a function of θ and α. The contrast and resolution of these designs are evaluated by Monte-Carlo scattering simulations and diffraction theory calculations, respectively. These results can be used for guiding the optimal designs of DAC-PS and DAC-LS microscopes.

Microscope-Based Fluid Physics Experiments in the Fluids and Combustion Facility on ISS

NASA Technical Reports Server (NTRS)

Doherty, Michael P.; Motil, Susan M.; Snead, John H.; Malarik, Diane C.

2000-01-01

At the NASA Glenn Research Center, the Microgravity Science Program is planning to conduct a large number of experiments on the International Space Station in both the Fluid Physics and Combustion Science disciplines, and is developing flight experiment hardware for use within the International Space Station's Fluids and Combustion Facility. Four fluids physics experiments that require an optical microscope will be sequentially conducted within a subrack payload to the Fluids Integrated Rack of the Fluids and Combustion Facility called the Light Microscopy Module, which will provide the containment, changeout, and diagnostic capabilities to perform the experiments. The Light Microscopy Module is planned as a fully remotely controllable on-orbit microscope facility, allowing flexible scheduling and control of experiments within International Space Station resources. This paper will focus on the four microscope-based experiments, specifically, their objectives and the sample cell and instrument hardware to accommodate their requirements.

Intercomparison of 3D pore-scale flow and solute transport simulation methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaofan; Mehmani, Yashar; Perkins, William A.

2016-09-01

Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include methods that 1) explicitly model the three-dimensional geometry of pore spaces and 2) those that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of class 1, based on direct numerical simulation using computational fluid dynamics (CFD) codes, against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of class 1 based on the immersed-boundary method (IMB),more » lattice Boltzmann method (LBM), smoothed particle hydrodynamics (SPH), as well as a model of class 2 (a pore-network model or PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and nonreactive solute transport, and intercompare the model results with previously reported experimental observations. Experimental observations are limited to measured pore-scale velocities, so solute transport comparisons are made only among the various models. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations).« less

Evaluating Red Reflex and Surgeon Preference Between Nearly-Collimated and Focused Beam Microscope Illumination Systems

PubMed Central

Cionni, Robert J.; Pei, Ron; Dimalanta, Ramon; Lubeck, David

2015-01-01

Purpose To evaluate the intensity and stability of the red reflex produced by ophthalmic surgical microscopes with nearly-collimated versus focused illumination systems and to assess surgeon preference in a simulated surgical setting. Methods This two-part evaluation consisted of postproduction surgical video analysis of red reflex intensity and a microscope use and preference survey completed by 13 experienced cataract surgeons. Survey responses were based on bench testing and experience in a simulated surgical setting. A microscope with nearly-collimated beam illumination and two focused beam microscopes were assessed. Results Red reflex intensity and stability were greater with the nearly-collimated microscope illumination system. In the bench testing survey, surgeons reported that the red reflex was maintained over significantly greater distances away from pupillary center, and depth of focus was numerically greater with nearly-collimated illumination relative to focused illumination. Most participating surgeons (≥64%) reported a preference for the microscope with nearly-collimated illumination with regard to red reflex stability, depth of focus, visualization, surgical working distance, and perceived patient comfort. Conclusions The microscope with nearly-collimated illumination produced a more intense and significantly more stable red reflex and was preferred overall by more surgeons. Translational Relevance This is the first report of an attempt to quantify red reflex intensity and stability and to evaluate surgically-relevant parameters between microscope systems. The data and methods presented here may provide a basis for future studies attempting to quantify differences between surgical microscopes that may affect surgeon preference and microscope use in ophthalmic surgery. PMID:26290778

Numerical Investigation of the Microscopic Heat Current Inside a Nanofluid System Based on Molecular Dynamics Simulation and Wavelet Analysis.

PubMed

Jia, Tao; Gao, Di

2018-04-03

Molecular dynamics simulation is employed to investigate the microscopic heat current inside an argon-copper nanofluid. Wavelet analysis of the microscopic heat current inside the nanofluid system is conducted. The signal of the microscopic heat current is decomposed into two parts: one is the approximation part; the other is the detail part. The approximation part is associated with the low-frequency part of the signal, and the detail part is associated with the high-frequency part of the signal. Both the probability distributions of the high-frequency and the low-frequency parts of the signals demonstrate Gaussian-like characteristics. The curves fit to data of the probability distribution of the microscopic heat current are established, and the parameters including the mean value and the standard deviation in the mathematical formulas of the curves show dramatic changes for the cases before and after adding copper nanoparticles into the argon base fluid.

Cavity losses for the dissipative Jaynes Cummings Hamiltonian beyond rotating wave approximation

NASA Astrophysics Data System (ADS)

Scala, M.; Militello, B.; Messina, A.; Maniscalco, S.; Piilo, J.; Suominen, K.-A.

2007-11-01

A microscopic derivation of the master equation for the Jaynes-Cummings model with cavity losses is given, taking into account the terms in the dissipator which vary with frequencies of the order of the vacuum Rabi frequency. Our approach allows us to single out physical contexts wherein the usual phenomenological dissipator turns out to be fully justified and constitutes an extension of our previous analysis (Scala et al 2007 Phys. Rev. A 75 013811), where a microscopic derivation was given in the framework of the rotating wave approximation.

Picosecond imaging of signal propagation in integrated circuits

NASA Astrophysics Data System (ADS)

Frohmann, Sven; Dietz, Enrico; Dittrich, Helmar; Hübers, Heinz-Wilhelm

2017-04-01

Optical analysis of integrated circuits (IC) is a powerful tool for analyzing security functions that are implemented in an IC. We present a photon emission microscope for picosecond imaging of hot carrier luminescence in ICs in the near-infrared spectral range from 900 to 1700 nm. It allows for a semi-invasive signal tracking in fully operational ICs on the gate or transistor level with a timing precision of approximately 6 ps. The capabilities of the microscope are demonstrated by imaging the operation of two ICs made by 180 and 60 nm process technology.

Microscopic approaches to liquid nitromethane detonation properties.

PubMed

Hervouët, Anaïs; Desbiens, Nicolas; Bourasseau, Emeric; Maillet, Jean-Bernard

2008-04-24

In this paper, thermodynamic and chemical properties of nitromethane are investigated using microscopic simulations. The Hugoniot curve of the inert explosive is computed using Monte Carlo simulations with a modified version of the adaptative Erpenbeck equation of state and a recently developed intermolecular potential. Molecular dynamic simulations of nitromethane decomposition have been performed using a reactive potential, allowing the calculation of kinetic rate constants and activation energies. Finally, the Crussard curve of detonation products as well as thermodynamic properties at the Chapman-Jouguet (CJ) point are computed using reactive ensemble Monte Carlo simulations. Results are in good agreement with both thermochemical calculations and experimental measurements.

FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

PubMed Central

Quammen, Cory W.; Richardson, Alvin C.; Haase, Julian; Harrison, Benjamin D.; Taylor, Russell M.; Bloom, Kerry S.

2010-01-01

Fluorescence microscopy provides a powerful method for localization of structures in biological specimens. However, aspects of the image formation process such as noise and blur from the microscope's point-spread function combine to produce an unintuitive image transformation on the true structure of the fluorescing molecules in the specimen, hindering qualitative and quantitative analysis of even simple structures in unprocessed images. We introduce FluoroSim, an interactive fluorescence microscope simulator that can be used to train scientists who use fluorescence microscopy to understand the artifacts that arise from the image formation process, to determine the appropriateness of fluorescence microscopy as an imaging modality in an experiment, and to test and refine hypotheses of model specimens by comparing the output of the simulator to experimental data. FluoroSim renders synthetic fluorescence images from arbitrary geometric models represented as triangle meshes. We describe three rendering algorithms on graphics processing units for computing the convolution of the specimen model with a microscope's point-spread function and report on their performance. We also discuss several cases where the microscope simulator has been used to solve real problems in biology. PMID:20431698

Microscopic description of fission dynamics: Toward a 3D computation of the time dependent GCM equation

NASA Astrophysics Data System (ADS)

Regnier, D.; Dubray, N.; Schunck, N.; Verrière, M.

2017-09-01

Accurate knowledge of fission fragment yields is an essential ingredient of numerous applications ranging from the formation of elements in the r-process to fuel cycle optimization in nuclear energy. The need for a predictive theory applicable where no data is available, together with the variety of potential applications, is an incentive to develop a fully microscopic approach to fission dynamics. One of the most promising theoretical frameworks is the time dependent generator coordinate method (TDGCM) applied under the Gaussian overlap approximation (GOA). However, the computational cost of this method makes it difficult to perform calculations with more than two collective degree of freedom. Meanwhile, it is well-known from both semi-phenomenological and fully microscopic approaches that at least four or five dimensions may play a role in the dynamics of fission. To overcome this limitation, we develop the code FELIX aiming to solve the TDGCM+GOA equation for an arbitrary number of collective variables. In this talk, we report the recent progress toward this enriched description of fission dynamics. We will briefly present the numerical methods adopted as well as the status of the latest version of FELIX. Finally, we will discuss fragments yields obtained within this approach for the low energy fission of major actinides.

Polarization in the social sciences: Assortative mixing in social science collaboration networks is resilient to interventions

NASA Astrophysics Data System (ADS)

Leifeld, Philip

2018-10-01

Academic collaboration in the social sciences is characterized by a polarization between hermeneutic and nomological researchers. This polarization is expressed in different publication strategies. The present article analyzes the complete co-authorship networks in a social science discipline in two separate countries over five years using an exponential random graph model. It examines whether and how assortative mixing in publication strategies is present and leads to a polarization in scientific collaboration. In the empirical analysis, assortative mixing is found to play a role in shaping the topology of the network and significantly explains collaboration. Co-authorship edges are more prevalent within each of the groups, but this mixing pattern does not fully account for the extent of polarization. Instead, a thought experiment reveals that other components of the complex system dampen or amplify polarization in the data-generating process and that microscopic interventions targeting behavior change with regard to assortativity would be hindered by the resilience of the system. The resilience to interventions is quantified in a series of simulations on the effect of microscopic behavior on macroscopic polarization. The empirical study controls for geographic proximity, supervision, and topical similarity (using a vector space model), and the interplay of these factors is likely responsible for this resilience. The paper also predicts the co-authorship network in one country based on the model of collaborations in the other country.

Microscopic analysis of saturable absorbers: Semiconductor saturable absorber mirrors versus graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hader, J.; Moloney, J. V.; College of Optical Sciences, University of Arizona, Tucson, Arizona 85721

2016-02-07

Fully microscopic many-body calculations are used to study the influence of strong sub-picosecond pulses on the carrier distributions and corresponding optical response in saturable absorbers used for mode-locking—semiconductor (quantum well) saturable absorber mirrors (SESAMs) and single layer graphene based saturable absorber mirrors (GSAMs). Unlike in GSAMs, the saturation fluence and recovery time in SESAMs show a strong spectral dependence. While the saturation fluence in the SESAM is minimal at the excitonic bandgap, the optimal recovery time and least pulse distortion due to group delay dispersion are found for excitation higher in the first subband. For excitation near the SESAM bandgap,more » the saturation fluence is about one tenth of that in the GSAM. At energies above the bandgap, the fluences in both systems become similar. A strong dependence of the saturation fluence on the pulse width in both systems is caused by carrier relaxation during the pulse. The recovery time in graphene is found to be about two to four times faster than that in the SESAMs. The occurrence of negative differential transmission in graphene is shown to be caused by dopant related carriers. In SESAMs, a negative differential transmission is found when exciting below the excitonic resonance where excitation induced dephasing leads to an enhancement of the absorption. Comparisons of the simulation data to the experiment show a very good quantitative agreement.« less

Dual-mode optical microscope based on single-pixel imaging

NASA Astrophysics Data System (ADS)

Rodríguez, A. D.; Clemente, P.; Tajahuerce, E.; Lancis, J.

2016-07-01

We demonstrate an inverted microscope that can image specimens in both reflection and transmission modes simultaneously with a single light source. The microscope utilizes a digital micromirror device (DMD) for patterned illumination altogether with two single-pixel photosensors for efficient light detection. The system, a scan-less device with no moving parts, works by sequential projection of a set of binary intensity patterns onto the sample that are codified onto a modified commercial DMD. Data to be displayed are geometrically transformed before written into a memory cell to cancel optical artifacts coming from the diamond-like shaped structure of the micromirror array. The 24-bit color depth of the display is fully exploited to increase the frame rate by a factor of 24, which makes the technique practicable for real samples. Our commercial DMD-based LED-illumination is cost effective and can be easily coupled as an add-on module for already existing inverted microscopes. The reflection and transmission information provided by our dual microscope complement each other and can be useful for imaging non-uniform samples and to prevent self-shadowing effects.

Directed polymers on a disordered tree with a defect subtree

NASA Astrophysics Data System (ADS)

Madras, Neal; Yıldırım, Gökhan

2018-04-01

We study the question of how the competition between bulk disorder and a localized microscopic defect affects the macroscopic behavior of a system in the directed polymer context at the free energy level. We consider the directed polymer model on a disordered d-ary tree and represent the localized microscopic defect by modifying the disorder distribution at each vertex in a single path (branch), or in a subtree, of the tree. The polymer must choose between following the microscopic defect and finding the best branches through the bulk disorder. We describe three possible phases, called the fully pinned, partially pinned and depinned phases. When the microscopic defect is associated only with a single branch, we compute the free energy and the critical curve of the model, and show that the partially pinned phase does not occur. When the localized microscopic defect is associated with a non-disordered regular subtree of the disordered tree, the picture is more complicated. We prove that all three phases are non-empty below a critical temperature, and that the partially pinned phase disappears above the critical temperature.

A modular designed ultra-high-vacuum spin-polarized scanning tunneling microscope with controllable magnetic fields for investigating epitaxial thin films.

PubMed

Wang, Kangkang; Lin, Wenzhi; Chinchore, Abhijit V; Liu, Yinghao; Smith, Arthur R

2011-05-01

A room-temperature ultra-high-vacuum scanning tunneling microscope for in situ scanning freshly grown epitaxial films has been developed. The core unit of the microscope, which consists of critical components including scanner and approach motors, is modular designed. This enables easy adaptation of the same microscope units to new growth systems with different sample-transfer geometries. Furthermore the core unit is designed to be fully compatible with cryogenic temperatures and high magnetic field operations. A double-stage spring suspension system with eddy current damping has been implemented to achieve ≤5 pm z stability in a noisy environment and in the presence of an interconnected growth chamber. Both tips and samples can be quickly exchanged in situ; also a tunable external magnetic field can be introduced using a transferable permanent magnet shuttle. This allows spin-polarized tunneling with magnetically coated tips. The performance of this microscope is demonstrated by atomic-resolution imaging of surface reconstructions on wide band-gap GaN surfaces and spin-resolved experiments on antiferromagnetic Mn(3)N(2)(010) surfaces.

Sirepo: a web-based interface for physical optics simulations - its deployment and use at NSLS-II

NASA Astrophysics Data System (ADS)

Rakitin, Maksim S.; Chubar, Oleg; Moeller, Paul; Nagler, Robert; Bruhwiler, David L.

2017-08-01

"Sirepo" is an open source cloud-based software framework which provides a convenient and user-friendly web-interface for scientific codes such as Synchrotron Radiation Workshop (SRW) running on a local machine or a remote server side. SRW is a physical optics code allowing to simulate the synchrotron radiation from various insertion devices (undulators and wigglers) and bending magnets. Another feature of SRW is a support of high-accuracy simulation of fully- and partially-coherent radiation propagation through X-ray optical beamlines, facilitated by so-called "Virtual Beamline" module. In the present work, we will discuss the most important features of Sirepo/SRW interface with emphasis on their use for commissioning of beamlines and simulation of experiments at National Synchrotron Light Source II. In particular, "Flux through Finite Aperture" and "Intensity" reports, visualizing results of the corresponding SRW calculations, are being routinely used for commissioning of undulators and X-ray optical elements. Material properties of crystals, compound refractive lenses, and some other optical elements can be dynamically obtained for the desired photon energy from the databases publicly available at Argonne National Lab and at Lawrence Berkeley Lab. In collaboration with the Center for Functional Nanomaterials (CFN) of BNL, a library of samples for coherent scattering experiments has been implemented in SRW and the corresponding Sample optical element was added to Sirepo. Electron microscope images of artificially created nanoscale samples can be uploaded to Sirepo to simulate scattering patterns created by synchrotron radiation in different experimental schemes that can be realized at beamlines.

KLASS: Kennedy Launch Academy Simulation System

NASA Technical Reports Server (NTRS)

Garner, Lesley C.

2007-01-01

Software provides access to many sophisticated scientific instrumentation (Scanning Electron Microscope (SEM), a Light Microscope, a Scanning Probe Microscope (covering Scanning Tunneling, Atomic Force, and Magnetic Force microscopy), and an Energy Dispersive Spectrometer for the SEM). Flash animation videos explain how each of the instruments work. Videos on how they are used at NASA and the sample preparation. Measuring and labeling tools provided with each instrument. Hands on experience of controlling the virtual instrument to conduct investigations, much like the real scientists at NASA do. Very open architecture. Open source on SourceForge. Extensive use of XML Target audience is high school and entry-level college students. "Many beginning students never get closer to an electron microscope than the photos in their textbooks. But anyone can get a sense of what the instrument can do by downloading this simulator from NASA's Kennedy Space Center." Science Magazine, April 8th, 2005

A two-dimensional Dirac fermion microscope

NASA Astrophysics Data System (ADS)

Bøggild, Peter; Caridad, José M.; Stampfer, Christoph; Calogero, Gaetano; Papior, Nick Rübner; Brandbyge, Mads

2017-06-01

The electron microscope has been a powerful, highly versatile workhorse in the fields of material and surface science, micro and nanotechnology, biology and geology, for nearly 80 years. The advent of two-dimensional materials opens new possibilities for realizing an analogy to electron microscopy in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2D electron guns, deflectors, tunable lenses and various detectors. The simulations show how simple objects can be imaged with well-controlled and collimated in-plane beams consisting of relativistic charge carriers. Finally, we discuss the potential of such microscopes for investigating edges, terminations and defects, as well as interfaces, including external nanoscale structures such as adsorbed molecules, nanoparticles or quantum dots.

A two-dimensional Dirac fermion microscope

PubMed Central

Bøggild, Peter; Caridad, José M.; Stampfer, Christoph; Calogero, Gaetano; Papior, Nick Rübner; Brandbyge, Mads

2017-01-01

The electron microscope has been a powerful, highly versatile workhorse in the fields of material and surface science, micro and nanotechnology, biology and geology, for nearly 80 years. The advent of two-dimensional materials opens new possibilities for realizing an analogy to electron microscopy in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2D electron guns, deflectors, tunable lenses and various detectors. The simulations show how simple objects can be imaged with well-controlled and collimated in-plane beams consisting of relativistic charge carriers. Finally, we discuss the potential of such microscopes for investigating edges, terminations and defects, as well as interfaces, including external nanoscale structures such as adsorbed molecules, nanoparticles or quantum dots. PMID:28598421

A versatile optical microscope for time-dependent single-molecule and single-particle spectroscopy

NASA Astrophysics Data System (ADS)

Li, Hao; Yang, Haw

2018-03-01

This work reports the design and implementation of a multi-function optical microscope for time-dependent spectroscopy on single molecules and single nanoparticles. It integrates the now-routine single-object measurements into one standalone platform so that no reconfiguration is needed when switching between different types of sample or spectroscopy modes. The illumination modes include evanescent field through total internal reflection, dark-field illumination, and epi-excitation onto a diffraction-limited spot suitable for confocal detection. The detection modes include spectrally resolved line imaging, wide-field imaging with dual-color capability, and two-color single-element photon-counting detection. The switch between different spectroscopy and data acquisition modes is fully automated and executed through computer programming. The capability of this microscope is demonstrated through selected proof-of-principle experiments.

A versatile optical microscope for time-dependent single-molecule and single-particle spectroscopy.

PubMed

Li, Hao; Yang, Haw

2018-03-28

This work reports the design and implementation of a multi-function optical microscope for time-dependent spectroscopy on single molecules and single nanoparticles. It integrates the now-routine single-object measurements into one standalone platform so that no reconfiguration is needed when switching between different types of sample or spectroscopy modes. The illumination modes include evanescent field through total internal reflection, dark-field illumination, and epi-excitation onto a diffraction-limited spot suitable for confocal detection. The detection modes include spectrally resolved line imaging, wide-field imaging with dual-color capability, and two-color single-element photon-counting detection. The switch between different spectroscopy and data acquisition modes is fully automated and executed through computer programming. The capability of this microscope is demonstrated through selected proof-of-principle experiments.

Foot pad dermatitis develops at an early age in commercial turkeys.

PubMed

Mayne, R K; Hocking, P M; Else, R W

2006-02-01

1. A field experiment was conducted to identify the macroscopic and histological changes associated with the development of foot pad dermatitis (FPD) in growing turkeys. Two affected and two unaffected turkeys were sampled weekly from 1 to 8 and at 10 and 21 weeks of age. 2. At one week old, birds with external signs of FPD (surface skin discolouration) showed abnormal cellular changes of the foot pad integument. As the flock aged the reactions intensified, with one sample exhibiting a fully developed macroscopic lesion at 3 weeks. 3. Major pathological changes had occurred by 6 weeks and all turkeys with external signs of lesions had fully developed microscopic inflammatory cellular lesions. From 6 weeks of age onwards lesions were increasingly numerous and became more overtly necrotic. 4. Externally normal foot pads showed microscopic evidence of lesions after the turkeys reached 4 weeks. 5. We conclude that FPD lesions become severe over a short period of time and at a very early age.

Comparisons of dense-plasma-focus kinetic simulations with experimental measurements.

PubMed

Schmidt, A; Link, A; Welch, D; Ellsworth, J; Falabella, S; Tang, V

2014-06-01

Dense-plasma-focus (DPF) Z-pinch devices are sources of copious high-energy electrons and ions, x rays, and neutrons. The mechanisms through which these physically simple devices generate such high-energy beams in a relatively short distance are not fully understood and past optimization efforts of these devices have been largely empirical. Previously we reported on fully kinetic simulations of a DPF and compared them with hybrid and fluid simulations of the same device. Here we present detailed comparisons between fully kinetic simulations and experimental data on a 1.2 kJ DPF with two electrode geometries, including neutron yield and ion beam energy distributions. A more intensive third calculation is presented which examines the effects of a fully detailed pulsed power driver model. We also compare simulated electromagnetic fluctuations with direct measurement of radiofrequency electromagnetic fluctuations in a DPF plasma. These comparisons indicate that the fully kinetic model captures the essential physics of these plasmas with high fidelity, and provide further evidence that anomalous resistivity in the plasma arises due to a kinetic instability near the lower hybrid frequency.

Traffic management simulation development.

DOT National Transportation Integrated Search

2011-01-03

Microscopic simulation can provide significant support to traffic management center (TMC) operations. However, traffic simulation applications require data that are expensive and time-consuming to collect. Data collected by TMCs can be used as a prim...

Surrogate safety measures from traffic simulation models

DOT National Transportation Integrated Search

2003-01-01

This project investigates the potential for deriving surrogate measures of safety from existing microscopic traffic simulation models for intersections. The process of computing the measures in the simulation, extracting the required data, and summar...

The contributions of Otto Scherzer (1909-1982) to the development of the electron microscope.

PubMed

Marko, Michael; Rose, Harald

2010-08-01

Otto Scherzer was one of the pioneers of theoretical electron optics. He was coauthor of the first comprehensive book on electron optics and was the first to understand that round electron lenses could not be combined to correct aberrations, as is the case in light optics. He subsequently was the first to describe several alternative means to correct spherical and chromatic aberration of electron lenses. These ideas were put into practice by his laboratory and students at Darmstadt and their successors, leading to the fully corrected electron microscopes now in operation.

Multiple Chirality in Nuclear Rotation: A Microscopic View

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, P. W.

Covariant density functional theory and three-dimensional tilted axis cranking are used to investigate multiple chirality in nuclear rotation for the first time in a fully self-consistent and microscopic way. Two distinct sets of chiral solutions with negative and positive parities, respectively, are found in the nucleus 106Rh. The negative-parity solutions reproduce well the corresponding experimental spectrum as well as the B(M1)/B(E2) ratios of the transition strengths. Finally, this indicates that a predicted positive-parity chiral band should also exist. Therefore, it provides a further strong hint that multiple chirality is realized in nuclei.

Note: Automated electrochemical etching and polishing of silver scanning tunneling microscope tips.

PubMed

Sasaki, Stephen S; Perdue, Shawn M; Rodriguez Perez, Alejandro; Tallarida, Nicholas; Majors, Julia H; Apkarian, V Ara; Lee, Joonhee

2013-09-01

Fabrication of sharp and smooth Ag tips is crucial in optical scanning probe microscope experiments. To ensure reproducible tip profiles, the polishing process is fully automated using a closed-loop laminar flow system to deliver the electrolytic solution to moving electrodes mounted on a motorized translational stage. The repetitive translational motion is controlled precisely on the μm scale with a stepper motor and screw-thread mechanism. The automated setup allows reproducible control over the tip profile and improves smoothness and sharpness of tips (radius 27 ± 18 nm), as measured by ultrafast field emission.

Multiple Chirality in Nuclear Rotation: A Microscopic View

DOE PAGES

Zhao, P. W.

2017-10-10

Covariant density functional theory and three-dimensional tilted axis cranking are used to investigate multiple chirality in nuclear rotation for the first time in a fully self-consistent and microscopic way. Two distinct sets of chiral solutions with negative and positive parities, respectively, are found in the nucleus 106Rh. The negative-parity solutions reproduce well the corresponding experimental spectrum as well as the B(M1)/B(E2) ratios of the transition strengths. Finally, this indicates that a predicted positive-parity chiral band should also exist. Therefore, it provides a further strong hint that multiple chirality is realized in nuclei.

Colloidal Microworms Propelling via a Cooperative Hydrodynamic Conveyor Belt.

PubMed

Martinez-Pedrero, Fernando; Ortiz-Ambriz, Antonio; Pagonabarraga, Ignacio; Tierno, Pietro

2015-09-25

We study propulsion arising from microscopic colloidal rotors dynamically assembled and driven in a viscous fluid upon application of an elliptically polarized rotating magnetic field. Close to a confining plate, the motion of this self-assembled microscopic worm results from the cooperative flow generated by the spinning particles which act as a hydrodynamic "conveyor belt." Chains of rotors propel faster than individual ones, until reaching a saturation speed at distances where induced-flow additivity vanishes. By combining experiments and theoretical arguments, we elucidate the mechanism of motion and fully characterize the propulsion speed in terms of the field parameters.

Analysis of improvement in performance and design parameters for enhancing resolution in an atmospheric scanning electron microscope.

PubMed

Yoon, Yeo Hun; Kim, Seung Jae; Kim, Dong Hwan

2015-12-01

The scanning electron microscope is used in various fields to go beyond diffraction limits of the optical microscope. However, the electron pathway should be conducted in a vacuum so as not to scatter electrons. The pretreatment of the sample is needed for use in the vacuum. To directly observe large and fully hydrophilic samples without pretreatment, the atmospheric scanning electron microscope (ASEM) is needed. We developed an electron filter unit and an electron detector unit for implementation of the ASEM. The key of the electron filter unit is that electrons are transmitted while air molecules remain untransmitted through the unit. The electron detector unit collected the backscattered electrons. We conducted experiments using the selected materials with Havar foil, carbon film and SiN film. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Development of Models for High Precision Simulation of the Space Mission Microscope

NASA Astrophysics Data System (ADS)

Bremer, Stefanie; List, Meike; Selig, Hanns; Lämmerzahl, Claus

MICROSCOPE is a French space mission for testing the Weak Equivalence Principle (WEP). The mission goal is the determination of the Eötvös parameter with an accuracy of 10-15. This will be achieved by means of two high-precision capacitive differential accelerometers, that are built by the French institute ONERA. At the German institute ZARM drop tower tests are carried out to verify the payload performance. Additionally, the mission data evaluation is prepared in close cooperation with the French partners CNES, ONERA and OCA. Therefore a comprehensive simulation of the real system including the science signal and all error sources is built for the development and testing of data reduction and data analysis algorithms to extract the WEP violation signal. Currently, the High Performance Satellite Dynamics Simulator (HPS), a cooperation project of ZARM and the DLR Institute of Space Systems, is adapted to the MICROSCOPE mission for the simulation of test mass and satellite dynamics. Models of environmental disturbances like solar radiation pressure are considered, too. Furthermore detailed modeling of the on-board capacitive sensors is done.

Simulation modeling of route guidance concept

DOT National Transportation Integrated Search

1997-01-01

The methodology of a simulation model developed at the University of New South Wales, Australia, for the evaluation of performance of Dynamic Route Guidance Systems (DRGS) is described. The microscopic simulation model adopts the event update simulat...

Integrating meso- and micro-simulation models to evaluate traffic management strategies - year 1 : final report.

DOT National Transportation Integrated Search

2016-06-01

In this project the researchers developed a hierarchical multi-resolution traffic simulation system for metropolitan areas, referred to as MetroSim. Categorically, the focus is on integrating two types of simulation: microscopic simulation in which i...

The effect of microscopic friction and size distributions on conditional probability distributions in soft particle packings

NASA Astrophysics Data System (ADS)

Saitoh, Kuniyasu; Magnanimo, Vanessa; Luding, Stefan

2017-10-01

Employing two-dimensional molecular dynamics (MD) simulations of soft particles, we study their non-affine responses to quasi-static isotropic compression where the effects of microscopic friction between the particles in contact and particle size distributions are examined. To quantify complicated restructuring of force-chain networks under isotropic compression, we introduce the conditional probability distributions (CPDs) of particle overlaps such that a master equation for distribution of overlaps in the soft particle packings can be constructed. From our MD simulations, we observe that the CPDs are well described by q-Gaussian distributions, where we find that the correlation for the evolution of particle overlaps is suppressed by microscopic friction, while it significantly increases with the increase of poly-dispersity.

Effectiveness of Dry Cell Microscopic Simulation (DCMS) to Promote Conceptual Understanding about Battery

NASA Astrophysics Data System (ADS)

Catur Wibowo, Firmanul; Suhandi, Andi; Rusdiana, Dadi; Samsudin, Achmad; Rahmi Darman, Dina; Faizin, M. Noor; Wiyanto; Supriyatman; Permanasari, Anna; Kaniawati, Ida; Setiawan, Wawan; Karyanto, Yudi; Linuwih, Suharto; Fatah, Abdul; Subali, Bambang; Hasani, Aceng; Hidayat, Sholeh

2017-07-01

Electricity is a concept that is abstract and difficult to see by eye directly, one example electric shock, but cannot see the movement of electric current so that students have difficulty by students. A computer simulation designed to improve the understanding of the concept of the workings of the dry cell (battery). This study was conducted to 82 students (aged 18-20 years) in the experimental group by learning to use the Dry Cell Microscopic Simulation (DCMS). The result shows the improving of students’ conceptual understanding scores from post test were statistically significantly of the workings of batteries. The implication using computer simulations designed to overcome the difficulties of conceptual understanding, can effectively help students in facilitating conceptual change.

Simulation of Tip-Sample Interaction in the Atomic Force Microscope

NASA Technical Reports Server (NTRS)

Good, Brian S.; Banerjea, Amitava

1994-01-01

Recent simulations of the interaction between planar surfaces and model Atomic Force Microscope (AFM) tips have suggested that there are conditions under which the tip may become unstable and 'avalanche' toward the sample surface. Here we investigate via computer simulation the stability of a variety of model AFM tip configurations with respect to the avalanche transition for a number of fcc metals. We perform Monte-Carlo simulations at room temperature using the Equivalent Crystal Theory (ECT) of Smith and Banerjea. Results are compared with recent experimental results as well as with our earlier work on the avalanche of parallel planar surfaces. Our results on a model single-atom tip are in excellent agreement with recent experiments on tunneling through mechanically-controlled break junctions.

Differentiating characteristic microstructural features of cancerous tissues using Mueller matrix microscope.

PubMed

Wang, Ye; He, Honghui; Chang, Jintao; Zeng, Nan; Liu, Shaoxiong; Li, Migao; Ma, Hui

2015-12-01

Polarized light imaging can provide rich microstructural information of samples, and has been applied to the detections of various abnormal tissues. In this paper, we report a polarized light microscope based on Mueller matrix imaging by adding the polarization state generator and analyzer (PSG and PSA) to a commercial transmission optical microscope. The maximum errors for the absolute values of Mueller matrix elements are reduced to 0.01 after calibration. This Mueller matrix microscope has been used to examine human cervical and liver cancerous tissues with fibrosis. Images of the transformed Mueller matrix parameters provide quantitative assessment on the characteristic features of the pathological tissues. Contrast mechanism of the experimental results are backed up by Monte Carlo simulations based on the sphere-cylinder birefringence model, which reveal the relationship between the pathological features in the cancerous tissues at the cellular level and the polarization parameters. Both the experimental and simulated data indicate that the microscopic transformed Mueller matrix parameters can distinguish the breaking down of birefringent normal tissues for cervical cancer, or the formation of birefringent surrounding structures accompanying the inflammatory reaction for liver cancer. With its simple structure, fast measurement and high precision, polarized light microscope based on Mueller matrix shows a good diagnosis application prospect. Copyright © 2015 Elsevier Ltd. All rights reserved.

Conformational Contribution to Thermodynamics of Binding in Protein-Peptide Complexes through Microscopic Simulation

PubMed Central

Das, Amit; Chakrabarti, J.; Ghosh, Mahua

2013-01-01

We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-energy changes and their contributions for different peptide-binding regions of calmodulin are evaluated microscopically. PMID:23528087

Longitudinal train dynamics model for a rail transit simulation system

DOE PAGES

Wang, Jinghui; Rakha, Hesham A.

2018-01-01

The paper develops a longitudinal train dynamics model in support of microscopic railway transportation simulation. The model can be calibrated without any mechanical data making it ideal for implementation in transportation simulators. The calibration and validation work is based on data collected from the Portland light rail train fleet. The calibration procedure is mathematically formulated as a constrained non-linear optimization problem. The validity of the model is assessed by comparing instantaneous model predictions against field observations, and also evaluated in the domains of acceleration/deceleration versus speed and acceleration/deceleration versus distance. A test is conducted to investigate the adequacy of themore » model in simulation implementation. The results demonstrate that the proposed model can adequately capture instantaneous train dynamics, and provides good performance in the simulation test. Thus, the model provides a simple theoretical foundation for microscopic simulators and will significantly support the planning, management and control of railway transportation systems.« less

Longitudinal train dynamics model for a rail transit simulation system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jinghui; Rakha, Hesham A.

The paper develops a longitudinal train dynamics model in support of microscopic railway transportation simulation. The model can be calibrated without any mechanical data making it ideal for implementation in transportation simulators. The calibration and validation work is based on data collected from the Portland light rail train fleet. The calibration procedure is mathematically formulated as a constrained non-linear optimization problem. The validity of the model is assessed by comparing instantaneous model predictions against field observations, and also evaluated in the domains of acceleration/deceleration versus speed and acceleration/deceleration versus distance. A test is conducted to investigate the adequacy of themore » model in simulation implementation. The results demonstrate that the proposed model can adequately capture instantaneous train dynamics, and provides good performance in the simulation test. Thus, the model provides a simple theoretical foundation for microscopic simulators and will significantly support the planning, management and control of railway transportation systems.« less

Computer Simulation of the Forces Acting on the Polystyrene Probe Submerged into the Succinonitrile Near Phase Transition

NASA Technical Reports Server (NTRS)

Bune, Andris V.; Kaukler, William F.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Modeling approach to simulate both mesoscale and microscopic forces acting in a typical AFM experiment is presented. At mesoscale level interaction between the cantilever tip and the sample surface is primarily described by the balance of attractive Van der Waals and repulsive forces. The model of cantilever oscillations is applicable to both non-contact and "tapping" AFM. This model can be farther enhanced to describe nanoparticle manipulation by cantilever. At microscopic level tip contamination and details of tip-surface interaction can be simulated using molecular dynamics approach. Integration of mesoscale model with molecular dynamic model is discussed.

Nonlinear saturation of the slab ITG instability and zonal flow generation with fully kinetic ions

NASA Astrophysics Data System (ADS)

Miecnikowski, Matthew T.; Sturdevant, Benjamin J.; Chen, Yang; Parker, Scott E.

2018-05-01

Fully kinetic turbulence models are of interest for their potential to validate or replace gyrokinetic models in plasma regimes where the gyrokinetic expansion parameters are marginal. Here, we demonstrate fully kinetic ion capability by simulating the growth and nonlinear saturation of the ion-temperature-gradient instability in shearless slab geometry assuming adiabatic electrons and including zonal flow dynamics. The ion trajectories are integrated using the Lorentz force, and the cyclotron motion is fully resolved. Linear growth and nonlinear saturation characteristics show excellent agreement with analogous gyrokinetic simulations across a wide range of parameters. The fully kinetic simulation accurately reproduces the nonlinearly generated zonal flow. This work demonstrates nonlinear capability, resolution of weak gradient drive, and zonal flow physics, which are critical aspects of modeling plasma turbulence with full ion dynamics.

Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats

NASA Astrophysics Data System (ADS)

Stalter, S.; Yelash, L.; Emamy, N.; Statt, A.; Hanke, M.; Lukáčová-Medvid'ová, M.; Virnau, P.

2018-03-01

Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations typically pose a computational bottleneck, which we investigate in detail in this study. We find that it is preferable to simulate many small systems as opposed to a few large systems, and that a choice of a simple isokinetic thermostat is typically sufficient while thermostats such as Lowe-Andersen allow for simulations at elevated viscosity. We discuss suitable choices for time steps and finite-size effects which arise in the limit of very small simulation boxes. We also argue that if colloidal systems are considered as opposed to atomistic systems, the gap between microscopic and macroscopic simulations regarding time and length scales is significantly smaller. We propose a novel reduced-order technique for the coupling to the macroscopic solver, which allows us to approximate a non-linear stress-strain relation efficiently and thus further reduce computational effort of microscopic simulations.

Modeling vehicle fuel consumption and emissions at signalized intersection approaches : integrating field-collected data into microscopic simulation.

DOT National Transportation Integrated Search

2012-07-01

Microscopic models produce emissions and fuel consumption estimates with higher temporal resolution than other scales of : models. Most emissions and fuel consumption models were developed with data from dynamometer testing which are : sufficiently a...

Using machine-learning to optimize phase contrast in a low-cost cellphone microscope

PubMed Central

Wartmann, Rolf; Schadwinkel, Harald; Heintzmann, Rainer

2018-01-01

Cellphones equipped with high-quality cameras and powerful CPUs as well as GPUs are widespread. This opens new prospects to use such existing computational and imaging resources to perform medical diagnosis in developing countries at a very low cost. Many relevant samples, like biological cells or waterborn parasites, are almost fully transparent. As they do not exhibit absorption, but alter the light’s phase only, they are almost invisible in brightfield microscopy. Expensive equipment and procedures for microscopic contrasting or sample staining often are not available. Dedicated illumination approaches, tailored to the sample under investigation help to boost the contrast. This is achieved by a programmable illumination source, which also allows to measure the phase gradient using the differential phase contrast (DPC) [1, 2] or even the quantitative phase using the derived qDPC approach [3]. By applying machine-learning techniques, such as a convolutional neural network (CNN), it is possible to learn a relationship between samples to be examined and its optimal light source shapes, in order to increase e.g. phase contrast, from a given dataset to enable real-time applications. For the experimental setup, we developed a 3D-printed smartphone microscope for less than 100 $ using off-the-shelf components only such as a low-cost video projector. The fully automated system assures true Koehler illumination with an LCD as the condenser aperture and a reversed smartphone lens as the microscope objective. We show that the effect of a varied light source shape, using the pre-trained CNN, does not only improve the phase contrast, but also the impression of an improvement in optical resolution without adding any special optics, as demonstrated by measurements. PMID:29494620

The HD molecule in small and medium cages of clathrate hydrates: Quantum dynamics studied by neutron scattering measurements and computation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colognesi, Daniele; Celli, Milva; Ulivi, Lorenzo, E-mail: lorenzo.ulivi@isc.cnr.it

2014-10-07

We report inelastic neutron scattering (INS) measurements on molecular hydrogen deuteride (HD) trapped in binary cubic (sII) and hexagonal (sH) clathrate hydrates, performed at low temperature using two different neutron spectrometers in order to probe both energy and momentum transfer. The INS spectra of binary clathrate samples exhibit a rich structure containing sharp bands arising from both the rotational transitions and the rattling modes of the guest molecule. For the clathrates with sII structure, there is a very good agreement with the rigorous fully quantum simulations which account for the subtle effects of the anisotropy, angular and radial, of themore » host cage on the HD microscopic dynamics. The sH clathrate sample presents a much greater challenge, due to the uncertainties regarding the crystal structure, which is known only for similar crystals with different promoter, but nor for HD (or H{sub 2}) plus methyl tert-butyl ether (MTBE-d12)« less

Rapid onset of decoherence in driven-dissipative Rydberg systems

NASA Astrophysics Data System (ADS)

Magnan, Eric; Boulier, Thomas; Bracamontes, Carlos; Maslek, James; Young, Jeremy; Gorshkov, Alexei; Porto, Trey; Rolston, Steven; JQI-Rubidium One Team

2017-04-01

Rydberg atoms have been strong candidates for the realization of quantum information processing and quantum simulation. Recently, however, there has been concerns about this approach due to the observation of a rapid onset of decoherence in large ensembles. In we provide experimental support for the hypothesis that this is due to the avalanche-like onset of exchange dipole interactions, fueled by blackbody transitions to nearby Rydberg states of opposite parity. Making a fully microscopic model has proven difficult as it requires beyond mean-field arguments, but the ubiquitousness of Rydberg-Rydberg blackbody transitions at room temperature and the always-resonant nature of dipole exchange interactions make it an interesting challenge, and argues for deeper study into the matter. In this poster, we present complementary measurements and analysis that confirm this mechanism. We also discuss several possibilities to reduce its impact on the system's coherence. This work was partially supported by NSF PIF, AFOSR, ARO, ARL-CDQI, and NSF PFC at JQI.

Comparison of skin responses from macroscopic and microscopic UV challenges

NASA Astrophysics Data System (ADS)

Seo, InSeok; Bargo, Paulo R.; Chu, Melissa; Ruvolo, Eduardo; Kollias, Nikiforos

2011-03-01

The minimal erythema dose induced by solar-simulated radiation is a useful measure of UV sensitivity of skin. Most skin phototests have been conducted by projecting a flat field of UV radiation onto the skin in an area greater than 15 cm × 15 cm with an increment of radiation doses. In this study, we investigated the responses of human skin to solar-simulated radiation of different field sizes. Twelve human subjects of skin phototype I-IV were exposed to solar-simulated radiation (SSR) on their upper inner arm or on their lower back with a series of doses in increments of 20% in order to determine the threshold dose to induce a minimal perceptible erythema response (MED). Each dose was delivered with a liquid light guide (8 mm diameter on the back or 6 mm on the upper inner arm) and with quartz optical fibers of 200 μm diameter. The resulting skin responses were evaluated visually and investigated with a reflectance confocal microscope and imaging. The erythema response to the microscopic challenge was always diffuse with no clear boundaries extending to several times the exposed site diameter at doses greater than 2 MED. The skin returned to normal appearance from the microscopic challenge after two weeks of exposure while change in appearance for the larger areas persisted for several weeks to months. This new modality of testing provides the possibility to study skin at the microscopic level with a rapid recovery following challenge.

A Fully Nonmetallic Gas Turbine Engine Enabled by Additive Manufacturing, Part II: Additive Manufacturing and Characterization of Polymer Composites

NASA Technical Reports Server (NTRS)

Chuang, Kathy C.; Grady, Joseph E.; Arnold, Steven M.; Draper, Robert D.; Shin, Eugene; Patterson, Clark; Santelle, Tom; Lao, Chao; Rhein, Morgan; Mehl, Jeremy

2015-01-01

This publication is the second part of the three part report of the project entitled "A Fully Nonmetallic Gas Turbine Engine Enabled by Additive Manufacturing" funded by NASA Aeronautics Research Institute (NARI). The objective of this project was to conduct additive manufacturing to produce aircraft engine components by Fused Deposition Modeling (FDM), using commercially available polyetherimides-Ultem 9085 and experimental Ultem 1000 mixed with 10% chopped carbon fiber. A property comparison between FDM-printed and injection molded coupons for Ultem 9085, Ultem 1000 resin and the fiber-filled composite Ultem 1000 was carried out. Furthermore, an acoustic liner was printed from Ultem 9085 simulating conventional honeycomb structured liners and tested in a wind tunnel. Composite compressor inlet guide vanes were also printed using fiber-filled Ultem 1000 filaments and tested in a cascade rig. The fiber-filled Ultem 1000 filaments and composite vanes were characterized by scanning electron microscope (SEM) and acid digestion to determine the porosity of FDM-printed articles which ranged from 25 to 31%. Coupons of Ultem 9085, experimental Ultem 1000 composites and XH6050 resin were tested at room temperature and 400F to evaluate their corresponding mechanical properties. A preliminary modeling was also initiated to predict the mechanical properties of FDM-printed Ultem 9085 coupons in relation to varied raster angles and void contents, using the GRC-developed MAC/GMC program.

Design and performance of an ultra-high vacuum scanning tunneling microscope operating at dilution refrigerator temperatures and high magnetic fields.

PubMed

Misra, S; Zhou, B B; Drozdov, I K; Seo, J; Urban, L; Gyenis, A; Kingsley, S C J; Jones, H; Yazdani, A

2013-10-01

We describe the construction and performance of a scanning tunneling microscope capable of taking maps of the tunneling density of states with sub-atomic spatial resolution at dilution refrigerator temperatures and high (14 T) magnetic fields. The fully ultra-high vacuum system features visual access to a two-sample microscope stage at the end of a bottom-loading dilution refrigerator, which facilitates the transfer of in situ prepared tips and samples. The two-sample stage enables location of the best area of the sample under study and extends the experiment lifetime. The successful thermal anchoring of the microscope, described in detail, is confirmed through a base temperature reading of 20 mK, along with a measured electron temperature of 250 mK. Atomically resolved images, along with complementary vibration measurements, are presented to confirm the effectiveness of the vibration isolation scheme in this instrument. Finally, we demonstrate that the microscope is capable of the same level of performance as typical machines with more modest refrigeration by measuring spectroscopic maps at base temperature both at zero field and in an applied magnetic field.

Fully microscopic analysis of laser-driven finite plasmas using the example of clusters

NASA Astrophysics Data System (ADS)

Peltz, Christian; Varin, Charles; Brabec, Thomas; Fennel, Thomas

2012-06-01

We discuss a microscopic particle-in-cell (MicPIC) approach that allows bridging of the microscopic and macroscopic realms of laser-driven plasma physics. The simultaneous resolution of collisions and electromagnetic field propagation in MicPIC enables the investigation of processes that have been inaccessible to rigorous numerical scrutiny so far. This is illustrated by the two main findings of our analysis of pre-ionized, resonantly laser-driven clusters, which can be realized experimentally in pump-probe experiments. In the linear response regime, MicPIC data are used to extract the individual microscopic contributions to the dielectric cluster response function, such as surface and bulk collision frequencies. We demonstrate that the competition between surface collisions and radiation damping is responsible for the maximum in the size-dependent lifetime of the Mie surface plasmon. The capacity to determine the microscopic underpinning of optical material parameters opens new avenues for modeling nano-plasmonics and nano-photonics systems. In the non-perturbative regime, we analyze the formation and evolution of recollision-induced plasma waves in laser-driven clusters. The resulting dynamics of the electron density and local field hot spots opens a new research direction for the field of attosecond science.

Open Source Surrogate Safety Assessment Model, 2017 Enhancement and Update: SSAM Version 3.0 [Tech Brief

DOT National Transportation Integrated Search

2016-11-17

The ETFOMM (Enhanced Transportation Flow Open Source Microscopic Model) Cloud Service (ECS) is a software product sponsored by the U.S. Department of Transportation in conjunction with the Microscopic Traffic Simulation Models and SoftwareAn Op...

In honour of N. Yngve Öhrn: surveying proton cancer therapy reactions with Öhrn's electron nuclear dynamics method. Aqueous clusters radiolysis and DNA-base damage by proton collisions

NASA Astrophysics Data System (ADS)

Mclaurin, Patrick M.; Privett, Austin J.; Stopera, Christopher; Grimes, Thomas V.; Perera, Ajith; Morales, Jorge A.

2015-02-01

Proton cancer therapy (PCT) utilises high-energy H+ projectiles to cure cancer. PCT healing arises from its DNA damage in cancerous cells, which is mostly inflicted by the products from PCT water radiolysis reactions. While clinically established, a complete microscopic understanding of PCT remains elusive. To help in the microscopic elucidation of PCT, Professor Öhrn's simplest-level electron nuclear dynamics (SLEND) method is herein applied to H+ + (H2O)3-4 and H+ + DNA-bases at ELab = 1.0 keV. These are two types of computationally feasible prototypes to study water radiolysis reactions and H+-induced DNA damage, respectively. SLEND is a time-dependent, variational, non-adiabatic and direct-dynamics method that adopts a nuclear classical-mechanics description and an electronic single-determinantal wavefunction. Additionally, our SLEND + effective-core-potential method is herein employed to simulate some computationally demanding PCT reactions. Due to these attributes, SLEND proves appropriate for the simulation of various types of PCT reactions accurately and feasibly. H+ + (H2O)3-4 simulations reveal two main processes: H+ projectile scattering and the simultaneous formation of H and OH fragments; the latter process is quantified through total integrals cross sections. H+ + DNA-base simulations reveal atoms and groups displacements, ring openings and base-to-proton electron transfers as predominant damage processes. The authors warmly dedicate this SLEND investigation in honour of Professor N. Yngve Öhrn on the occasion of his 80th birthday celebration during the 54th Sanibel Symposium in St. Simons' Island, Georgia, on February 16-21, 2014. Associate Professor Jorge A. Morales was a former chemistry PhD student under the mentorship of Professor Öhrn and Dr Ajith Perera took various quantum chemistry courses taught by Professor Öhrn during his chemistry PhD studies. Both Jorge and Ajith look back to those great times of their scientific formation under Yngve's guidance during the 1990s with a strong sense of gratitude toward him (and even with a sense of nostalgia). The authors are pleased to present to Professor Öhrn this birthday gift of fully mature SLEND developments that now venture to treat systems of biochemical interest.

Ultrafast 2D IR microscopy

PubMed Central

Baiz, Carlos R.; Schach, Denise; Tokmakoff, Andrei

2014-01-01

We describe a microscope for measuring two-dimensional infrared (2D IR) spectra of heterogeneous samples with μm-scale spatial resolution, sub-picosecond time resolution, and the molecular structure information of 2D IR, enabling the measurement of vibrational dynamics through correlations in frequency, time, and space. The setup is based on a fully collinear “one beam” geometry in which all pulses propagate along the same optics. Polarization, chopping, and phase cycling are used to isolate the 2D IR signals of interest. In addition, we demonstrate the use of vibrational lifetime as a contrast agent for imaging microscopic variations in molecular environments. PMID:25089490

Image formation of thick three-dimensional objects in differential-interference-contrast microscopy.

PubMed

Trattner, Sigal; Kashdan, Eugene; Feigin, Micha; Sochen, Nir

2014-05-01

The differential-interference-contrast (DIC) microscope is of widespread use in life sciences as it enables noninvasive visualization of transparent objects. The goal of this work is to model the image formation process of thick three-dimensional objects in DIC microscopy. The model is based on the principles of electromagnetic wave propagation and scattering. It simulates light propagation through the components of the DIC microscope to the image plane using a combined geometrical and physical optics approach and replicates the DIC image of the illuminated object. The model is evaluated by comparing simulated images of three-dimensional spherical objects with the recorded images of polystyrene microspheres. Our computer simulations confirm that the model captures the major DIC image characteristics of the simulated object, and it is sensitive to the defocusing effects.

An ODE-Based Wall Model for Turbulent Flow Simulations

NASA Technical Reports Server (NTRS)

Berger, Marsha J.; Aftosmis, Michael J.

2017-01-01

Fully automated meshing for Reynolds-Averaged Navier-Stokes Simulations, Mesh generation for complex geometry continues to be the biggest bottleneck in the RANS simulation process; Fully automated Cartesian methods routinely used for inviscid simulations about arbitrarily complex geometry; These methods lack of an obvious & robust way to achieve near wall anisotropy; Goal: Extend these methods for RANS simulation without sacrificing automation, at an affordable cost; Note: Nothing here is limited to Cartesian methods, and much becomes simpler in a body-fitted setting.

Modelling and simulation of [18F]fluoromisonidazole dynamics based on histology-derived microvessel maps

NASA Astrophysics Data System (ADS)

Mönnich, David; Troost, Esther G. C.; Kaanders, Johannes H. A. M.; Oyen, Wim J. G.; Alber, Markus; Thorwarth, Daniela

2011-04-01

Hypoxia can be assessed non-invasively by positron emission tomography (PET) using radiotracers such as [18F]fluoromisonidazole (Fmiso) accumulating in poorly oxygenated cells. Typical features of dynamic Fmiso PET data are high signal variability in the first hour after tracer administration and slow formation of a consistent contrast. The purpose of this study is to investigate whether these characteristics can be explained by the current conception of the underlying microscopic processes and to identify fundamental effects. This is achieved by modelling and simulating tissue oxygenation and tracer dynamics on the microscopic scale. In simulations, vessel structures on histology-derived maps act as sources and sinks for oxygen as well as tracer molecules. Molecular distributions in the extravascular space are determined by reaction-diffusion equations, which are solved numerically using a two-dimensional finite element method. Simulated Fmiso time activity curves (TACs), though not directly comparable to PET TACs, reproduce major characteristics of clinical curves, indicating that the microscopic model and the parameter values are adequate. Evidence for dependence of the early PET signal on the vascular fraction is found. Further, possible effects leading to late contrast formation and potential implications on the quantification of Fmiso PET data are discussed.

Microscopic structure of liquid 1-1-1-2-tetrafluoroethane (R134a) from Monte Carlo simulation.

PubMed

Do, Hainam; Wheatley, Richard J; Hirst, Jonathan D

2010-10-28

1-1-1-2-tetrafluoroethane (R134a) is one of the most commonly used refrigerants. Its thermophysical properties are important for evaluating the performance of refrigeration cycles. These can be obtained via computer simulation, with an insight into the microscopic structure of the liquid, which is not accessible to experiment. In this paper, vapour-liquid equilibrium properties of R134a and its liquid microscopic structure are investigated using coupled-decoupled configurational-bias Monte Carlo simulation in the Gibbs ensemble, with a recent potential [J. Phys. Chem. B 2009, 113, 178]. We find that the simulations agree well with the experimental data, except at the vicinity of the critical region. Liquid R134a packs like liquid argon, with a coordination number in the first solvation shell of 12 at 260 K. The nearest neighbours prefer to be localized in three different spaces around the central molecule, in such a manner that the dipole moments are in a parallel alignment. Analysis of the pair interaction energy shows clear association of R134a molecules, but no evidence for C-HF type hydrogen bonding is found. The above findings should be of relevance to a broad range of fluoroalkanes.

Ultimate scaling of TiN/ZrO2/TiN capacitors: Leakage currents and limitations due to electrode roughness

NASA Astrophysics Data System (ADS)

Jegert, Gunther; Kersch, Alfred; Weinreich, Wenke; Lugli, Paolo

2011-01-01

In this paper, we investigate the influence of electrode roughness on the leakage current in TiN/high-κ ZrO2/TiN (TZT) thin-film capacitors which are used in dynamic random access memory cells. Based on a microscopic transport model, which is expanded to incorporate electrode roughness, we assess the ultimate scaling potential of TZT capacitors in terms of equivalent oxide thickness, film smoothness, thickness fluctuations, defect density and distribution, and conduction band offset (CBO). The model is based on three-dimensional, fully self-consistent, kinetic Monte Carlo transport simulations. Tunneling transport in the bandgap of the dielectric is treated, which includes defect-assisted transport mechanisms. Electrode roughness is described in the framework of fractal geometry. While the short-range roughness of the electrodes is found not to influence significantly the leakage current, thickness fluctuations of the dielectric have a major impact. For thinner dielectric films they cause a transformation of the dominant transport mechanism from Poole-Frenkel conduction to trap-assisted tunneling. Consequently, the sensitivity of the leakage current on electrode roughness drastically increases on downscaling. Based on the simulations, optimization of the CBO is suggested as the most viable strategy to extend the scalability of TZT capacitors over the next chip generations.

Influence of Cyclic Straining on Fatigue, Deformation, and Fracture Behavior of High-Strength Alloy Steel

NASA Astrophysics Data System (ADS)

Manigandan, K.; Srivatsan, T. S.; Vasudevan, V. K.; Tammana, D.; Poorganji, B.

2016-01-01

In this paper, the results of a study on microstructural influences on mechanical behavior of the high-strength alloy steel Tenax™ 310 are presented and discussed. Under the influence of fully reversed strain cycling, the stress response of this alloy steel revealed softening from the onset of deformation. Cyclic strain resistance exhibited a linear trend for the variation of both elastic strain amplitude with reversals-to-failure, and plastic strain amplitude with reversals-to-failure. Fracture morphology was essentially the same at the macroscopic level over the entire range of cyclic strain amplitudes examined. However, at the fine microscopic level, this high-strength alloy steel revealed fracture to be mixed-mode with features reminiscent of "locally" ductile and brittle mechanisms. The macroscopic mechanisms governing stress response at the fine microscopic level, resultant fatigue life, and final fracture behavior are presented and discussed in light of the mutually interactive influences of intrinsic microstructural effects, deformation characteristics of the microstructural constituents during fully reversed strain cycling, cyclic strain amplitude, and resultant response stress.

Monte-Carlo Geant4 numerical simulation of experiments at 247-MeV proton microscope

NASA Astrophysics Data System (ADS)

Kantsyrev, A. V.; Skoblyakov, A. V.; Bogdanov, A. V.; Golubev, A. A.; Shilkin, N. S.; Yuriev, D. S.; Mintsev, V. B.

2018-01-01

A radiographic facility for an investigation of fast dynamic processes with areal density of targets up to 5 g/cm2 is under development on the basis of high-current proton linear accelerator at the Institute for Nuclear Research (Troitsk, Russia). A virtual model of the proton microscope developed in a software toolkit Geant4 is presented in the article. Fullscale Monte-Carlo numerical simulation of static radiographic experiments at energy of a proton beam 247 MeV was performed. The results of simulation of proton radiography experiments with static model of shock-compressed xenon are presented. The results of visualization of copper and polymethyl methacrylate step wedges static targets also described.

Determining transport coefficients for a microscopic simulation of a hadron gas

NASA Astrophysics Data System (ADS)

Pratt, Scott; Baez, Alexander; Kim, Jane

2017-02-01

Quark-gluon plasmas produced in relativistic heavy-ion collisions quickly expand and cool, entering a phase consisting of multiple interacting hadronic resonances just below the QCD deconfinement temperature, T ˜155 MeV. Numerical microscopic simulations have emerged as the principal method for modeling the behavior of the hadronic stage of heavy-ion collisions, but the transport properties that characterize these simulations are not well understood. Methods are presented here for extracting the shear viscosity and two transport parameters that emerge in Israel-Stewart hydrodynamics. The analysis is based on studying how the stress-energy tensor responds to velocity gradients. Results are consistent with Kubo relations if viscous relaxation times are twice the collision time.

Microscopic information processing and communication in crowd dynamics

NASA Astrophysics Data System (ADS)

Henein, Colin Marc; White, Tony

2010-11-01

Due, perhaps, to the historical division of crowd dynamics research into psychological and engineering approaches, microscopic crowd models have tended toward modelling simple interchangeable particles with an emphasis on the simulation of physical factors. Despite the fact that people have complex (non-panic) behaviours in crowd disasters, important human factors in crowd dynamics such as information discovery and processing, changing goals and communication have not yet been well integrated at the microscopic level. We use our Microscopic Human Factors methodology to fuse a microscopic simulation of these human factors with a popular microscopic crowd model. By tightly integrating human factors with the existing model we can study the effects on the physical domain (movement, force and crowd safety) when human behaviour (information processing and communication) is introduced. In a large-room egress scenario with ample exits, information discovery and processing yields a crowd of non-interchangeable individuals who, despite close proximity, have different goals due to their different beliefs. This crowd heterogeneity leads to complex inter-particle interactions such as jamming transitions in open space; at high crowd energies, we found a freezing by heating effect (reminiscent of the disaster at Central Lenin Stadium in 1982) in which a barrier formation of naïve individuals trying to reach blocked exits prevented knowledgeable ones from exiting. Communication, when introduced, reduced this barrier formation, increasing both exit rates and crowd safety.

Microscopic Studies of Quantum Phase Transitions in Optical Lattices

NASA Astrophysics Data System (ADS)

Bakr, Waseem S.

2011-12-01

In this thesis, I report on experiments that microscopically probe quantum phase transitions of ultracold atoms in optical lattices. We have developed a "quantum gas microscope" that allowed, for the first time, optical imaging and manipulation of single atoms in a quantum-degenerate gas on individual sites of an optical lattice. This system acts as a quantum simulator of strongly correlated materials, which are currently the subject of intense research because of the technological potential of high--T c superconductors and spintronic materials. We have used our microscope to study the superfluid to Mott insulator transition in bosons and a magnetic quantum phase transition in a spin system. In our microscopic study of the superfluid-insulator transition, we have characterized the on-site number statistics in a space- and time-resolved manner. We observed Mott insulators with fidelities as high as 99%, corresponding to entropies of 0.06kB per particle. We also measured local quantum dynamics and directly imaged the shell structure of the Mott insulator. I report on the first quantum magnetism experiments in optical lattices. We have realized a quantum Ising chain in a magnetic field, and observed a quantum phase transition between a paramagnet and antiferromagnet. We achieved strong spin interactions by encoding spins in excitations of a Mott insulator in a tilted lattice. We detected the transition by measuring the total magnetization of the system across the transition using in-situ measurements as well as the Neel ordering in the antiferromagnetic state using noise-correlation techniques. We characterized the dynamics of domain formation in the system. The spin mapping introduced opens up a new path to realizing more exotic states in optical lattices including spin liquids and quantum valence bond solids. As our system sizes become larger, simulating their physics on classical computers will require exponentially larger resources because of entanglement build-up near a quantum phase transition. We have demonstrated a quantum simulator in which all degrees of freedom can be read out microscopically, allowing the simulation of quantum many-body systems with manageable resources. More generally, the ability to image and manipulate individual atoms in optical lattices opens an avenue towards scalable quantum computation.

Microscopic Description of Le Chatelier's Principle

ERIC Educational Resources Information Center

Novak, Igor

2005-01-01

A simple approach that "demystifies" Le Chatelier's principle (LCP) and simulates students to think about fundamental physical background behind the well-known principles is presented. The approach uses microscopic descriptors of matter like energy levels and populations and does not require any assumption about the fixed amount of substance being…

Dating Fossil Pollen: A Simulation.

ERIC Educational Resources Information Center

Sheridan, Philip

1992-01-01

Describes a hands-on simulation in which students determine the age of "fossil" pollen samples based on the pollen types present when examined microscopically. Provides instructions for the preparation of pollen slides. (MDH)

Universality of emergent states in diverse physical systems

NASA Astrophysics Data System (ADS)

Guidry, Mike

2017-12-01

Our physics textbooks are dominated by examples of simple weakly-interacting microscopic states, but most of the real world around us is most effectively described in terms of emergent states that have no clear connection to simple textbook states. Emergent states are strongly-correlated and dominated by properties that emerge as a consequence of interactions and are not part of the description of the corresponding weakly-interacting system. This paper proposes a connection of weakly-interacting textbook states and realistic emergent states through fermion dynamical symmetries having fully-microscopic generators of the emergent states. These imply unique truncation of the Hilbert space for the weakly-interacting system to a collective subspace where the emergent states live. Universality arises because the possible symmetries under commutation of generators, which transcend the microscopic structure of the generators, are highly restricted in character and determine the basic structure of the emergent state, with the microscopic structure of the generators influencing emergent state only parametrically. In support of this idea we show explicit evidence that high-temperature superconductors, collective states in heavy atomic nuclei, and graphene quantum Hall states in strong magnetic fields exhibit a near-universal emergent behavior in their microscopically-computed total energy surfaces, even though these systems share essentially nothing in common at the microscopic level and their emergent states are characterized by fundamentally different order parameters.

Systematic parameter inference in stochastic mesoscopic modeling

NASA Astrophysics Data System (ADS)

Lei, Huan; Yang, Xiu; Li, Zhen; Karniadakis, George Em

2017-02-01

We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the prior knowledge that the coefficients are "sparse". The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.

Wettability effect on capillary trapping of supercritical CO2 at pore-scale: micromodel experiment and numerical modeling

NASA Astrophysics Data System (ADS)

Hu, R.; Wan, J.

2015-12-01

Wettability of reservoir minerals along pore surfaces plays a controlling role in capillary trapping of supercritical (sc) CO2 in geologic carbon sequestration. The mechanisms controlling scCO2 residual trapping are still not fully understood. We studied the effect of pore surface wettability on CO2 residual saturation at the pore-scale using engineered high pressure and high temperature micromodel (transparent pore networks) experiments and numerical modeling. Through chemical treatment of the micromodel pore surfaces, water-wet, intermediate-wet, and CO2-wet micromodels can be obtained. Both drainage and imbibition experiments were conducted at 8.5 MPa and 45 °C with controlled flow rate. Dynamic images of fluid-fluid displacement processes were recorded using a microscope with a CCD camera. Residual saturations were determined by analysis of late stage imbibition images of flow path structures. We performed direct numerical simulations of the full Navier-Stokes equations using a volume-of-fluid based finite-volume framework for the primary drainage and the followed imbibition for the micromodel experiments with different contact angles. The numerical simulations agreed well with our experimental observations. We found that more scCO2 can be trapped within the CO2-wet micromodel whereas lower residual scCO2 saturation occurred within the water-wet micromodels in both our experiments and the numerical simulations. These results provide direct and consistent evidence of the effect of wettability, and have important implications for scCO2 trapping in geologic carbon sequestration.

Buckling vs. particle desorption in a particle-covered drop subject to compressive surface stresses: a simulation study.

PubMed

Gu, Chuan; Botto, Lorenzo

2018-01-31

Predicting the behaviour of particle-covered fluid interfaces under compression has implications in several fields. The surface-tension driven adhesion of particles to drops and bubbles is exploited for example to enhance the stability of foams and emulsion and develop new generation materials. When a particle-covered fluid interface is compressed, one can observe either smooth buckling or particle desorption from the interface. The microscopic mechanisms leading to the buckling-to-desorption transition are not fully understood. In this paper we simulate a spherical drop covered by a monolayer of spherical particles. The particle-covered interface is subject to time-dependent compressive surface stresses that mimic the slow deflation of the drop. The buckling-to-desorption transition depends in a non-trivial way on three non-dimensional parameters: the ratio Π s /γ of particle-induced surface pressure and bare surface tension, the ratio a/R of particle and drop radii, and the parameter f characterising the strength of adhesion of each particle to the interface. Based on the insights from the simulations, we propose a configuration diagram describing the effect of these controlling parameters. We find that particle desorption is highly correlated with a mechanical instability that produces small-scale undulations of the monolayer of the order of the particle size that grow when the surface pressure is sufficiently large. We argue that the large local curvature associated with these small undulations can produce large normal forces, enhancing the probability of desorption.

WE-D-BRF-01: FEATURED PRESENTATION - Investigating Particle Track Structures Using Fluorescent Nuclear Track Detectors and Monte Carlo Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dowdell, S; Paganetti, H; Schuemann, J

Purpose: To report on the efforts funded by the AAPM seed funding grant to develop the basis for fluorescent nuclear track detector (FNTD) based radiobiological experiments in combination with dedicated Monte Carlo simulations (MCS) on the nanometer scale. Methods: Two confocal microscopes were utilized in this study. Two FNTD samples were used to find the optimal microscope settings, one FNTD irradiated with 11.1 MeV/u Gold ions and one irradiated with 428.77 MeV/u Carbon ions. The first sample provided a brightly luminescent central track while the latter is used to test the capabilities to observe secondary electrons. MCS were performed usingmore » TOPAS beta9 version, layered on top of Geant4.9.6p02. Two sets of simulations were performed, one with the Geant4-DNA physics list and approximating the FNTDs by water, a second set using the Penelope physics list in a water-approximated FNTD and a aluminum-oxide FNTD. Results: Within the first half of the funding period, we have successfully established readout capabilities of FNTDs at our institute. Due to technical limitations, our microscope setup is significantly different from the approach implemented at the DKFZ, Germany. However, we can clearly reconstruct Carbon tracks in 3D with electron track resolution of 200 nm. A second microscope with superior readout capabilities will be tested in the second half of the funding period, we expect an improvement in signal to background ratio with the same the resolution.We have successfully simulated tracks in FNTDs. The more accurate Geant4-DNA track simulations can be used to reconstruct the track energy from the size and brightness of the observed tracks. Conclusion: We have achieved the goals set in the seed funding proposal: the setup of FNTD readout and simulation capabilities. We will work on improving the readout resolution to validate our MCS track structures down to the nanometer scales.« less

A high-throughput screening system for barley/powdery mildew interactions based on automated analysis of light micrographs.

PubMed

Ihlow, Alexander; Schweizer, Patrick; Seiffert, Udo

2008-01-23

To find candidate genes that potentially influence the susceptibility or resistance of crop plants to powdery mildew fungi, an assay system based on transient-induced gene silencing (TIGS) as well as transient over-expression in single epidermal cells of barley has been developed. However, this system relies on quantitative microscopic analysis of the barley/powdery mildew interaction and will only become a high-throughput tool of phenomics upon automation of the most time-consuming steps. We have developed a high-throughput screening system based on a motorized microscope which evaluates the specimens fully automatically. A large-scale double-blind verification of the system showed an excellent agreement of manual and automated analysis and proved the system to work dependably. Furthermore, in a series of bombardment experiments an RNAi construct targeting the Mlo gene was included, which is expected to phenocopy resistance mediated by recessive loss-of-function alleles such as mlo5. In most cases, the automated analysis system recorded a shift towards resistance upon RNAi of Mlo, thus providing proof of concept for its usefulness in detecting gene-target effects. Besides saving labor and enabling a screening of thousands of candidate genes, this system offers continuous operation of expensive laboratory equipment and provides a less subjective analysis as well as a complete and enduring documentation of the experimental raw data in terms of digital images. In general, it proves the concept of enabling available microscope hardware to handle challenging screening tasks fully automatically.

A Closed-Loop Proportional-Integral (PI) Control Software for Fully Mechanically Controlled Automated Electron Microscopic Tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

REN, GANG; LIU, JINXIN; LI, HONGCHANG

A closed-loop proportional-integral (PI) control software is provided for fully mechanically controlled automated electron microscopic tomography. The software is developed based on Gatan DigitalMicrograph, and is compatible with Zeiss LIBRA 120 transmission electron microscope. However, it can be expanded to other TEM instrument with modification. The software consists of a graphical user interface, a digital PI controller, an image analyzing unit, and other drive units (i.e.: image acquire unit and goniometer drive unit). During a tomography data collection process, the image analyzing unit analyzes both the accumulated shift and defocus value of the latest acquired image, and provides the resultsmore » to the digital PI controller. The digital PI control compares the results with the preset values and determines the optimum adjustments of the goniometer. The goniometer drive unit adjusts the spatial position of the specimen according to the instructions given by the digital PI controller for the next tilt angle and image acquisition. The goniometer drive unit achieves high precision positioning by using a backlash elimination method. The major benefits of the software are: 1) the goniometer drive unit keeps pre-aligned/optimized beam conditions unchanged and achieves position tracking solely through mechanical control; 2) the image analyzing unit relies on only historical data and therefore does not require additional images/exposures; 3) the PI controller enables the system to dynamically track the imaging target with extremely low system error.« less

Thermalization of oscillator chains with onsite anharmonicity and comparison with kinetic theory

DOE PAGES

Mendl, Christian B.; Lu, Jianfeng; Lukkarinen, Jani

2016-12-02

We perform microscopic molecular dynamics simulations of particle chains with an onsite anharmonicity to study relaxation of spatially homogeneous states to equilibrium, and directly compare the simulations with the corresponding Boltzmann-Peierls kinetic theory. The Wigner function serves as a common interface between the microscopic and kinetic level. We demonstrate quantitative agreement after an initial transient time interval. In particular, besides energy conservation, we observe the additional quasiconservation of the phonon density, defined via an ensemble average of the related microscopic field variables and exactly conserved by the kinetic equations. On superkinetic time scales, density quasiconservation is lost while energy remainsmore » conserved, and we find evidence for eventual relaxation of the density to its canonical ensemble value. Furthermore, the precise mechanism remains unknown and is not captured by the Boltzmann-Peierls equations.« less

Thermalization of oscillator chains with onsite anharmonicity and comparison with kinetic theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mendl, Christian B.; Lu, Jianfeng; Lukkarinen, Jani

We perform microscopic molecular dynamics simulations of particle chains with an onsite anharmonicity to study relaxation of spatially homogeneous states to equilibrium, and directly compare the simulations with the corresponding Boltzmann-Peierls kinetic theory. The Wigner function serves as a common interface between the microscopic and kinetic level. We demonstrate quantitative agreement after an initial transient time interval. In particular, besides energy conservation, we observe the additional quasiconservation of the phonon density, defined via an ensemble average of the related microscopic field variables and exactly conserved by the kinetic equations. On superkinetic time scales, density quasiconservation is lost while energy remainsmore » conserved, and we find evidence for eventual relaxation of the density to its canonical ensemble value. Furthermore, the precise mechanism remains unknown and is not captured by the Boltzmann-Peierls equations.« less

Large Scale Traffic Simulations

DOT National Transportation Integrated Search

1997-01-01

Large scale microscopic (i.e. vehicle-based) traffic simulations pose high demands on computation speed in at least two application areas: (i) real-time traffic forecasting, and (ii) long-term planning applications (where repeated "looping" between t...

Intercomparison of 3D pore-scale flow and solute transport simulation methods

DOE PAGES

Mehmani, Yashar; Schoenherr, Martin; Pasquali, Andrea; ...

2015-09-28

Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based onmore » the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This paper provides support for confidence in a variety of pore-scale modeling methods and motivates further development and application of pore-scale simulation methods.« less

Intercomparison of 3D pore-scale flow and solute transport simulation methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaofan; Mehmani, Yashar; Perkins, William A.

2016-09-01

Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based onmore » the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This study provides support for confidence in a variety of pore-scale modeling methods and motivates further development and application of pore-scale simulation methods.« less

Implementation of PSF engineering in high-resolution 3D microscopy imaging with a LCoS (reflective) SLM

NASA Astrophysics Data System (ADS)

King, Sharon V.; Doblas, Ana; Patwary, Nurmohammed; Saavedra, Genaro; Martínez-Corral, Manuel; Preza, Chrysanthe

2014-03-01

Wavefront coding techniques are currently used to engineer unique point spread functions (PSFs) that enhance existing microscope modalities or create new ones. Previous work in this field demonstrated that simulated intensity PSFs encoded with a generalized cubic phase mask (GCPM) are invariant to spherical aberration or misfocus; dependent on parameter selection. Additional work demonstrated that simulated PSFs encoded with a squared cubic phase mask (SQUBIC) produce a depth invariant focal spot for application in confocal scanning microscopy. Implementation of PSF engineering theory with a liquid crystal on silicon (LCoS) spatial light modulator (SLM) enables validation of WFC phase mask designs and parameters by manipulating optical wavefront properties with a programmable diffractive element. To validate and investigate parameters of the GCPM and SQUBIC WFC masks, we implemented PSF engineering in an upright microscope modified with a dual camera port and a LCoS SLM. We present measured WFC PSFs and compare them to simulated PSFs through analysis of their effect on the microscope imaging system properties. Experimentally acquired PSFs show the same intensity distribution as simulation for the GCPM phase mask, the SQUBIC-mask and the well-known and characterized cubic-phase mask (CPM), first applied to high NA microscopy by Arnison et al.10, for extending depth of field. These measurements provide experimental validation of new WFC masks and demonstrate the use of the LCoS SLM as a WFC design tool. Although efficiency improvements are needed, this application of LCoS technology renders the microscope capable of switching among multiple WFC modes.

Optimising electron microscopy experiment through electron optics simulation.

PubMed

Kubo, Y; Gatel, C; Snoeck, E; Houdellier, F

2017-04-01

We developed a new type of electron trajectories simulation inside a complete model of a modern transmission electron microscope (TEM). Our model incorporates the precise and real design of each element constituting a TEM, i.e. the field emission (FE) cathode, the extraction optic and acceleration stages of a 300kV cold field emission gun, the illumination lenses, the objective lens, the intermediate and projection lenses. Full trajectories can be computed using magnetically saturated or non-saturated round lenses, magnetic deflectors and even non-cylindrical symmetry elements like electrostatic biprism. This multi-scale model gathers nanometer size components (FE tip) with parts of meter length (illumination and projection systems). We demonstrate that non-trivial TEM experiments requiring specific and complex optical configurations can be simulated and optimized prior to any experiment using such model. We show that all the currents set in all optical elements of the simulated column can be implemented in the real column (I2TEM in CEMES) and used as starting alignment for the requested experiment. We argue that the combination of such complete electron trajectory simulations in the whole TEM column with automatic optimization of the microscope parameters for optimal experimental data (images, diffraction, spectra) allows drastically simplifying the implementation of complex experiments in TEM and will facilitate the development of advanced use of the electron microscope in the near future. Copyright © 2017 Elsevier B.V. All rights reserved.

Microscopic Car Modeling for Intelligent Traffic and Scenario Generation in the UCF Driving Simulator : Year 2

DOT National Transportation Integrated Search

2000-01-01

A multi-year project was initiated to introduce autonomous vehicles in the University of Central Florida (UCF) Driving Simulator for real-time interaction with the simulator vehicle. This report describes the progress during the second year. In the f...

Monte Carlo Simulation of Microscopic Stock Market Models

NASA Astrophysics Data System (ADS)

Stauffer, Dietrich

Computer simulations with random numbers, that is, Monte Carlo methods, have been considerably applied in recent years to model the fluctuations of stock market or currency exchange rates. Here we concentrate on the percolation model of Cont and Bouchaud, to simulate, not to predict, the market behavior.

Reactive Transport Modeling of Induced Calcite Precipitation Reaction Fronts in Porous Media Using A Parallel, Fully Coupled, Fully Implicit Approach

NASA Astrophysics Data System (ADS)

Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.; Fox, D. T.; Fujita, Y.

2010-12-01

Inducing mineral precipitation in the subsurface is one potential strategy for immobilizing trace metal and radionuclide contaminants. Generating mineral precipitates in situ can be achieved by manipulating chemical conditions, typically through injection or in situ generation of reactants. How these reactants transport, mix and react within the medium controls the spatial distribution and composition of the resulting mineral phases. Multiple processes, including fluid flow, dispersive/diffusive transport of reactants, biogeochemical reactions and changes in porosity-permeability, are tightly coupled over a number of scales. Numerical modeling can be used to investigate the nonlinear coupling effects of these processes which are quite challenging to explore experimentally. Many subsurface reactive transport simulators employ a de-coupled or operator-splitting approach where transport equations and batch chemistry reactions are solved sequentially. However, such an approach has limited applicability for biogeochemical systems with fast kinetics and strong coupling between chemical reactions and medium properties. A massively parallel, fully coupled, fully implicit Reactive Transport simulator (referred to as “RAT”) based on a parallel multi-physics object-oriented simulation framework (MOOSE) has been developed at the Idaho National Laboratory. Within this simulator, systems of transport and reaction equations can be solved simultaneously in a fully coupled, fully implicit manner using the Jacobian Free Newton-Krylov (JFNK) method with additional advanced computing capabilities such as (1) physics-based preconditioning for solution convergence acceleration, (2) massively parallel computing and scalability, and (3) adaptive mesh refinements for 2D and 3D structured and unstructured mesh. The simulator was first tested against analytical solutions, then applied to simulating induced calcium carbonate mineral precipitation in 1D columns and 2D flow cells as analogs to homogeneous and heterogeneous porous media, respectively. In 1D columns, calcium carbonate mineral precipitation was driven by urea hydrolysis catalyzed by urease enzyme, and in 2D flow cells, calcium carbonate mineral forming reactants were injected sequentially, forming migrating reaction fronts that are typically highly nonuniform. The RAT simulation results for the spatial and temporal distributions of precipitates, reaction rates and major species in the system, and also for changes in porosity and permeability, were compared to both laboratory experimental data and computational results obtained using other reactive transport simulators. The comparisons demonstrate the ability of RAT to simulate complex nonlinear systems and the advantages of fully coupled approaches, over de-coupled methods, for accurate simulation of complex, dynamic processes such as engineered mineral precipitation in subsurface environments.

A fully coupled method for massively parallel simulation of hydraulically driven fractures in 3-dimensions: FULLY COUPLED PARALLEL SIMULATION OF HYDRAULIC FRACTURES IN 3-D

DOE PAGES

Settgast, Randolph R.; Fu, Pengcheng; Walsh, Stuart D. C.; ...

2016-09-18

This study describes a fully coupled finite element/finite volume approach for simulating field-scale hydraulically driven fractures in three dimensions, using massively parallel computing platforms. The proposed method is capable of capturing realistic representations of local heterogeneities, layering and natural fracture networks in a reservoir. A detailed description of the numerical implementation is provided, along with numerical studies comparing the model with both analytical solutions and experimental results. The results demonstrate the effectiveness of the proposed method for modeling large-scale problems involving hydraulically driven fractures in three dimensions.

A fully coupled method for massively parallel simulation of hydraulically driven fractures in 3-dimensions: FULLY COUPLED PARALLEL SIMULATION OF HYDRAULIC FRACTURES IN 3-D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Settgast, Randolph R.; Fu, Pengcheng; Walsh, Stuart D. C.

This study describes a fully coupled finite element/finite volume approach for simulating field-scale hydraulically driven fractures in three dimensions, using massively parallel computing platforms. The proposed method is capable of capturing realistic representations of local heterogeneities, layering and natural fracture networks in a reservoir. A detailed description of the numerical implementation is provided, along with numerical studies comparing the model with both analytical solutions and experimental results. The results demonstrate the effectiveness of the proposed method for modeling large-scale problems involving hydraulically driven fractures in three dimensions.

Finite-size effects in Monte Carlo simulations of two stock market models

NASA Astrophysics Data System (ADS)

Egenter, E.; Lux, T.; Stauffer, D.

The microscopic market models of Kim-Markowitz and of Lux-Marchesi are simulated for varying number of investors. If this number goes to infinity, in some quantities nearly periodic oscillations occur.

Microscopic model for the isotope effect in the high-Tc oxides

NASA Astrophysics Data System (ADS)

Kresin, V. Z.; Wolf, S. A.

1994-02-01

An unconventional microscopic mechanism relating Tc and the isotope substitution for the doped superconductors such as the high-Tc oxides is proposed. Strong nonadiabaticity, when it is impossible, strictly speaking, to separate fully the nuclear and electronic degrees of freedom, leads to a peculiar dependence of the carrier concentration n on the ionic mass M. This case corresponds, for example, to the isotopic substitution of the axial oxygen in YBa2Cu3O7-x. Because of the dependence of Tc on n, this leads to the dependence of Tc on M, that is to the isotope effect. The minimum value of the isotope coefficient corresponds to Tc=Tmaxc.

Atomic resolution ultrafast scanning tunneling microscope with scan rate breaking the resonant frequency of a quartz tuning fork resonator.

PubMed

Li, Quanfeng; Lu, Qingyou

2011-05-01

We present an ultra-fast scanning tunneling microscope with atomic resolution at 26 kHz scan rate which surpasses the resonant frequency of the quartz tuning fork resonator used as the fast scan actuator. The main improvements employed in achieving this new record are (1) fully low voltage design (2) independent scan control and data acquisition, where the tuning fork (carrying a tip) is blindly driven to scan by a function generator with the scan voltage and tunneling current (I(T)) being measured as image data (this is unlike the traditional point-by-point move and measure method where data acquisition and scan control are switched many times).

Plastic deformation at surface during unlubricated sliding

NASA Technical Reports Server (NTRS)

Yamamoto, T.; Buckley, D. H.

1982-01-01

The plastic deformation and wear of 304 stainless-steel surface slid against an aluminum oxide rider were observed by using a scanning electron microscope and an optical microscope. Experiments were conducted in a vacuum of 0.000001 Pa and in an environment of 0.0005 Pa chlorine gas at 25 C. The load was 500 grams and the sliding velocity was 0.5 centimeter per second. The deformed surface layer which accumulates and develops successively is left behind the rider, and step-shaped protuberances are developed even after single pass sliding under both environmental conditions. A fully developed surface layer is gradually torn off leaving a characteristic pattern. These observations result from both adhesion and an adhesive wear mechanism.

Epistemological Issues Concerning Computer Simulations in Science and Their Implications for Science Education

ERIC Educational Resources Information Center

Greca, Ileana M.; Seoane, Eugenia; Arriassecq, Irene

2014-01-01

Computers and simulations represent an undeniable aspect of daily scientific life, the use of simulations being comparable to the introduction of the microscope and the telescope, in the development of knowledge. In science education, simulations have been proposed for over three decades as useful tools to improve the conceptual understanding of…

Super-rogue waves in simulations based on weakly nonlinear and fully nonlinear hydrodynamic equations.

PubMed

Slunyaev, A; Pelinovsky, E; Sergeeva, A; Chabchoub, A; Hoffmann, N; Onorato, M; Akhmediev, N

2013-07-01

The rogue wave solutions (rational multibreathers) of the nonlinear Schrödinger equation (NLS) are tested in numerical simulations of weakly nonlinear and fully nonlinear hydrodynamic equations. Only the lowest order solutions from 1 to 5 are considered. A higher accuracy of wave propagation in space is reached using the modified NLS equation, also known as the Dysthe equation. This numerical modeling allowed us to directly compare simulations with recent results of laboratory measurements in Chabchoub et al. [Phys. Rev. E 86, 056601 (2012)]. In order to achieve even higher physical accuracy, we employed fully nonlinear simulations of potential Euler equations. These simulations provided us with basic characteristics of long time evolution of rational solutions of the NLS equation in the case of near-breaking conditions. The analytic NLS solutions are found to describe the actual wave dynamics of steep waves reasonably well.

Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning.

PubMed

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2017-12-21

The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian dynamics or Green's function reaction dynamics, the RDME can be orders of magnitude faster if the lattice spacing can be chosen coarse enough. However, strongly diffusion-controlled reactions mandate a very fine mesh resolution for acceptable accuracy. It is common that reactions in the same model differ in their degree of diffusion control and therefore require different degrees of mesh resolution. This renders mesoscopic simulation inefficient for systems with multiscale properties. Mesoscopic-microscopic hybrid methods address this problem by resolving the most challenging reactions with a microscale, off-lattice simulation. However, all methods to date require manual partitioning of a system, effectively limiting their usefulness as "black-box" simulation codes. In this paper, we propose a hybrid simulation algorithm with automatic system partitioning based on indirect a priori error estimates. We demonstrate the accuracy and efficiency of the method on models of diffusion-controlled networks in 3D.

Effect of Microscopic Damage Events on Static and Ballistic Impact Strength of Triaxial Braid Composites

NASA Technical Reports Server (NTRS)

Littell, Justin D.; Binienda, Wieslaw K.; Arnold, William A.; Roberts, Gary d.; Goldberg, Robert K.

2008-01-01

In previous work, the ballistic impact resistance of triaxial braided carbon/epoxy composites made with large flat tows (12k and 24k) was examined by impacting 2 X2 X0.125" composite panels with gelatin projectiles. Several high strength, intermediate modulus carbon fibers were used in combination with both untoughened and toughened matrix materials. A wide range of penetration thresholds were measured for the various fiber/matrix combinations. However, there was no clear relationship between the penetration threshold and the properties of the constituents. During some of these experiments high speed cameras were used to view the failure process, and full-field strain measurements were made to determine the strain at the onset of failure. However, these experiments provided only limited insight into the microscopic failure processes responsible for the wide range of impact resistance observed. In order to investigate potential microscopic failure processes in more detail, quasi-static tests were performed in tension, compression, and shear. Full-field strain measurement techniques were used to identify local regions of high strain resulting from microscopic failures. Microscopic failure events near the specimen surface, such as splitting of fiber bundles in surface plies, were easily identified. Subsurface damage, such as fiber fracture or fiber bundle splitting, could be identified by its effect on in-plane surface strains. Subsurface delamination could be detected as an out-of-plane deflection at the surface. Using this data, failure criteria could be established at the fiber tow level for use in analysis. An analytical formulation was developed to allow the microscopic failure criteria to be used in place of macroscopic properties as input to simulations performed using the commercial explicit finite element code, LS-DYNA. The test methods developed to investigate microscopic failure will be presented along with methods for determining local failure criteria that can be used in analysis. Results of simulations performed using LS-DYNA will be presented to illustrate the capabilities and limitations for simulating failure during quasi-static deformation and during ballistic impact of large unit cell size triaxial braid composites.

A comparison between electromechanical and pneumatic-controlled knee simulators for the investigation of wear of total knee replacements.

PubMed

Abdelgaied, Abdellatif; Fisher, John; Jennings, Louise M

2017-07-01

More robust preclinical experimental wear simulation methods are required in order to simulate a wider range of activities, observed in different patient populations such as younger more active patients, as well as to fully meet and be capable of going well beyond the existing requirements of the relevant international standards. A new six-station electromechanically driven simulator (Simulation Solutions, UK) with five fully independently controlled axes of articulation for each station, capable of replicating deep knee bending as well as other adverse conditions, which can be operated in either force or displacement control with improved input kinematic following, has been developed to meet these requirements. This study investigated the wear of a fixed-bearing total knee replacement using this electromechanically driven fully independent knee simulator and compared it to previous data from a predominantly pneumatically controlled simulator in which each station was not fully independently controlled. In addition, the kinematic performance and the repeatability of the simulators have been investigated and compared to the international standard requirements. The wear rates from the electromechanical and pneumatic knee simulators were not significantly different, with wear rates of 2.6 ± 0.9 and 2.7 ± 0.9 mm 3 /million cycles (MC; mean ± 95% confidence interval, p = 0.99) and 5.4 ± 1.4 and 6.7 ± 1.5 mm 3 /MC (mean ± 95 confidence interval, p = 0.54) from the electromechanical and pneumatic simulators under intermediate levels (maximum 5 mm) and high levels (maximum 10 mm) of anterior-posterior displacements, respectively. However, the output kinematic profiles of the control system, which drive the motion of the simulator, followed the input kinematic profiles more closely on the electromechanical simulator than the pneumatic simulator. In addition, the electromechanical simulator was capable of following kinematic and loading input cycles within the tolerances of the international standard requirements (ISO 14243-3). The new-generation electromechanical knee simulator with fully independent control has the potential to be used for a much wider range of kinematic conditions, including high-flexion and other severe conditions, due to its improved capability and performance in comparison to the previously used pneumatic-controlled simulators.

A comparison between electromechanical and pneumatic-controlled knee simulators for the investigation of wear of total knee replacements

PubMed Central

Abdelgaied, Abdellatif; Fisher, John; Jennings, Louise M

2017-01-01

More robust preclinical experimental wear simulation methods are required in order to simulate a wider range of activities, observed in different patient populations such as younger more active patients, as well as to fully meet and be capable of going well beyond the existing requirements of the relevant international standards. A new six-station electromechanically driven simulator (Simulation Solutions, UK) with five fully independently controlled axes of articulation for each station, capable of replicating deep knee bending as well as other adverse conditions, which can be operated in either force or displacement control with improved input kinematic following, has been developed to meet these requirements. This study investigated the wear of a fixed-bearing total knee replacement using this electromechanically driven fully independent knee simulator and compared it to previous data from a predominantly pneumatically controlled simulator in which each station was not fully independently controlled. In addition, the kinematic performance and the repeatability of the simulators have been investigated and compared to the international standard requirements. The wear rates from the electromechanical and pneumatic knee simulators were not significantly different, with wear rates of 2.6 ± 0.9 and 2.7 ± 0.9 mm3/million cycles (MC; mean ± 95% confidence interval, p = 0.99) and 5.4 ± 1.4 and 6.7 ± 1.5 mm3/MC (mean ± 95 confidence interval, p = 0.54) from the electromechanical and pneumatic simulators under intermediate levels (maximum 5 mm) and high levels (maximum 10 mm) of anterior–posterior displacements, respectively. However, the output kinematic profiles of the control system, which drive the motion of the simulator, followed the input kinematic profiles more closely on the electromechanical simulator than the pneumatic simulator. In addition, the electromechanical simulator was capable of following kinematic and loading input cycles within the tolerances of the international standard requirements (ISO 14243-3). The new-generation electromechanical knee simulator with fully independent control has the potential to be used for a much wider range of kinematic conditions, including high-flexion and other severe conditions, due to its improved capability and performance in comparison to the previously used pneumatic-controlled simulators. PMID:28661228

Lensless high-resolution on-chip optofluidic microscopes for Caenorhabditis elegans and cell imaging

PubMed Central

Cui, Xiquan; Lee, Lap Man; Heng, Xin; Zhong, Weiwei; Sternberg, Paul W.; Psaltis, Demetri; Yang, Changhuei

2008-01-01

Low-cost and high-resolution on-chip microscopes are vital for reducing cost and improving efficiency for modern biomedicine and bioscience. Despite the needs, the conventional microscope design has proven difficult to miniaturize. Here, we report the implementation and application of two high-resolution (≈0.9 μm for the first and ≈0.8 μm for the second), lensless, and fully on-chip microscopes based on the optofluidic microscopy (OFM) method. These systems abandon the conventional microscope design, which requires expensive lenses and large space to magnify images, and instead utilizes microfluidic flow to deliver specimens across array(s) of micrometer-size apertures defined on a metal-coated CMOS sensor to generate direct projection images. The first system utilizes a gravity-driven microfluidic flow for sample scanning and is suited for imaging elongate objects, such as Caenorhabditis elegans; and the second system employs an electrokinetic drive for flow control and is suited for imaging cells and other spherical/ellipsoidal objects. As a demonstration of the OFM for bioscience research, we show that the prototypes can be used to perform automated phenotype characterization of different Caenorhabditis elegans mutant strains, and to image spores and single cellular entities. The optofluidic microscope design, readily fabricable with existing semiconductor and microfluidic technologies, offers low-cost and highly compact imaging solutions. More functionalities, such as on-chip phase and fluorescence imaging, can also be readily adapted into OFM systems. We anticipate that the OFM can significantly address a range of biomedical and bioscience needs, and engender new microscope applications. PMID:18663227

3D Cryo-Imaging: A Very High-Resolution View of the Whole Mouse

PubMed Central

Roy, Debashish; Steyer, Grant J.; Gargesha, Madhusudhana; Stone, Meredith E.; Wilson, David L.

2009-01-01

We developed the Case Cryo-imaging system that provides information rich, very high-resolution, color brightfield, and molecular fluorescence images of a whole mouse using a section-and-image block-face imaging technology. The system consists of a mouse-sized, motorized cryo-microtome with special features for imaging, a modified, brightfield/ fluorescence microscope, and a robotic xyz imaging system positioner, all of which is fully automated by a control system. Using the robotic system, we acquired microscopic tiled images at a pixel size of 15.6 µm over the block face of a whole mouse sectioned at 40 µm, with a total data volume of 55 GB. Viewing 2D images at multiple resolutions, we identified small structures such as cardiac vessels, muscle layers, villi of the small intestine, the optic nerve, and layers of the eye. Cryo-imaging was also suitable for imaging embryo mutants in 3D. A mouse, in which enhanced green fluorescent protein was expressed under gamma actin promoter in smooth muscle cells, gave clear 3D views of smooth muscle in the urogenital and gastrointestinal tracts. With cryo-imaging, we could obtain 3D vasculature down to 10 µm, over very large regions of mouse brain. Software is fully automated with fully programmable imaging/sectioning protocols, email notifications, and automatic volume visualization. With a unique combination of field-of-view, depth of field, contrast, and resolution, the Case Cryo-imaging system fills the gap between whole animal in vivo imaging and histology. PMID:19248166

3D electrostatic gyrokinetic electron and fully kinetic ion simulation of lower-hybrid drift instability of Harris current sheet

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Zhenyu; Lin, Yu; Wang, Xueyi

The eigenmode stability properties of three-dimensional lower-hybrid-drift-instabilities (LHDI) in a Harris current sheet with a small but finite guide magnetic field have been systematically studied by employing the gyrokinetic electron and fully kinetic ion (GeFi) particle-in-cell (PIC) simulation model with a realistic ion-to-electron mass ratio m i/m e. In contrast to the fully kinetic PIC simulation scheme, the fast electron cyclotron motion and plasma oscillations are systematically removed in the GeFi model, and hence one can employ the realistic m i/m e. The GeFi simulations are benchmarked against and show excellent agreement with both the fully kinetic PIC simulation and the analytical eigenmode theory. Our studies indicate that, for small wavenumbers, ky, along the current direction, the most unstable eigenmodes are peaked at the location wheremore » $$\\vec{k}$$• $$\\vec{B}$$ =0, consistent with previous analytical and simulation studies. Here, $$\\vec{B}$$ is the equilibrium magnetic field and $$\\vec{k}$$ is the wavevector perpendicular to the nonuniformity direction. As ky increases, however, the most unstable eigenmodes are found to be peaked at $$\\vec{k}$$ •$$\\vec{B}$$ ≠0. Additionally, the simulation results indicate that varying m i/m e, the current sheet width, and the guide magnetic field can affect the stability of LHDI. Simulations with the varying mass ratio confirm the lower hybrid frequency and wave number scalings.« less

3D electrostatic gyrokinetic electron and fully kinetic ion simulation of lower-hybrid drift instability of Harris current sheet

DOE PAGES

Wang, Zhenyu; Lin, Yu; Wang, Xueyi; ...

2016-07-07

The eigenmode stability properties of three-dimensional lower-hybrid-drift-instabilities (LHDI) in a Harris current sheet with a small but finite guide magnetic field have been systematically studied by employing the gyrokinetic electron and fully kinetic ion (GeFi) particle-in-cell (PIC) simulation model with a realistic ion-to-electron mass ratio m i/m e. In contrast to the fully kinetic PIC simulation scheme, the fast electron cyclotron motion and plasma oscillations are systematically removed in the GeFi model, and hence one can employ the realistic m i/m e. The GeFi simulations are benchmarked against and show excellent agreement with both the fully kinetic PIC simulation and the analytical eigenmode theory. Our studies indicate that, for small wavenumbers, ky, along the current direction, the most unstable eigenmodes are peaked at the location wheremore » $$\\vec{k}$$• $$\\vec{B}$$ =0, consistent with previous analytical and simulation studies. Here, $$\\vec{B}$$ is the equilibrium magnetic field and $$\\vec{k}$$ is the wavevector perpendicular to the nonuniformity direction. As ky increases, however, the most unstable eigenmodes are found to be peaked at $$\\vec{k}$$ •$$\\vec{B}$$ ≠0. Additionally, the simulation results indicate that varying m i/m e, the current sheet width, and the guide magnetic field can affect the stability of LHDI. Simulations with the varying mass ratio confirm the lower hybrid frequency and wave number scalings.« less

Influence of atomic kinetics in the simulation of plasma microscopic properties and thermal instabilities for radiative bow shock experiments.

PubMed

Espinosa, G; Rodríguez, R; Gil, J M; Suzuki-Vidal, F; Lebedev, S V; Ciardi, A; Rubiano, J G; Martel, P

2017-03-01

Numerical simulations of laboratory astrophysics experiments on plasma flows require plasma microscopic properties that are obtained by means of an atomic kinetic model. This fact implies a careful choice of the most suitable model for the experiment under analysis. Otherwise, the calculations could lead to inaccurate results and inappropriate conclusions. First, a study of the validity of the local thermodynamic equilibrium in the calculation of the average ionization, mean radiative properties, and cooling times of argon plasmas in a range of plasma conditions of interest in laboratory astrophysics experiments on radiative shocks is performed in this work. In the second part, we have made an analysis of the influence of the atomic kinetic model used to calculate plasma microscopic properties of experiments carried out on magpie on radiative bow shocks propagating in argon. The models considered were developed assuming both local and nonlocal thermodynamic equilibrium and, for the latter situation, we have considered in the kinetic model different effects such as external radiation field and plasma mixture. The microscopic properties studied were the average ionization, the charge state distributions, the monochromatic opacities and emissivities, the Planck mean opacity, and the radiative power loss. The microscopic study was made as a postprocess of a radiative-hydrodynamic simulation of the experiment. We have also performed a theoretical analysis of the influence of these atomic kinetic models in the criteria for the onset possibility of thermal instabilities due to radiative cooling in those experiments in which small structures were experimentally observed in the bow shock that could be due to this kind of instability.

Influence of atomic kinetics in the simulation of plasma microscopic properties and thermal instabilities for radiative bow shock experiments

NASA Astrophysics Data System (ADS)

Espinosa, G.; Rodríguez, R.; Gil, J. M.; Suzuki-Vidal, F.; Lebedev, S. V.; Ciardi, A.; Rubiano, J. G.; Martel, P.

2017-03-01

Numerical simulations of laboratory astrophysics experiments on plasma flows require plasma microscopic properties that are obtained by means of an atomic kinetic model. This fact implies a careful choice of the most suitable model for the experiment under analysis. Otherwise, the calculations could lead to inaccurate results and inappropriate conclusions. First, a study of the validity of the local thermodynamic equilibrium in the calculation of the average ionization, mean radiative properties, and cooling times of argon plasmas in a range of plasma conditions of interest in laboratory astrophysics experiments on radiative shocks is performed in this work. In the second part, we have made an analysis of the influence of the atomic kinetic model used to calculate plasma microscopic properties of experiments carried out on magpie on radiative bow shocks propagating in argon. The models considered were developed assuming both local and nonlocal thermodynamic equilibrium and, for the latter situation, we have considered in the kinetic model different effects such as external radiation field and plasma mixture. The microscopic properties studied were the average ionization, the charge state distributions, the monochromatic opacities and emissivities, the Planck mean opacity, and the radiative power loss. The microscopic study was made as a postprocess of a radiative-hydrodynamic simulation of the experiment. We have also performed a theoretical analysis of the influence of these atomic kinetic models in the criteria for the onset possibility of thermal instabilities due to radiative cooling in those experiments in which small structures were experimentally observed in the bow shock that could be due to this kind of instability.

Elastically driven intermittent microscopic dynamics in soft solids

NASA Astrophysics Data System (ADS)

Bouzid, Mehdi; Colombo, Jader; Barbosa, Lucas Vieira; Del Gado, Emanuela

2017-06-01

Soft solids with tunable mechanical response are at the core of new material technologies, but a crucial limit for applications is their progressive aging over time, which dramatically affects their functionalities. The generally accepted paradigm is that such aging is gradual and its origin is in slower than exponential microscopic dynamics, akin to the ones in supercooled liquids or glasses. Nevertheless, time- and space-resolved measurements have provided contrasting evidence: dynamics faster than exponential, intermittency and abrupt structural changes. Here we use 3D computer simulations of a microscopic model to reveal that the timescales governing stress relaxation, respectively, through thermal fluctuations and elastic recovery are key for the aging dynamics. When thermal fluctuations are too weak, stress heterogeneities frozen-in upon solidification can still partially relax through elastically driven fluctuations. Such fluctuations are intermittent, because of strong correlations that persist over the timescale of experiments or simulations, leading to faster than exponential dynamics.

Characterization of a subwavelength-scale 3D void structure using the FDTD-based confocal laser scanning microscopic image mapping technique.

PubMed

Choi, Kyongsik; Chon, James W; Gu, Min; Lee, Byoungho

2007-08-20

In this paper, a simple confocal laser scanning microscopic (CLSM) image mapping technique based on the finite-difference time domain (FDTD) calculation has been proposed and evaluated for characterization of a subwavelength-scale three-dimensional (3D) void structure fabricated inside polymer matrix. The FDTD simulation method adopts a focused Gaussian beam incident wave, Berenger's perfectly matched layer absorbing boundary condition, and the angular spectrum analysis method. Through the well matched simulation and experimental results of the xz-scanned 3D void structure, we first characterize the exact position and the topological shape factor of the subwavelength-scale void structure, which was fabricated by a tightly focused ultrashort pulse laser. The proposed CLSM image mapping technique based on the FDTD can be widely applied from the 3D near-field microscopic imaging, optical trapping, and evanescent wave phenomenon to the state-of-the-art bio- and nanophotonics.

Analysis of Decomposition for Structure I Methane Hydrate by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Wei, Na; Sun, Wan-Tong; Meng, Ying-Feng; Liu, An-Qi; Zhou, Shou-Wei; Guo, Ping; Fu, Qiang; Lv, Xin

2018-05-01

Under multi-nodes of temperatures and pressures, microscopic decomposition mechanisms of structure I methane hydrate in contact with bulk water molecules have been studied through LAMMPS software by molecular dynamics simulation. Simulation system consists of 482 methane molecules in hydrate and 3027 randomly distributed bulk water molecules. Through analyses of simulation results, decomposition number of hydrate cages, density of methane molecules, radial distribution function for oxygen atoms, mean square displacement and coefficient of diffusion of methane molecules have been studied. A significant result shows that structure I methane hydrate decomposes from hydrate-bulk water interface to hydrate interior. As temperature rises and pressure drops, the stabilization of hydrate will weaken, decomposition extent will go deep, and mean square displacement and coefficient of diffusion of methane molecules will increase. The studies can provide important meanings for the microscopic decomposition mechanisms analyses of methane hydrate.

Quasi-Dynamic Versus Fully-Dynamic Simulations of Slip Accumulation on Faults with Enhanced Dynamic Weakening

NASA Astrophysics Data System (ADS)

Lapusta, N.; Thomas, M.; Noda, H.; Avouac, J.

2012-12-01

Long-term simulations that incorporate both seismic events and aseismic slip are quite important for studies of earthquake physics but challenging computationally. To study long deformation histories, most simulation methods do not incorporate full inertial effects (wave propagation) during simulated earthquakes, using quasi-dynamic approximations instead. Here we compare the results of quasi-dynamic simulations to the fully dynamic ones for a range of problems to determine the applicability of the quasi-dynamic approach. Intuitively, the quasi-dynamic approach should do relatively well in problems where wave-mediated effects are relatively simple but should have substantially different (and hence wrong) response when the wave-mediated stress transfers dominate the character of the seismic events. This is exactly what we observe in our simulations. We consider a 2D model of a rate-and-state fault with a seismogenic (steady-state velocity-weakening) zone surrounded by creeping (steady-state velocity-strengthening) areas. If the seismogenic zone is described by the standard Dieterich-Ruina rate-and-state friction, the resulting earthquake sequences consist of relatively simple crack-like ruptures, and the inclusion of true wave-propagation effects mostly serves to concentrate stress more efficiently at the rupture front. Hence, in such models, rupture speeds and slip rates are significantly (several times) lower in the quasi-dynamic simulations compared to the fully dynamic ones, but the total slip, the crack-like nature of seismic events, and the overall pattern of earthquake sequences is comparable, consistently with prior studies. Such behavior can be classified as qualitatively similar but quantitatively different, and it motivates the popularity of the quasi-dynamic methods in simulations. However, the comparison changes dramatically once we consider a model with enhanced dynamic weakening in the seismogenic zone in the form of flash heating. In this case, the fully dynamic simulations produce seismic ruptures in the form of short-duration slip pulses, where the pulses form due to a combination of enhanced weakening and wave effects. The quasi-dynamic simulations in the same model produce completely different results, with large crack-like ruptures, different total slips, different rupture patterns, and different prestress state before large, model-spanning events. Such qualitative differences between the quasi-dynamic and fully-dynamic simulation should result in any model where inertial effects lead to qualitative differences, such as cases with supershear transition or fault with different materials on the two sides. We will present results on our current work on how the quasi-dynamic and fully dynamic simulations compare for the cases with heterogeneous fault properties.

Microscopic calculations of the characteristics of radiative nuclear reactions for double-magic nuclei

NASA Astrophysics Data System (ADS)

Achakovskiy, Oleg; Kamerdzhiev, Sergei; Tselyaev, Victor; Shitov, Mikhail

2016-01-01

The neutron capture cross sections and average radiative widths Γγ of neutron resonances for two double-magic nuclei 132Sn and 208Pb have been calculated using the microscopic photon strength functions (PSF), which were obtained within the microscopic self-consistent version of the extended theory of finite Fermi systems in the time blocking approximation. For the first time, the microscopic PSFs have been obtained within the fully self-consistent approach with exact accounting for the single particle continuum (for 208Pb). The approach includes phonon coupling effects in addition to the standard RPA approach. The known Skyrme force has been used. The calculations of nuclear reaction characteristics have been performed with the EMPIRE 3.1 nuclear reaction code. Here, three nuclear level density (NLD) models have been used: the so-called phenomenological GSM, the EMPIRE specific (or Enhanced GSM) and the microscopical combinatorial HFB NLD models. For both considered characteristics we found a significant disagreement between the results obtained with the GSM and HFB NLD models. For 208Pb, a reasonable agreement has been found with systematic for the Γγ values with HFB NLD and with the experimental data for the HFB NLD average resonance spacing D0, while for these two quantities the differences between the values obtained with GSM and HFB NLD are of several orders of magnitude. The discrepancies between the results with the phenomenological EGLO PSF and microscopic RPA or TBA are much less for the same NLD model.

Microscopic Simulation and Macroscopic Modeling for Thermal and Chemical Non-Equilibrium

NASA Technical Reports Server (NTRS)

Liu, Yen; Panesi, Marco; Vinokur, Marcel; Clarke, Peter

2013-01-01

This paper deals with the accurate microscopic simulation and macroscopic modeling of extreme non-equilibrium phenomena, such as encountered during hypersonic entry into a planetary atmosphere. The state-to-state microscopic equations involving internal excitation, de-excitation, dissociation, and recombination of nitrogen molecules due to collisions with nitrogen atoms are solved time-accurately. Strategies to increase the numerical efficiency are discussed. The problem is then modeled using a few macroscopic variables. The model is based on reconstructions of the state distribution function using the maximum entropy principle. The internal energy space is subdivided into multiple groups in order to better describe the non-equilibrium gases. The method of weighted residuals is applied to the microscopic equations to obtain macroscopic moment equations and rate coefficients. The modeling is completely physics-based, and its accuracy depends only on the assumed expression of the state distribution function and the number of groups used. The model makes no assumption at the microscopic level, and all possible collisional and radiative processes are allowed. The model is applicable to both atoms and molecules and their ions. Several limiting cases are presented to show that the model recovers the classical twotemperature models if all states are in one group and the model reduces to the microscopic equations if each group contains only one state. Numerical examples and model validations are carried out for both the uniform and linear distributions. Results show that the original over nine thousand microscopic equations can be reduced to 2 macroscopic equations using 1 to 5 groups with excellent agreement. The computer time is decreased from 18 hours to less than 1 second.

Global MHD simulation of magnetosphere using HPF

NASA Astrophysics Data System (ADS)

Ogino, T.

We have translated a 3-dimensional magnetohydrodynamic (MHD) simulation code of the Earth's magnetosphere from VPP Fortran to HPF/JA on the Fujitsu VPP5000/56 vector-parallel supercomputer and the MHD code was fully vectorized and fully parallelized in VPP Fortran. The entire performance and capability of the HPF MHD code could be shown to be almost comparable to that of VPP Fortran. A 3-dimensional global MHD simulation of the earth's magnetosphere was performed at a speed of over 400 Gflops with an efficiency of 76.5% using 56 PEs of Fujitsu VPP5000/56 in vector and parallel computation that permitted comparison with catalog values. We have concluded that fluid and MHD codes that are fully vectorized and fully parallelized in VPP Fortran can be translated with relative ease to HPF/JA, and a code in HPF/JA may be expected to perform comparably to the same code written in VPP Fortran.

Schematic microscopic approach to the description of M1 transitions between mixed-symmetry and fully symmetric collective states in {gamma}-soft nuclei based on RPA-IBM boson mapping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jolos, R. V.; Shirikova, N. Yu.; Voronov, V. V.

A schematic microscopic method is developed to calculate the M1 transition probabilities between the mixed-symmetry and the fully symmetric states in {gamma}-soft nuclei. The method is based on the random-phase approximation-interacting boson model (RPA-IBM) boson mapping of the most collective isoscalar boson. All other boson modes with higher excitation energies, including the mixed-symmetry boson, are described in the framework of RPA. As an example the M1 transition probabilities are calculated for the {sup 124-134}Xe isotopes and compared with the experimental data. The results agree well with the data for the ratio B(M1;1{sub ms}{sup +}{yields}2{sub 2}{sup +})/B(M1;1{sub ms}{sup +}{yields}0{sub 1}{sup +}).more » However, the calculated ratio B(M1;2{sub ms}{sup +}{yields}2{sub 1}{sup +})/B(M1;1{sub ms}{sup +}{yields}0{sub 1}{sup +}) shows a significantly weaker dependence on the mass number than the experimental data.« less

On the Specific Role of Microstructure in Governing Cyclic Fatigue, Deformation, and Fracture Behavior of a High-Strength Alloy Steel

NASA Astrophysics Data System (ADS)

Manigandan, K.; Srivatsan, T. S.

2015-06-01

In this paper, the results of an experimental study that focused on evaluating the conjoint influence of microstructure and test specimen orientation on fully reversed strain-controlled fatigue behavior of the high alloy steel X2M are presented and discussed. The cyclic stress response of this high-strength alloy steel revealed initial hardening during the first few cycles followed by gradual softening for most of fatigue life. Cyclic strain resistance exhibited a linear trend for the variation of elastic strain amplitude with reversals to failure, and plastic strain amplitude with reversals to failure. Fracture morphology was the same at the macroscopic level over the entire range of cyclic strain amplitudes examined. However, at the fine microscopic level, the alloy steel revealed fracture to be essentially ductile with features reminiscent of predominantly "locally" ductile and isolated brittle mechanisms. The mechanisms governing stress response at the fine microscopic level, fatigue life, and final fracture behavior are presented and discussed in light of the mutually interactive influences of intrinsic microstructural effects, deformation characteristics of the microstructural constituents during fully reversed strain cycling, cyclic strain amplitude, and resultant response stress.

Maximizing fluorescence collection efficiency in multiphoton microscopy

PubMed Central

Zinter, Joseph P.; Levene, Michael J.

2011-01-01

Understanding fluorescence propagation through a multiphoton microscope is of critical importance in designing high performance systems capable of deep tissue imaging. Optical models of a scattering tissue sample and the Olympus 20X 0.95NA microscope objective were used to simulate fluorescence propagation as a function of imaging depth for physiologically relevant scattering parameters. The spatio-angular distribution of fluorescence at the objective back aperture derived from these simulations was used to design a simple, maximally efficient post-objective fluorescence collection system. Monte Carlo simulations corroborated by data from experimental tissue phantoms demonstrate collection efficiency improvements of 50% – 90% over conventional, non-optimized fluorescence collection geometries at large imaging depths. Imaging performance was verified by imaging layer V neurons in mouse cortex to a depth of 850 μm. PMID:21934897

Fully dynamical simulation of central nuclear collisions.

PubMed

van der Schee, Wilke; Romatschke, Paul; Pratt, Scott

2013-11-27

We present a fully dynamical simulation of central nuclear collisions around midrapidity at LHC energies. Unlike previous treatments, we simulate all phases of the collision, including the equilibration of the system. For the simulation, we use numerical relativity solutions to anti-de Sitter space/conformal field theory for the preequilibrium stage, viscous hydrodynamics for the plasma equilibrium stage, and kinetic theory for the low-density hadronic stage. Our preequilibrium stage provides initial conditions for hydrodynamics, resulting in sizable radial flow. The resulting light particle spectra reproduce the measurements from the ALICE experiment at all transverse momenta.

Report Viewgraphs for IC project: Fully-coupled climate simulations with an eddy-permitting ocean component

DOE Office of Scientific and Technical Information (OSTI.GOV)

Veneziani, Carmela

Two sets of simulations were performed within this allocation: 1) a 12-year fully-coupled experiment in preindustrial conditions, using the CICE4 version of the sea-ice model; 2) a set of multi-decadal ocean-ice-only experiments, forced with CORE-I atmospheric fields and using the CICE5 version of the sea-ice model. Results from simulation 1) are presented in Figures 1-3, and specific results from a simulation in 2) with tracer releases are presented in Figure 4.

Development of a Tool for an Efficient Calibration of CORSIM Models

DOT National Transportation Integrated Search

2014-08-01

This project proposes a Memetic Algorithm (MA) for the calibration of microscopic traffic flow simulation models. The proposed MA includes a combination of genetic and simulated annealing algorithms. The genetic algorithm performs the exploration of ...

Transient Droplet Behavior and Droplet Breakup during Bulk and Confined Shear Flow in Blends with One Viscoelastic Component: Experiments, Modelling and Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardinaels, Ruth; Verhulst, Kristof; Moldenaers, Paula

2008-07-07

The transient droplet deformation and droplet orientation after inception of shear, the shape relaxation after cessation of shear and droplet breakup during shear, are microscopically studied, both under bulk and confined conditions. The studied blends contain one viscoelastic Boger fluid phase. A counter rotating setup, based on a Paar Physica MCR300, is used for the droplet visualisation. For bulk shear flow, it is shown that the droplet deformation during startup of shear flow and the shape relaxation after cessation of shear flow are hardly influenced by droplet viscoelasticity, even at moderate to high capillary and Deborah numbers. The effects ofmore » droplet viscoelasticity only become visible close to the critical conditions and a novel break-up mechanism is observed. Matrix viscoelasticity has a more pronounced effect, causing overshoots in the deformation and significantly inhibiting relaxation. However, different applied capillary numbers prior to cessation of shear flow, with the Deborah number fixed, still result in a single master curve for shape retraction, as in fully Newtonian systems. The long tail in the droplet relaxation can be qualitatively described with a phenomenological model for droplet deformation, when using a 5-mode Giesekus model for the fluid rheology. It is found that the shear flow history significantly affects the droplet shape evolution and the breakup process in blends with one viscoelastic component. Confining a droplet between two plates accelerates the droplet deformation kinetics, similar to fully Newtonian systems. However, the increased droplet deformation, due to wall effects, causes the steady state to be reached at a later instant in time. Droplet relaxation is less sensitive to confinement, leading to slower relaxation kinetics only for highly confined droplets. For the blend with a viscoelastic droplet, a non-monotonous trend is found for the critical capillary number as a function of the confinement ratio. Finally, experimental data are compared with 3D simulations, performed with a volume-of-fluid algorithm.« less

Historical roots of centrosome research: discovery of Boveri's microscope slides in Würzburg

PubMed Central

Scheer, Ulrich

2014-01-01

Boveri's visionary monograph ‘Ueber die Natur der Centrosomen’ (On the nature of centrosomes) in 1900 was founded primarily on microscopic observations of cleaving eggs of sea urchins and the roundworm parasite Ascaris. As Boveri wrote in the introductory paragraph, his interests were less about morphological aspects of centrosomes, but rather aimed at an understanding of their physiological role during cell division. The remarkable transition from observations of tiny dot-like structures in fixed and sectioned material to a unified theory of centrosome function (which in essence still holds true today) cannot be fully appreciated without examining Boveri's starting material, the histological specimens. It was generally assumed that the microscope slides were lost during the bombing of the Zoological Institute in Würzburg at the end of WWII. Here, I describe the discovery of a number of Boveri's original microscope slides with serial sections of early sea urchin and Ascaris embryos, stained by Heidenhain's iron haematoxylin method. Some slides bear handwritten notes and sketches by Boveri. Evidence is presented that the newly discovered slides are part of the original material used by Boveri for his seminal centrosome monograph. PMID:25047623

Effect of silica nanoparticle filler on microscopic polymer α-relaxation dynamics

NASA Astrophysics Data System (ADS)

Saito, Makina; Mashita, Ryo; Kishimoto, Hiroyuki; Masuda, Ryo; Yoda, Yoshitaka; Seto, Makoto

2017-11-01

Tyre rubber has been continuously developed to improve its performance, but the microscopic mechanisms behind these improvements, e.g. by adding nanoparticles to the rubber, are still not fully understood. We study the microscopic polymer dynamics of a rubber nanocomposite system consisting of polymer polybutadiene with 20 volume% of silica nanoparticles with diameters of 100 nm via quasi-elastic scattering experiments using gamma-ray time-domain interferometry. The result shows that the presence of silica nanoparticles caused the inter-chain α-relaxation dynamics to slow down in a shallowly supercooled state suggesting that the presence of the nanoparticles that came in contact with the polymer controlled the timescale of the polymer's α-relaxation dynamics. Conversely, the presence of nanoparticles less affects the dynamics in a lower temperature region near T g. It is consistent with the result of the differential scanning calorimetry study showing negligible T g difference among the pure polymer and the nanocomposite system. It also shows that the quasi-elastic scattering experiment can be used to reveal the polymer dynamics in nanocomposites and is appropriate for characterising their microscopic dynamics for the purpose of improving tyre performance.

Telepathology. Long-distance diagnosis.

PubMed

Weinstein, R S; Bloom, K J; Rozek, L S

1989-04-01

Telepathology is defined as the practice of pathology at a distance, by visualizing an image on a video monitor rather than viewing a specimen directly through a microscope. Components of a telepathology system include the following: (1) a workstation equipped with a high-resolution video camera attached to a remote-controlled light microscope; (2) a pathologist workstation incorporating controls for manipulating the robotic microscope as well as a high-resolution video monitor; and (3) a telecommunications link. Progress has been made in designing and constructing telepathology workstations and fully motorized, computer-controlled light microscopes suitable for telepathology. In addition, components such as video signal digital encoders and decoders that produce remarkably stable, high-color fidelity, and high-resolution images have been incorporated into the workstations. Resolution requirements for the video microscopy component of telepathology have been formally examined in receiver operator characteristic (ROC) curve analyses. Test-of-concept demonstrations have been completed with the use of geostationary satellites as the broadband communication linkages for 750-line resolution video. Potential benefits of telepathology include providing a means of conveniently delivering pathology services in real-time to remote sites or underserviced areas, time-sharing of pathologists' services by multiple institutions, and increasing accessibility to specialty pathologists.

Use of a night vision intensifier for direct visualization by eye of far-red and near-infrared fluorescence through an optical microscope.

PubMed

Siddiqi, M A; Kilduff, G M; Gearhart, J D

2003-11-01

We describe the design, construction and testing of a prototype device that allows the direct visualization by eye of far-red and near-infrared (NIR) fluorescence through an optical microscope. The device incorporates a gallium arsenide (GaAs) image intensifier, typically utilized in low-light or 'night vision' applications. The intensifier converts far-red and NIR light into electrons and then into green light, which is visible to the human eye. The prototype makes possible the direct, real-time viewing by eye of normally invisible far-red and NIR fluorescence from a wide variety of fluorophores, using the full field of view of the microscope to which it is applied. The high sensitivity of the image intensifier facilitates the viewing of a wide variety of photosensitive specimens, including live cells and embryos, at vastly reduced illumination levels in both fluorescence and bright-field microscopy. Modifications to the microscope are not required in order to use the prototype, which is fully compatible with all current fluorescence techniques. Refined versions of the prototype device will have broad research and clinical applications.

Review of current progress in nanometrology with the helium ion microscope

NASA Astrophysics Data System (ADS)

Postek, Michael T.; Vladár, András; Archie, Charles; Ming, Bin

2011-02-01

Scanning electron microscopy has been employed as an imaging and measurement tool for more than 50 years and it continues as a primary tool in many research and manufacturing facilities across the world. A new challenger to this work is the helium ion microscope (HIM). The HIM is a new imaging and metrology technology. Essentially, substitution of the electron source with a helium ion source yields a tool visually similar in function to the scanning electron microscope, but very different in the fundamental imaging and measurement process. The imaged and measured signal originates differently than in the scanning electron microscope and that fact and its single atom source diameter may be able to push the obtainable resolution lower, provide greater depth-of-field and ultimately improve the metrology. Successful imaging and metrology with this instrument entails understanding and modeling of new ion beam/specimen interaction physics. As a new methodology, HIM is beginning to show promise and the abundance of potentially advantageous applications for nanometrology has yet to be fully exploited. This paper discusses some of the progress made at NIST in collaboration with IBM to understand the science behind this new technology.

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Vos, Winnok H., E-mail: winnok.devos@uantwerpen.be; Cell Systems and Imaging Research Group, Department of Molecular Biotechnology, Ghent University, Ghent; Beghuin, Didier

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALMmore » ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.« less

Characteristics of Al2O3, MnS, and TiN inclusions in the remelting process of bearing steel

NASA Astrophysics Data System (ADS)

Yang, Liang; Cheng, Guo-guang

2017-08-01

The Al2O3, MnS, and TiN inclusions in bearing steel will deteriorate the steel's mechanical properties. Therefore, elucidating detailed characteristics of these inclusions in consumable electrode during the electroslag remelting process is important for achieving a subsequently clean ingot. In this study, a confocal scanning violet laser microscope was used to simulate the remelting process and observe, in real time, the behaviors of inclusions. The obtained images show that, after the temperature exceeded the steel solidus temperature, MnS and TiN inclusions in the specimen began to dissolve. Higher temperatures led to faster dissolution, and the inclusions disappeared before the steel was fully liquid. In the case of an observed Al2O3 inclusion, its shape changed from angular to a smooth ellipsoid in the region where the solid and liquid coexisted and it began to dissolve as the temperature continued to increase. This dissolution was driven by the difference in oxygen potential between the inclusion and the liquid steel.

A simple and efficient alternative to implementing systematic random sampling in stereological designs without a motorized microscope stage.

PubMed

Melvin, Neal R; Poda, Daniel; Sutherland, Robert J

2007-10-01

When properly applied, stereology is a very robust and efficient method to quantify a variety of parameters from biological material. A common sampling strategy in stereology is systematic random sampling, which involves choosing a random sampling [corrected] start point outside the structure of interest, and sampling relevant objects at [corrected] sites that are placed at pre-determined, equidistant intervals. This has proven to be a very efficient sampling strategy, and is used widely in stereological designs. At the microscopic level, this is most often achieved through the use of a motorized stage that facilitates the systematic random stepping across the structure of interest. Here, we report a simple, precise and cost-effective software-based alternative to accomplishing systematic random sampling under the microscope. We believe that this approach will facilitate the use of stereological designs that employ systematic random sampling in laboratories that lack the resources to acquire costly, fully automated systems.

Acquisition of a High Resolution Field Emission Scanning Electron Microscope for the Analysis of Returned Samples

NASA Technical Reports Server (NTRS)

Nittler, Larry R.

2003-01-01

This grant furnished funds to purchase a state-of-the-art scanning electron microscope (SEM) to support our analytical facilities for extraterrestrial samples. After evaluating several instruments, we purchased a JEOL 6500F thermal field emission SEM with the following analytical accessories: EDAX energy-dispersive x-ray analysis system with fully automated control of instrument and sample stage; EDAX LEXS wavelength-dispersive x-ray spectrometer for high sensitivity light-element analysis; EDAX/TSL electron backscatter diffraction (EBSD) system with software for phase identification and crystal orientation mapping; Robinson backscatter electron detector; and an in situ micro-manipulator (Kleindiek). The total price was $550,000 (with $150,000 of the purchase supported by Carnegie institution matching funds). The microscope was delivered in October 2002, and most of the analytical accessories were installed by January 2003. With the exception of the wavelength spectrometer (which has been undergoing design changes) everything is working well and the SEM is in routine use in our laboratory.

Data reduction of digitized images processed from calibrated photographic and spectroscopic films obtained from terrestial, rocket and space shuttle telescopic instruments

NASA Technical Reports Server (NTRS)

Hammond, Ernest C., Jr.

1990-01-01

The Microvax 2 computer, the basic software in VMS, and the Mitsubishi High Speed Disk were received and installed. The digital scanning tunneling microscope is fully installed and operational. A new technique was developed for pseudocolor analysis of the line plot images of a scanning tunneling microscope. Computer studies and mathematical modeling of the empirical data associated with many of the film calibration studies were presented. A gas can follow-up experiment which will be launched in September, on the Space Shuttle STS-50, was prepared and loaded. Papers were presented on the structure of the human hair strand using scanning electron microscopy and x ray analysis and updated research on the annual rings produced by the surf clam of the ocean estuaries of Maryland. Scanning electron microscopic work was conducted by the research team for the study of the Mossbauer and Magnetic Susceptibility Studies on NmNi(4.25)Fe(.85) and its Hydride.

Telepresence in neurosurgery: the integrated remote neurosurgical system.

PubMed

Kassell, N F; Downs, J H; Graves, B S

1997-01-01

This paper describes the Integrated Remote Neurosurgical System (IRNS), a remotely-operated neurosurgical microscope with high-speed communications and a surgeon-accessible user interface. The IRNS will allow high quality bidirectional mentoring in the neurosurgical suite. The research goals of this effort are twofold: to develop a clinical system allowing a remote neurosurgeon to lend expertise to the OR-based neurosurgical team and to provide an integrated training environment. The IRNS incorporates a generic microscope/transport model, Called SuMIT (Surgical Manipulator Interface Translator). Our system is currently under test using the Zeiss MKM surgical transport. A SuMIT interface is also being constructed for the Robotics Research 1607. The IRNS Remote Planning and Navigation Workstation incorporates surgical planning capabilities, real-time, 30 fps video from the microscope and overhead video camera. The remote workstation includes a force reflecting handcontroller which gives the remote surgeon an intuitive way to position the microscope head. Bidirectional audio, video whiteboarding, and image archiving are also supported by the remote workstation. A simulation mode permits pre-surgical simulation, post-surgical critique, and training for surgeons without access to an actual microscope transport system. The components of the IRNS are integrated using ATM switching to provide low latency data transfer. The research, along with the more sophisticated systems that will follow, will serve as a foundation and test-bed for extending the surgeon's skills without regard to time zone or geographic boundaries.

Measurement with microscopic MRI and simulation of flow in different aneurysm models.

PubMed

Edelhoff, Daniel; Walczak, Lars; Frank, Frauke; Heil, Marvin; Schmitz, Inge; Weichert, Frank; Suter, Dieter

2015-10-01

The impact and the development of aneurysms depend to a significant degree on the exchange of liquid between the regular vessel and the pathological extension. A better understanding of this process will lead to improved prediction capabilities. The aim of the current study was to investigate fluid-exchange in aneurysm models of different complexities by combining microscopic magnetic resonance measurements with numerical simulations. In order to evaluate the accuracy and applicability of these methods, the fluid-exchange process between the unaltered vessel lumen and the aneurysm phantoms was analyzed quantitatively using high spatial resolution. Magnetic resonance flow imaging was used to visualize fluid-exchange in two different models produced with a 3D printer. One model of an aneurysm was based on histological findings. The flow distribution in the different models was measured on a microscopic scale using time of flight magnetic resonance imaging. The whole experiment was simulated using fast graphics processing unit-based numerical simulations. The obtained simulation results were compared qualitatively and quantitatively with the magnetic resonance imaging measurements, taking into account flow and spin-lattice relaxation. The results of both presented methods compared well for the used aneurysm models and the chosen flow distributions. The results from the fluid-exchange analysis showed comparable characteristics concerning measurement and simulation. Similar symmetry behavior was observed. Based on these results, the amount of fluid-exchange was calculated. Depending on the geometry of the models, 7% to 45% of the liquid was exchanged per second. The result of the numerical simulations coincides well with the experimentally determined velocity field. The rate of fluid-exchange between vessel and aneurysm was well-predicted. Hence, the results obtained by simulation could be validated by the experiment. The observed deviations can be caused by the noise in the measurement and by the limited resolution of the simulation. The resulting differences are small enough to allow reliable predictions of the flow distribution in vessels with stents and for pulsed blood flow.

Relationship between pore size and reversible and irreversible immobilization of ionic liquid electrolytes in porous carbon under applied electric potential

DOE PAGES

Mahurin, Shannon M.; Mamontov, Eugene; Thompson, Matthew W.; ...

2016-10-04

Transport of electrolytes in nanoporous carbon-based electrodes largely defines the function and performance of energy storage devices. Here, using molecular dynamics simulation and quasielastic neutron scattering, we investigate the microscopic dynamics of a prototypical ionic liquid electrolyte, [emim][Tf 2N], under applied electric potential in carbon materials with 6.7 nm and 1.5 nm pores. The simulations demonstrate the formation of dense layers of counter-ions near the charged surfaces, which is reversible when the polarity is reversed. In the experiment, the ions immobilized near the surface manifest themselves in the elastic scattering signal. The experimentally observed ion immobilization near the wall ismore » fully reversible as a function of the applied electric potential in the 6.7 nm, but not in the 1.5 nm nanopores. In the latter case, remarkably, the first application of the electric potential leads to apparently irreversible immobilization of cations or anions, depending on the polarity, near the carbon pore walls. This unexpectedly demonstrates that in carbon electrode materials with the small pores, which are optimal for energy storage applications, the polarity of the electrical potential applied for the first time after the introduction of an ionic liquid electrolyte may define the decoration of the small pore walls with ions for prolonged periods of time and possibly for the lifetime of the electrode.« less

Discrete Element Method and its application to materials failure problem on the example of Brazilian Test

NASA Astrophysics Data System (ADS)

Klejment, Piotr; Kosmala, Alicja; Foltyn, Natalia; Dębski, Wojciech

2017-04-01

The earthquake focus is the point where a rock under external stress starts to fracture. Understanding earthquake nucleation and earthquake dynamics requires thus understanding of fracturing of brittle materials. This, however, is a continuing problem and enduring challenge to geoscience. In spite of significant progress we still do not fully understand the failure of rock materials due to extreme stress concentration in natural condition. One of the reason of this situation is that information about natural or induced seismic events is still not sufficient for precise description of physical processes in seismic foci. One of the possibility of improving this situation is using numerical simulations - a powerful tool of contemporary physics. For this reason we used an advanced implementation of the Discrete Element Method (DEM). DEM's main task is to calculate physical properties of materials which are represented as an assembly of a great number of particles interacting with each other. We analyze the possibility of using DEM for describing materials during so called Brazilian Test. Brazilian Test is a testing method to obtain the tensile strength of brittle material. One of the primary reasons for conducting such simulations is to measure macroscopic parameters of the rock sample. We would like to report our efforts of describing the fracturing process during the Brazilian Test from the microscopic point of view and give an insight into physical processes preceding materials failure.

Increased hematuria following hypergravic exposure in middle-aged women

NASA Technical Reports Server (NTRS)

Goldwater, D. J.; Ohara, D. B.; Sandler, H.

1982-01-01

The effects of simulated weightlessness on orthostatic tolerance were studied in 9 women (55 to 65 years old) who underwent acceleration and lower body negative pressure before and after 10 days of horizontal bed rest. The results of this study show the first known association of microscopic hematuria with hypergravic and orthostatic stress which suggests similarities to the 'stress hematuria syndrome' previously seen with heavy exercise (Boileau et al., 1980). In addition, the sporadic occurrence of this phenomenon indicates a multifactorial etiology in predisposed individuals. Bedrest or weightlessness simulation per se does not seem to significantly alter renal function, but may decrease microscopic hematuria with an orthostatic component.

A Numerical Method for Simulating the Microscopic Damage Evolution in Composites Under Uniaxial Transverse Tension

NASA Astrophysics Data System (ADS)

Zhi, Jie; Zhao, Libin; Zhang, Jianyu; Liu, Zhanli

2016-06-01

In this paper, a new numerical method that combines a surface-based cohesive model and extended finite element method (XFEM) without predefining the crack paths is presented to simulate the microscopic damage evolution in composites under uniaxial transverse tension. The proposed method is verified to accurately capture the crack kinking into the matrix after fiber/matrix debonding. A statistical representative volume element (SRVE) under periodic boundary conditions is used to approximate the microstructure of the composites. The interface parameters of the cohesive models are investigated, in which the initial interface stiffness has a great effect on the predictions of the fiber/matrix debonding. The detailed debonding states of SRVE with strong and weak interfaces are compared based on the surface-based and element-based cohesive models. The mechanism of damage in composites under transverse tension is described as the appearance of the interface cracks and their induced matrix micro-cracking, both of which coalesce into transversal macro-cracks. Good agreement is found between the predictions of the model and the in situ experimental observations, demonstrating the efficiency of the presented model for simulating the microscopic damage evolution in composites.

Electronic structure of polycrystalline CVD-graphene revealed by Nano-ARPES

NASA Astrophysics Data System (ADS)

Chen, Chaoyu; Avila, José; Asensio, Maria C.

2017-06-01

The ability to explore electronic structure and their role in determining material’s macroscopic behaviour is essential to explain and engineer functions of material and device. Since its debut in 2004, graphene has attracted global research interest due to its unique properties. Chemical vapor deposition (CVD) has emerged as an important method for the massive preparation and production of graphene for various applications. Here by employing angle-resolved photoemission spectroscopy with nanoscale spatial resolution ˜ 100 nm (Nano-ARPES), we describe the approach to measure the electronic structure of polycrystalline graphene on copper foils, demonstrating the power of Nano-ARPES to detect the electronic structure of microscopic single crystalline domains, being fully compatible with conventional ARPES. Similar analysis could be employed to other microscopic materials

In situ scanning tunneling microscope tip treatment device for spin polarization imaging

DOEpatents

Li, An-Ping [Oak Ridge, TN; Jianxing, Ma [Oak Ridge, TN; Shen, Jian [Knoxville, TN

2008-04-22

A tip treatment device for use in an ultrahigh vacuum in situ scanning tunneling microscope (STM). The device provides spin polarization functionality to new or existing variable temperature STM systems. The tip treatment device readily converts a conventional STM to a spin-polarized tip, and thereby converts a standard STM system into a spin-polarized STM system. The tip treatment device also has functions of tip cleaning and tip flashing a STM tip to high temperature (>2000.degree. C.) in an extremely localized fashion. Tip coating functions can also be carried out, providing the tip sharp end with monolayers of coating materials including magnetic films. The device is also fully compatible with ultrahigh vacuum sample transfer setups.

A modular, open-source, slide-scanning microscope for diagnostic applications in resource-constrained settings

PubMed Central

Lu, Qiang; Liu, Guanghui; Xiao, Chuanli; Hu, Chuanzhen; Zhang, Shiwu; Xu, Ronald X.; Chu, Kaiqin; Xu, Qianming

2018-01-01

In this paper we report the development of a cost-effective, modular, open source, and fully automated slide-scanning microscope, composed entirely of easily available off-the-shelf parts, and capable of bright field and fluorescence modes. The automated X-Y stage is composed of two low-cost micrometer stages coupled to stepper motors operated in open-loop mode. The microscope is composed of a low-cost CMOS sensor and low-cost board lenses placed in a 4f configuration. The system has approximately 1 micron resolution, limited by the f/# of available board lenses. The microscope is compact, measuring just 25×25×30 cm, and has an absolute positioning accuracy of ±1 μm in the X and Y directions. A Z-stage enables autofocusing and imaging over large fields of view even on non-planar samples, and custom software enables automatic determination of sample boundaries and image mosaicking. We demonstrate the utility of our device through imaging of fluorescent- and transmission-dye stained blood and fecal smears containing human and animal parasites, as well as several prepared tissue samples. These results demonstrate image quality comparable to high-end commercial microscopes at a cost of less than US$400 for a bright-field system, with an extra US$100 needed for the fluorescence module. PMID:29543835

Systematic parameter inference in stochastic mesoscopic modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lei, Huan; Yang, Xiu; Li, Zhen

2017-02-01

We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the priormore » knowledge that the coefficients are “sparse”. The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.« less

Microscopic transport model animation visualisation on KML base

NASA Astrophysics Data System (ADS)

Yatskiv, I.; Savrasovs, M.

2012-10-01

By reading classical literature devoted to the simulation theory it could be found that one of the greatest possibilities of simulation is the ability to present processes inside the system by animation. This gives to the simulation model additional value during presentation of simulation results for the public and authorities who are not familiar enough with simulation. That is why most of universal and specialised simulation tools have the ability to construct 2D and 3D representation of the model. Usually the development of such representation could take much time and there must be put a lot forces into creating an adequate 3D representation of the model. For long years such well-known microscopic traffic flow simulation software tools as VISSIM, AIMSUN and PARAMICS have had a possibility to produce 2D and 3D animation. But creation of realistic 3D model of the place where traffic flows are simulated, even in these professional software tools it is a hard and time consuming action. The goal of this paper is to describe the concepts of use the existing on-line geographical information systems for visualisation of animation produced by simulation software. For demonstration purposes the following technologies and tools have been used: PTV VISION VISSIM, KML and Google Earth.

Towards a Fine-Resolution Global Coupled Climate System for Prediction on Decadal/Centennial Scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

McClean, Julie L.

The over-arching goal of this project was to contribute to the realization of a fully coupled fine resolution Earth System Model simulation in which a weather-scale atmosphere is coupled to an ocean in which mesoscale eddies are largely resolved. Both a prototype fine-resolution fully coupled ESM simulation and a first-ever multi-decadal forced fine-resolution global coupled ocean/ice simulation were configured, tested, run, and analyzed as part of this grant. Science questions focused on the gains from the use of high horizontal resolution, particularly in the ocean and sea-ice, with respect to climatically important processes. Both these fine resolution coupled ocean/sea icemore » and fully-coupled simulations and precedent stand-alone eddy-resolving ocean and eddy-permitting coupled ocean/ice simulations were used to explore the high resolution regime. Overall, these studies showed that the presence of mesoscale eddies significantly impacted mixing processes and the global meridional overturning circulation in the ocean simulations. Fourteen refereed publications and a Ph.D. dissertation resulted from this grant.« less

Correlative SEM SERS for quantitative analysis of dimer nanoparticles.

PubMed

Timmermans, F J; Lenferink, A T M; van Wolferen, H A G M; Otto, C

2016-11-14

A Raman microscope integrated with a scanning electron microscope was used to investigate plasmonic structures by correlative SEM-SERS analysis. The integrated Raman-SEM microscope combines high-resolution electron microscopy information with SERS signal enhancement from selected nanostructures with adsorbed Raman reporter molecules. Correlative analysis is performed for dimers of two gold nanospheres. Dimers were selected on the basis of SEM images from multi aggregate samples. The effect of the orientation of the dimer with respect to the polarization state of the laser light and the effect of the particle gap size on the Raman signal intensity is observed. Additionally, calculations are performed to simulate the electric near field enhancement. These simulations are based on the morphologies observed by electron microscopy. In this way the experiments are compared with the enhancement factor calculated with near field simulations and are subsequently used to quantify the SERS enhancement factor. Large differences between experimentally observed and calculated enhancement factors are regularly detected, a phenomenon caused by nanoscale differences between the real and 'simplified' simulated structures. Quantitative SERS experiments reveal the structure induced enhancement factor, ranging from ∼200 to ∼20 000, averaged over the full nanostructure surface. The results demonstrate correlative Raman-SEM microscopy for the quantitative analysis of plasmonic particles and structures, thus enabling a new analytical method in the field of SERS and plasmonics.

Comprehensive study of unexpected microscope condensers formed in sample arrangements commonly used in optical microscopy.

PubMed

Desai, Darshan B; Aldawsari, Mabkhoot Mudith S; Alharbi, Bandar Mohammed H; Sen, Sanchari; Grave de Peralta, Luis

2015-09-01

We show that various setups for optical microscopy which are commonly used in biomedical laboratories behave like efficient microscope condensers that are responsible for observed subwavelength resolution. We present a series of experiments and simulations that reveal how inclined illumination from such unexpected condensers occurs when the sample is perpendicularly illuminated by a microscope's built-in white-light source. In addition, we demonstrate an inexpensive add-on optical module that serves as an efficient and lightweight microscope condenser. Using such add-on optical module in combination with a low-numerical-aperture objective lens and Fourier plane imaging microscopy technique, we demonstrate detection of photonic crystals with a period nearly eight times smaller than the Rayleigh resolution limit.

Assessing various Infrared (IR) microscopic imaging techniques for post-mortem interval evaluation of human skeletal remains.

PubMed

Woess, Claudia; Unterberger, Seraphin Hubert; Roider, Clemens; Ritsch-Marte, Monika; Pemberger, Nadin; Cemper-Kiesslich, Jan; Hatzer-Grubwieser, Petra; Parson, Walther; Pallua, Johannes Dominikus

2017-01-01

Due to the influence of many environmental processes, a precise determination of the post-mortem interval (PMI) of skeletal remains is known to be very complicated. Although methods for the investigation of the PMI exist, there still remains much room for improvement. In this study the applicability of infrared (IR) microscopic imaging techniques such as reflection-, ATR- and Raman- microscopic imaging for the estimation of the PMI of human skeletal remains was tested. PMI specific features were identified and visualized by overlaying IR imaging data with morphological tissue structures obtained using light microscopy to differentiate between forensic and archaeological bone samples. ATR and reflection spectra revealed that a more prominent peak at 1042 cm-1 (an indicator for bone mineralization) was observable in archeological bone material when compared with forensic samples. Moreover, in the case of the archaeological bone material, a reduction in the levels of phospholipids, proteins, nucleic acid sugars, complex carbohydrates as well as amorphous or fully hydrated sugars was detectable at (reciprocal wavelengths/energies) between 3000 cm-1 to 2800 cm-1. Raman spectra illustrated a similar picture with less ν2PO43-at 450 cm-1 and ν4PO43- from 590 cm-1 to 584 cm-1, amide III at 1272 cm-1 and protein CH2 deformation at 1446 cm-1 in archeological bone material/samples/sources. A semi-quantitative determination of various distributions of biomolecules by chemi-maps of reflection- and ATR- methods revealed that there were less carbohydrates and complex carbohydrates as well as amorphous or fully hydrated sugars in archaeological samples compared with forensic bone samples. Raman- microscopic imaging data showed a reduction in B-type carbonate and protein α-helices after a PMI of 3 years. The calculated mineral content ratio and the organic to mineral ratio displayed that the mineral content ratio increases, while the organic to mineral ratio decreases with time. Cluster-analyses of data from Raman microscopic imaging reconstructed histo-anatomical features in comparison to the light microscopic image and finally, by application of principal component analyses (PCA), it was possible to see a clear distinction between forensic and archaeological bone samples. Hence, the spectral characterization of inorganic and organic compounds by the afore mentioned techniques, followed by analyses such as multivariate imaging analysis (MIAs) and principal component analyses (PCA), appear to be suitable for the post mortem interval (PMI) estimation of human skeletal remains.

Assessing various Infrared (IR) microscopic imaging techniques for post-mortem interval evaluation of human skeletal remains

PubMed Central

Roider, Clemens; Ritsch-Marte, Monika; Pemberger, Nadin; Cemper-Kiesslich, Jan; Hatzer-Grubwieser, Petra; Parson, Walther; Pallua, Johannes Dominikus

2017-01-01

Due to the influence of many environmental processes, a precise determination of the post-mortem interval (PMI) of skeletal remains is known to be very complicated. Although methods for the investigation of the PMI exist, there still remains much room for improvement. In this study the applicability of infrared (IR) microscopic imaging techniques such as reflection-, ATR- and Raman- microscopic imaging for the estimation of the PMI of human skeletal remains was tested. PMI specific features were identified and visualized by overlaying IR imaging data with morphological tissue structures obtained using light microscopy to differentiate between forensic and archaeological bone samples. ATR and reflection spectra revealed that a more prominent peak at 1042 cm-1 (an indicator for bone mineralization) was observable in archeological bone material when compared with forensic samples. Moreover, in the case of the archaeological bone material, a reduction in the levels of phospholipids, proteins, nucleic acid sugars, complex carbohydrates as well as amorphous or fully hydrated sugars was detectable at (reciprocal wavelengths/energies) between 3000 cm-1 to 2800 cm-1. Raman spectra illustrated a similar picture with less ν2PO43−at 450 cm-1 and ν4PO43− from 590 cm-1 to 584 cm-1, amide III at 1272 cm-1 and protein CH2 deformation at 1446 cm-1 in archeological bone material/samples/sources. A semi-quantitative determination of various distributions of biomolecules by chemi-maps of reflection- and ATR- methods revealed that there were less carbohydrates and complex carbohydrates as well as amorphous or fully hydrated sugars in archaeological samples compared with forensic bone samples. Raman- microscopic imaging data showed a reduction in B-type carbonate and protein α-helices after a PMI of 3 years. The calculated mineral content ratio and the organic to mineral ratio displayed that the mineral content ratio increases, while the organic to mineral ratio decreases with time. Cluster-analyses of data from Raman microscopic imaging reconstructed histo-anatomical features in comparison to the light microscopic image and finally, by application of principal component analyses (PCA), it was possible to see a clear distinction between forensic and archaeological bone samples. Hence, the spectral characterization of inorganic and organic compounds by the afore mentioned techniques, followed by analyses such as multivariate imaging analysis (MIAs) and principal component analyses (PCA), appear to be suitable for the post mortem interval (PMI) estimation of human skeletal remains. PMID:28334006

Physics-based simulation models for EBSD: advances and challenges

NASA Astrophysics Data System (ADS)

Winkelmann, A.; Nolze, G.; Vos, M.; Salvat-Pujol, F.; Werner, W. S. M.

2016-02-01

EBSD has evolved into an effective tool for microstructure investigations in the scanning electron microscope. The purpose of this contribution is to give an overview of various simulation approaches for EBSD Kikuchi patterns and to discuss some of the underlying physical mechanisms.

Fully Scalable Porous Metal Electrospray Propulsion

DTIC Science & Technology

2012-03-20

particular emphasis on the variation of specific impulse for multi-modal propulsion is currently carried out by MIT and the Busek Company under an...Beam profile distributions in the negative (left) and positive (center) modes as visualized directly thorough a multi-channel plate and phosphor...screen. These profiles are parabolic (right) indicating the non-thermal character of these type of ion beams. Microscopic Image of pattern imprinted on Si

Microscopic approach to string gas cosmology

NASA Astrophysics Data System (ADS)

Evnin, Oleg

2014-03-01

In this contribution to the proceedings of the Conference on Modern Physics of Compact Stars and Relativistic Gravity in Yerevan, Armenia (September 18-21, 2013), I review recent work attempting to give a fundamental definition to string evolution in a dynamical, fully compact universe, and present a sketch of how the resulting formalism can be used for addressing questions of phenomenological significance in the field of string gas cosmology.

Microscopic modeling of multi-lane highway traffic flow

NASA Astrophysics Data System (ADS)

Hodas, Nathan O.; Jagota, Anand

2003-12-01

We discuss a microscopic model for the study of multi-lane highway traffic flow dynamics. Each car experiences a force resulting from a combination of the desire of the driver to attain a certain velocity, aerodynamic drag, and change of the force due to car-car interactions. The model also includes multi-lane simulation capability and the ability to add and remove obstructions. We implement the model via a Java applet, which is used to simulate traffic jam formation, the effect of bottlenecks on traffic flow, and the existence of light, medium, and heavy traffic flow. The simulations also provide insight into how the properties of individual cars result in macroscopic behavior. Because the investigation of emergent characteristics is so common in physics, the study of traffic in this manner sheds new light on how the micro-to-macro transition works in general.

GeoLab: A Geological Workstation for Future Missions

NASA Technical Reports Server (NTRS)

Evans, Cynthia; Calaway, Michael; Bell, Mary Sue; Li, Zheng; Tong, Shuo; Zhong, Ye; Dahiwala, Ravi

2014-01-01

The GeoLab glovebox was, until November 2012, fully integrated into NASA's Deep Space Habitat (DSH) Analog Testbed. The conceptual design for GeoLab came from several sources, including current research instruments (Microgravity Science Glovebox) used on the International Space Station, existing Astromaterials Curation Laboratory hardware and clean room procedures, and mission scenarios developed for earlier programs. GeoLab allowed NASA scientists to test science operations related to contained sample examination during simulated exploration missions. The team demonstrated science operations that enhance theThe GeoLab glovebox was, until November 2012, fully integrated into NASA's Deep Space Habitat (DSH) Analog Testbed. The conceptual design for GeoLab came from several sources, including current research instruments (Microgravity Science Glovebox) used on the International Space Station, existing Astromaterials Curation Laboratory hardware and clean room procedures, and mission scenarios developed for earlier programs. GeoLab allowed NASA scientists to test science operations related to contained sample examination during simulated exploration missions. The team demonstrated science operations that enhance the early scientific returns from future missions and ensure that the best samples are selected for Earth return. The facility was also designed to foster the development of instrument technology. Since 2009, when GeoLab design and construction began, the GeoLab team [a group of scientists from the Astromaterials Acquisition and Curation Office within the Astromaterials Research and Exploration Science (ARES) Directorate at JSC] has progressively developed and reconfigured the GeoLab hardware and software interfaces and developed test objectives, which were to 1) determine requirements and strategies for sample handling and prioritization for geological operations on other planetary surfaces, 2) assess the scientific contribution of selective in-situ sample characterization for mission planning, operations, and sample prioritization, 3) evaluate analytical instruments and tools for providing efficient and meaningful data in advance of sample return and 4) identify science operations that leverage human presence with robotic tools. In the first year of tests (2010), GeoLab examined basic glovebox operations performed by one and two crewmembers and science operations performed by a remote science team. The 2010 tests also examined the efficacy of basic sample characterization [descriptions, microscopic imagery, X-ray fluorescence (XRF) analyses] and feedback to the science team. In year 2 (2011), the GeoLab team tested enhanced software and interfaces for the crew and science team (including Web-based and mobile device displays) and demonstrated laboratory configurability with a new diagnostic instrument (the Multispectral Microscopic Imager from the JPL and Arizona State University). In year 3 (2012), the GeoLab team installed and tested a robotic sample manipulator and evaluated robotic-human interfaces for science operations.

Simulating land surface energy fluxes using a microscopic root water uptake approach in a northern temperate forest

NASA Astrophysics Data System (ADS)

He, L.; Ivanov, V. Y.; Schneider, C.

2012-12-01

The predictive accuracy of current land surface models has been limited by uncertainties in modeling transpiration and its sensitivity to the plant-available water in the root zone. Models usually distribute vegetation transpiration demand as sink terms in one-dimensional soil-water accounting model, according to the vertical root density profile. During water-limited situations, the sink terms are constrained using a heuristic "Feddes-type" water stress function. This approach significantly simplifies the actual three-dimensional physical process of root water uptake and may predict an early onset of water-limited transpiration. Recently, a microscopic root water uptake approach was proposed to simulate the three-dimensional radial moisture fluxes from the soil to roots, and water flux transfer processes along the root systems. During dry conditions, this approach permits the compensation of decreased root water uptake in water-stressed regions by increasing uptake density in moister regions. This effect cannot be captured by the Feddes heuristic function. This study "loosely" incorporates the microscopic root water uptake approach based on aRoot model into an ecohydrological model tRIBS+VEGGIE. The ecohydrological model provides boundary conditions for the microscopic root water uptake model (e.g., potential transpiration, soil evaporation, and precipitation influx), and the latter computes the actual transpiration and profiles of sink terms. Based on the departure of the actual latent heat flux from the potential value, the other energy budget components are adjusted. The study is conducted for a northern temperate mixed forest near the University of Michigan Biological Station. Observational evidence for this site suggests little-to-no control of transpiration by soil moisture yet the commonly used Feddes-type approach implies severe water limitation on transpiration during dry episodes. The study addresses two species: oak and aspen. The effects of differences in root architecture on actual transpiration are explored. The energy components simulated with the microscopic modeling approach are tested against observational data. Through the improved spatiotemporal representation of small-scale root water uptake process, the microscopic modeling framework leads to a better agreement with the observational data than the Feddes-type approach. During dry periods, relatively high transpiration is sustained, as water uptake regions shift from densely to sparsely rooted layers, or from drier to moister soil areas. Implications and approaches for incorporating microscopic modeling methodologies within large-scale land-surface parameterizations are discussed.

Efficient coarse simulation of a growing avascular tumor

PubMed Central

Kavousanakis, Michail E.; Liu, Ping; Boudouvis, Andreas G.; Lowengrub, John; Kevrekidis, Ioannis G.

2013-01-01

The subject of this work is the development and implementation of algorithms which accelerate the simulation of early stage tumor growth models. Among the different computational approaches used for the simulation of tumor progression, discrete stochastic models (e.g., cellular automata) have been widely used to describe processes occurring at the cell and subcell scales (e.g., cell-cell interactions and signaling processes). To describe macroscopic characteristics (e.g., morphology) of growing tumors, large numbers of interacting cells must be simulated. However, the high computational demands of stochastic models make the simulation of large-scale systems impractical. Alternatively, continuum models, which can describe behavior at the tumor scale, often rely on phenomenological assumptions in place of rigorous upscaling of microscopic models. This limits their predictive power. In this work, we circumvent the derivation of closed macroscopic equations for the growing cancer cell populations; instead, we construct, based on the so-called “equation-free” framework, a computational superstructure, which wraps around the individual-based cell-level simulator and accelerates the computations required for the study of the long-time behavior of systems involving many interacting cells. The microscopic model, e.g., a cellular automaton, which simulates the evolution of cancer cell populations, is executed for relatively short time intervals, at the end of which coarse-scale information is obtained. These coarse variables evolve on slower time scales than each individual cell in the population, enabling the application of forward projection schemes, which extrapolate their values at later times. This technique is referred to as coarse projective integration. Increasing the ratio of projection times to microscopic simulator execution times enhances the computational savings. Crucial accuracy issues arising for growing tumors with radial symmetry are addressed by applying the coarse projective integration scheme in a cotraveling (cogrowing) frame. As a proof of principle, we demonstrate that the application of this scheme yields highly accurate solutions, while preserving the computational savings of coarse projective integration. PMID:22587128

Global Magnetohydrodynamic Simulation Using High Performance FORTRAN on Parallel Computers

NASA Astrophysics Data System (ADS)

Ogino, T.

High Performance Fortran (HPF) is one of modern and common techniques to achieve high performance parallel computation. We have translated a 3-dimensional magnetohydrodynamic (MHD) simulation code of the Earth's magnetosphere from VPP Fortran to HPF/JA on the Fujitsu VPP5000/56 vector-parallel supercomputer and the MHD code was fully vectorized and fully parallelized in VPP Fortran. The entire performance and capability of the HPF MHD code could be shown to be almost comparable to that of VPP Fortran. A 3-dimensional global MHD simulation of the earth's magnetosphere was performed at a speed of over 400 Gflops with an efficiency of 76.5 VPP5000/56 in vector and parallel computation that permitted comparison with catalog values. We have concluded that fluid and MHD codes that are fully vectorized and fully parallelized in VPP Fortran can be translated with relative ease to HPF/JA, and a code in HPF/JA may be expected to perform comparably to the same code written in VPP Fortran.

Comprehensive modelling and simulation of cylindrical nanoparticles manipulation by using a virtual reality environment.

PubMed

Korayem, Moharam Habibnejad; Hoshiar, Ali Kafash; Ghofrani, Maedeh

2017-08-01

With the expansion of nanotechnology, robots based on atomic force microscope (AFM) have been widely used as effective tools for displacing nanoparticles and constructing nanostructures. One of the most limiting factors in AFM-based manipulation procedures is the inability of simultaneously observing the controlled pushing and displacing of nanoparticles while performing the operation. To deal with this limitation, a virtual reality environment has been used in this paper for observing the manipulation operation. In the simulations performed in this paper, first, the images acquired by the atomic force microscope have been processed and the positions and dimensions of nanoparticles have been determined. Then, by dynamically modelling the transfer of nanoparticles and simulating the critical force-time diagrams, a controlled displacement of nanoparticles has been accomplished. The simulations have been further developed for the use of rectangular, V-shape and dagger-shape cantilevers. The established virtual reality environment has made it possible to simulate the manipulation of biological particles in a liquid medium. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular Dynamic Simulation of Diffusion Coefficients for Alkanols in Supercritical CO2 1

NASA Astrophysics Data System (ADS)

Li, Zhiwei; Lai, Shuhui; Gao, Wei; Chen, Liuping

2018-07-01

The infinite dilution diffusion coefficients ( D 12) of methanol, ethanol, 1-propanol, 1-butanol and 1-pentanol in supercritical CO2 (scCO2) at 313.2 K and 10-16 MPa were simulated by molecular dynamics (MD) simulation. The microscopic structure was also analyzed by calculation of the radial distribution function, coordination number (CN) between the center mass of solute and solvent molecules, and the average number of hydrogen bonding of this system. In infinite dilute solution, the probability of forming hydrogen bond between alkanol molecules is greatly reduced relative to pure alkanol fluid, and the weak hydrogen bonds formed between alkanol and CO2 molecules. In general, this work provides a reliable simulation method for transfer properties of solutes in scCO2. The prediction data were provides for the design and development of chemical processing. The results are helpful for one to deeper understand the relationship between microscopic structures of fluid and its transfer properties.

A constitutive model and numerical simulation of sintering processes at macroscopic level

NASA Astrophysics Data System (ADS)

Wawrzyk, Krzysztof; Kowalczyk, Piotr; Nosewicz, Szymon; Rojek, Jerzy

2018-01-01

This paper presents modelling of both single and double-phase powder sintering processes at the macroscopic level. In particular, its constitutive formulation, numerical implementation and numerical tests are described. The macroscopic constitutive model is based on the assumption that the sintered material is a continuous medium. The parameters of the constitutive model for material under sintering are determined by simulation of sintering at the microscopic level using a micro-scale model. Numerical tests were carried out for a cylindrical specimen under hydrostatic and uniaxial pressure. Results of macroscopic analysis are compared against the microscopic model results. Moreover, numerical simulations are validated by comparison with experimental results. The simulations and preparation of the model are carried out by Abaqus FEA - a software for finite element analysis and computer-aided engineering. A mechanical model is defined by the user procedure "Vumat" which is developed by the first author in Fortran programming language. Modelling presented in the paper can be used to optimize and to better understand the process.

Comparison of semi-automated center-dot and fully automated endothelial cell analyses from specular microscopy images.

PubMed

Maruoka, Sachiko; Nakakura, Shunsuke; Matsuo, Naoko; Yoshitomi, Kayo; Katakami, Chikako; Tabuchi, Hitoshi; Chikama, Taiichiro; Kiuchi, Yoshiaki

2017-10-30

To evaluate two specular microscopy analysis methods across different endothelial cell densities (ECDs). Endothelial images of one eye from each of 45 patients were taken by using three different specular microscopes (three replicates each). To determine the consistency of the center-dot method, we compared SP-6000 and SP-2000P images. CME-530 and SP-6000 images were compared to assess the consistency of the fully automated method. The SP-6000 images from the two methods were compared. Intraclass correlation coefficients (ICCs) for the three measurements were calculated, and parametric multiple comparisons tests and Bland-Altman analysis were performed. The ECD mean value was 2425 ± 883 (range 516-3707) cells/mm 2 . ICC values were > 0.9 for all three microscopes for ECD, but the coefficients of variation (CVs) were 0.3-0.6. For ECD measurements, Bland-Altman analysis revealed that the mean difference was 42 cells/mm 2 between the SP-2000P and SP-6000 for the center-dot method; 57 cells/mm 2 between the SP-6000 measurements from both methods; and -5 cells/mm 2 between the SP-6000 and CME-530 for the fully automated method (95% limits of agreement: - 201 to 284 cell/mm 2 , - 410 to 522 cells/mm 2 , and - 327 to 318 cells/mm 2 , respectively). For CV measurements, the mean differences were - 3, - 12, and 13% (95% limits of agreement - 18 to 11, - 26 to 2, and - 5 to 32%, respectively). Despite using three replicate measurements, the precision of the center-dot method with the SP-2000P and SP-6000 software was only ± 10% for ECD data and was even worse for the fully automated method. Japan Clinical Trials Register ( http://www.umin.ac.jp/ctr/index/htm9 ) number UMIN 000015236.

Quantitative comparison between full-spectrum and filter-based imaging in hyperspectral fluorescence microscopy

PubMed Central

GAO, L.; HAGEN, N.; TKACZYK, T.S.

2012-01-01

Summary We implement a filterless illumination scheme on a hyperspectral fluorescence microscope to achieve full-range spectral imaging. The microscope employs polarisation filtering, spatial filtering and spectral unmixing filtering to replace the role of traditional filters. Quantitative comparisons between full-spectrum and filter-based microscopy are provided in the context of signal dynamic range and accuracy of measured fluorophores’ emission spectra. To show potential applications, a five-colour cell immunofluorescence imaging experiment is theoretically simulated. Simulation results indicate that the use of proposed full-spectrum imaging technique may result in three times improvement in signal dynamic range compared to that can be achieved in the filter-based imaging. PMID:22356127

A Geant4 simulation of the depth dose percentage in brain tumors treatments using protons and carbon ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diaz, José A. M., E-mail: joadiazme@unal.edu.co; Torres, D. A., E-mail: datorresg@unal.edu.co

2016-07-07

The deposited energy and dose distribution of beams of protons and carbon over a head are simulated using the free tool package Geant4 and the data analysis package ROOT-C++. The present work shows a methodology to understand the microscopical process occurring in a session of hadron-therapy using advance simulation tools.

Mueller matrix microscope: a quantitative tool to facilitate detections and fibrosis scorings of liver cirrhosis and cancer tissues.

PubMed

Wang, Ye; He, Honghui; Chang, Jintao; He, Chao; Liu, Shaoxiong; Li, Migao; Zeng, Nan; Wu, Jian; Ma, Hui

2016-07-01

Today the increasing cancer incidence rate is becoming one of the biggest threats to human health.Among all types of cancers, liver cancer ranks in the top five in both frequency and mortality rate all over the world. During the development of liver cancer, fibrosis often evolves as part of a healing process in response to liver damage, resulting in cirrhosis of liver tissues. In a previous study, we applied the Mueller matrix microscope to pathological liver tissue samples and found that both the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters are closely related to the fibrous microstructures. In this paper,we take this one step further to quantitatively facilitate the fibrosis detections and scorings of pathological liver tissue samples in different stages from cirrhosis to cancer using the Mueller matrix microscope. The experimental results of MMPD and MMT parameters for the fibrotic liver tissue samples in different stages are measured and analyzed. We also conduct Monte Carlo simulations based on the sphere birefringence model to examine in detail the influence of structural changes in different fibrosis stages on the imaging parameters. Both the experimental and simulated results indicate that the polarized light microscope and transformed Mueller matrix parameter scan provide additional quantitative information helpful for fibrosis detections and scorings of liver cirrhosis and cancers. Therefore, the polarized light microscope and transformed Mueller matrix parameters have a good application prospect in liver cancer diagnosis.

Mueller matrix microscope: a quantitative tool to facilitate detections and fibrosis scorings of liver cirrhosis and cancer tissues

NASA Astrophysics Data System (ADS)

Wang, Ye; He, Honghui; Chang, Jintao; He, Chao; Liu, Shaoxiong; Li, Migao; Zeng, Nan; Wu, Jian; Ma, Hui

2016-07-01

Today the increasing cancer incidence rate is becoming one of the biggest threats to human health. Among all types of cancers, liver cancer ranks in the top five in both frequency and mortality rate all over the world. During the development of liver cancer, fibrosis often evolves as part of a healing process in response to liver damage, resulting in cirrhosis of liver tissues. In a previous study, we applied the Mueller matrix microscope to pathological liver tissue samples and found that both the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters are closely related to the fibrous microstructures. In this paper, we take this one step further to quantitatively facilitate the fibrosis detections and scorings of pathological liver tissue samples in different stages from cirrhosis to cancer using the Mueller matrix microscope. The experimental results of MMPD and MMT parameters for the fibrotic liver tissue samples in different stages are measured and analyzed. We also conduct Monte Carlo simulations based on the sphere birefringence model to examine in detail the influence of structural changes in different fibrosis stages on the imaging parameters. Both the experimental and simulated results indicate that the polarized light microscope and transformed Mueller matrix parameters can provide additional quantitative information helpful for fibrosis detections and scorings of liver cirrhosis and cancers. Therefore, the polarized light microscope and transformed Mueller matrix parameters have a good application prospect in liver cancer diagnosis.

Laser speckle contrast imaging using light field microscope approach

NASA Astrophysics Data System (ADS)

Ma, Xiaohui; Wang, Anting; Ma, Fenghua; Wang, Zi; Ming, Hai

2018-01-01

In this paper, a laser speckle contrast imaging (LSCI) system using light field (LF) microscope approach is proposed. As far as we known, it is first time to combine LSCI with LF. To verify this idea, a prototype consists of a modified LF microscope imaging system and an experimental device was built. A commercially used Lytro camera was modified for microscope imaging. Hollow glass tubes with different depth fixed in glass dish were used to simulate the vessels in brain and test the performance of the system. Compared with conventional LSCI, three new functions can be realized by using our system, which include refocusing, extending the depth of field (DOF) and gathering 3D information. Experiments show that the principle is feasible and the proposed system works well.

Recent progress in understanding the imaging and metrology using the helium ion microscope

NASA Astrophysics Data System (ADS)

Postek, Michael T.; Vladar, Andras E.; Ming, Bin

2009-05-01

Nanotechnology is pushing imaging and measurement instrument technology to high levels of required performance. As this continues, new barriers confronting innovation in this field are encountered. Particle beam instrument resolution remains one of these barriers. A new tool for imaging and metrology for nanotechnology is the scanning Helium Ion Microscope (HIM). The HIM is a new approach to imaging and metrology for nanotechnology which may be able to push this barrier lower. As a new methodology, it is just beginning to show promise and the number of potentially advantageous applications for nanotechnology and nanometrology has yet to be fully exploited. This presentation will discuss some of the progress made at NIST in collaboration with the manufacturing community in understanding the imaging and metrology for this new technology.

The Width Distribution of Loops and Strands in the Solar Corona—Are We Hitting Rock Bottom?

NASA Astrophysics Data System (ADS)

Aschwanden, Markus J.; Peter, Hardi

2017-05-01

In this study, we analyze Atmospheric Imaging Assembly (AIA) and Hi-C images in order to investigate absolute limits for the finest loop strands. We develop a model of the occurrence-size distribution function of coronal loop widths, characterized by the lower limit of widths w min, the peak (or most frequent) width w p , the peak occurrence number n p , and a power-law slope a. Our data analysis includes automated tracing of curvilinear features with the OCCULT-2 code, automated sampling of the cross-sectional widths of coronal loops, and fitting of the theoretical size distribution to the observed distribution. With Monte Carlo simulations and variable pixel sizes {{Δ }}x, we derive a first diagnostic criterion to discriminate whether the loop widths are unresolved ({w}p/{{Δ }}x≈ 2.5+/- 0.2) or fully resolved (if {w}p/{{Δ }}x≳ 2.7). For images with resolved loop widths, we can apply a second diagnostic criterion that predicts the lower limit of loop widths as a function of the spatial resolution. We find that the loop widths are marginally resolved in AIA images but are fully resolved in Hi-C images, where our model predicts a most frequent (peak) value at {w}p≈ 550 {km}, in agreement with recent results of Brooks et al. This result agrees with the statistics of photospheric granulation sizes and thus supports coronal heating mechanisms operating on the macroscopic scale of photospheric magneto-convection, rather than nanoflare braiding models on unresolved microscopic scales.

Down to the roughness scale assessment of piston-ring/liner contacts

NASA Astrophysics Data System (ADS)

Checo, H. M.; Jaramillo, A.; Ausas, R. F.; Jai, M.; Buscaglia, G. C.

2017-02-01

The effects of surface roughness in hydrodynamic bearings been accounted for through several approaches, the most widely used being averaging or stochastic techniques. With these the surface is not treated “as it is”, but by means of an assumed probability distribution for the roughness. The so called direct, deterministic or measured-surface simulation) solve the lubrication problem with realistic surfaces down to the roughness scale. This leads to expensive computational problems. Most researchers have tackled this problem considering non-moving surfaces and neglecting the ring dynamics to reduce the computational burden. What is proposed here is to solve the fully-deterministic simulation both in space and in time, so that the actual movement of the surfaces and the rings dynamics are taken into account. This simulation is much more complex than previous ones, as it is intrinsically transient. The feasibility of these fully-deterministic simulations is illustrated two cases: fully deterministic simulation of liner surfaces with diverse finishings (honed and coated bores) with constant piston velocity and load on the ring and also in real engine conditions.

Modulus design multiwavelength polarization microscope for transmission Mueller matrix imaging

NASA Astrophysics Data System (ADS)

Zhou, Jialing; He, Honghui; Chen, Zhenhua; Wang, Ye; Ma, Hui

2018-01-01

We have developed a polarization microscope based on a commercial transmission microscope. We replace the halogen light source by a collimated LED light source module of six different colors. We use achromatic polarized optical elements that can cover the six different wavelength ranges in the polarization state generator (PSG) and polarization state analyzer (PSA) modules. The dual-rotating wave plate method is used to measure the Mueller matrix of samples, which requires the simultaneous rotation of the two quarter-wave plates in both PSG and PSA at certain angular steps. A scientific CCD detector is used as the image receiving module. A LabView-based software is developed to control the rotation angels of the wave plates and the exposure time of the detector to allow the system to run fully automatically in preprogrammed schedules. Standard samples, such as air, polarizers, and quarter-wave plates, are used to calibrate the intrinsic Mueller matrix of optical components, such as the objectives, using the eigenvalue calibration method. Errors due to the images walk-off in the PSA are studied. Errors in the Mueller matrices are below 0.01 using air and polarizer as standard samples. Data analysis based on Mueller matrix transformation and Mueller matrix polarization decomposition is used to demonstrate the potential application of this microscope in pathological diagnosis.

Application of Environmental Scanning Electron Microscope-Nanomanipulation System on Spheroplast Yeast Cells Surface Observation.

PubMed

Rad, Maryam Alsadat; Ahmad, Mohd Ridzuan; Nakajima, Masahiro; Kojima, Seiji; Homma, Michio; Fukuda, Toshio

2017-01-01

The preparation and observations of spheroplast W303 cells are described with Environmental Scanning Electron Microscope (ESEM). The spheroplasting conversion was successfully confirmed qualitatively, by the evaluation of the morphological change between the normal W303 cells and the spheroplast W303 cells, and quantitatively, by determining the spheroplast conversion percentage based on the OD 800 absorbance data. From the optical microscope observations as expected, the normal cells had an oval shape whereas spheroplast cells resemble a spherical shape. This was also confirmed under four different mediums, that is, yeast peptone-dextrose (YPD), sterile water, sorbitol-EDTA-sodium citrate buffer (SCE), and sorbitol-Tris-Hcl-CaCl 2 (CaS). It was also observed that the SCE and CaS mediums had a higher number of spheroplast cells as compared to the YPD and sterile water mediums. The OD 800 absorbance data also showed that the whole W303 cells were fully converted to the spheroplast cells after about 15 minutes. The observations of the normal and the spheroplast W303 cells were then performed under an environmental scanning electron microscope (ESEM). The normal cells showed a smooth cell surface whereas the spheroplast cells had a bleb-like surface after the loss of its integrity when removing the cell wall.

Noise induced chaos in optically driven colloidal rings.

NASA Astrophysics Data System (ADS)

Roichman, Yael; Zaslavsky, George; Grier, David G.

2007-03-01

Given a constant flux of energy, many driven dissipative systems rapidly organize themselves into configurations that support steady state motion. Examples include swarming of bacterial colonies, convection in shaken sandpiles, and synchronization in flowing traffic. How simple objects interacting in simple ways self-organize generally is not understood, mainly because so few of the available experimental systems afford the necessary access to their microscopic degrees of freedom. This talk introduces a new class of model driven dissipative systems typified by three colloidal spheres circulating around a ring-like optical trap known as an optical vortex. By controlling the interplay between hydrodynamic interactions and fixed disorder we are able to drive a transition from a previously predicted periodic steady state to fully developed chaos. In addition, by tracking both microscopic trajectories and macroscopic collective fluctuations the relation between the onset of microscopic weak chaos and the evolution of space-time self-similarity in macroscopic transport properties is revealed. In a broader scope, several optical vortices can be coupled to create a large dissipative system where each building block has internal degrees of freedom. In such systems the little understood dynamics of processes like frustration and jamming, fluctuation-dissipation relations and the propagation of collective motion can be tracked microscopically.

Microscopic insights into the NMR relaxation based protein conformational entropy meter

PubMed Central

Kasinath, Vignesh; Sharp, Kim A.; Wand, A. Joshua

2013-01-01

Conformational entropy is a potentially important thermodynamic parameter contributing to protein function. Quantitative measures of conformational entropy are necessary for an understanding of its role but have been difficult to obtain. An empirical method that utilizes changes in conformational dynamics as a proxy for changes in conformational entropy has recently been introduced. Here we probe the microscopic origins of the link between conformational dynamics and conformational entropy using molecular dynamics simulations. Simulation of seven pro! teins gave an excellent correlation with measures of side-chain motion derived from NMR relaxation. The simulations show that the motion of methyl-bearing side-chains are sufficiently coupled to that of other side chains to serve as excellent reporters of the overall side-chain conformational entropy. These results tend to validate the use of experimentally accessible measures of methyl motion - the NMR-derived generalized order parameters - as a proxy from which to derive changes in protein conformational entropy. PMID:24007504

Ultrastructural localization of hair keratins, high sulfur keratin-associated proteins and sulfhydryl oxidase in the human hair.

PubMed

Alibardi, Lorenzo

2017-03-01

Hardening of the human hair shaft during cornification results from the bonding of keratins and keratin-associated proteins. In situ hybridization and light immunocytochemical studies have shown the general distribution of different keratins and some associated proteins but not determined their ultrastructural localization. I report here the localization of hair keratins, two high-sulfur keratin-associated proteins and sulfhydryl oxidase has been studied under the transmission electron microscope in the cornification zone of the human hair. The ultrastructural study on keratin distribution in general confirms previous light microscopic studies. Sulfur-rich KAP1 is mainly cortical but the labeling disappears in fully cornified cortical cells while a diffuse labeling is also present in differentiating cuticle cells. Sulfur-rich K26 immunolocalization is only detected in the exocuticle and endocuticle. Sparse labeling for sulfhydryl oxidase occurs in differentiating cortical cells but is weak and uneven in cuticle cells and absent in medulla and inner root sheath. Labeling disappears in the upper fully cornified cortex and cuticle. The observations indicate that sulfhydryl oxidase and keratin associated proteins are initially produced in the cytoplasm among keratin bundles accumulating in cortical and cuticle cells but these proteins undergo changes during the following cornification that alter the epitopes tagged by the antibodies.

18/20 T high magnetic field scanning tunneling microscope with fully low voltage operability, high current resolution, and large scale searching ability.

PubMed

Li, Quanfeng; Wang, Qi; Hou, Yubin; Lu, Qingyou

2012-04-01

We present a home-built 18/20 T high magnetic field scanning tunneling microscope (STM) featuring fully low voltage (lower than ±15 V) operability in low temperatures, large scale searching ability, and 20 fA high current resolution (measured by using a 100 GOhm dummy resistor to replace the tip-sample junction) with a bandwidth of 3.03 kHz. To accomplish low voltage operation which is important in achieving high precision, low noise, and low interference with the strong magnetic field, the coarse approach is implemented with an inertial slider driven by the lateral bending of a piezoelectric scanner tube (PST) whose inner electrode is axially split into two for enhanced bending per volt. The PST can also drive the same sliding piece to inertial slide in the other bending direction (along the sample surface) of the PST, which realizes the large area searching ability. The STM head is housed in a three segment tubular chamber, which is detachable near the STM head for the convenience of sample and tip changes. Atomic resolution images of a graphite sample taken under 17.6 T and 18.0001 T are presented to show its performance. © 2012 American Institute of Physics

Multiscale pore structure and its effect on gas transport in organic-rich shale

NASA Astrophysics Data System (ADS)

Wu, Tianhao; Li, Xiang; Zhao, Junliang; Zhang, Dongxiao

2017-07-01

A systematic investigation of multiscale pore structure in organic-rich shale by means of the combination of various imaging techniques is presented, including the state-of-the-art Helium-Ion-Microscope (HIM). The study achieves insight into the major features at each scale and suggests the affordable techniques for specific objectives from the aspects of resolution, dimension, and cost. The pores, which appear to be isolated, are connected by smaller pores resolved by higher-resolution imaging. This observation provides valuable information, from the microscopic perspective of pore structure, for understanding how gas accumulates and transports from where it is generated. A comprehensive workflow is proposed based on the characteristics acquired from the multiscale pore structure analysis to simulate the gas transport process. The simulations are completed with three levels: the microscopic mechanisms should be taken into consideration at level I; the spatial distribution features of organic matter, inorganic matter, and macropores constitute the major issue at level II; and the microfracture orientation and topological structure are dominant factors at level III. The results of apparent permeability from simulations agree well with the values acquired from experiments. By means of the workflow, the impact of various gas transport mechanisms at different scales can be investigated more individually and precisely than conventional experiments.

Methodology of modeling and measuring computer architectures for plasma simulations

NASA Technical Reports Server (NTRS)

Wang, L. P. T.

1977-01-01

A brief introduction to plasma simulation using computers and the difficulties on currently available computers is given. Through the use of an analyzing and measuring methodology - SARA, the control flow and data flow of a particle simulation model REM2-1/2D are exemplified. After recursive refinements the total execution time may be greatly shortened and a fully parallel data flow can be obtained. From this data flow, a matched computer architecture or organization could be configured to achieve the computation bound of an application problem. A sequential type simulation model, an array/pipeline type simulation model, and a fully parallel simulation model of a code REM2-1/2D are proposed and analyzed. This methodology can be applied to other application problems which have implicitly parallel nature.

Impact of gastric acidic challenge on surface topography and optical properties of monolithic zirconia.

PubMed

Sulaiman, Taiseer A; Abdulmajeed, Aous A; Shahramian, Khalil; Hupa, Leena; Donovan, Terrence E; Vallittu, Pekka; Närhi, Timo O

2015-12-01

To evaluate the surface topography and optical properties of monolithic zirconia after immersion in simulated gastric acid. Four partially stabilized (PSZ) and one fully stabilized (FSZ) zirconia materials were selected for the study: Prettau (PRT, Zirkonzahn), Zenostar (ZEN, Ivoclar), Bruxzir (BRX, Glidewell), Katana (KAT, Noritake) and FSZ Prettau Anterior (PRTA, Zirkonzahn). IPS e.max (Ivoclar) was used as a control. The specimens (10×10×1.2mm, n=5 per material) were cut, sintered, polished and cleaned before immersed in 5ml of simulated gastric acid solution (Hydrochloric acid (HCl) 0.06M, 0.113% solution in deionized distal water, pH 1.2) for 96h in a 37°C incubator. Specimens were weighed and examined for morphological changes under scanning electron microscope (SEM) coupled with energy dispersive X-ray spectroscopy (EDX). Surface roughness was evaluated by a confocal microscope. Surface gloss and translucency parameter (TP) values were determined by a reflection spectrophotometer before and after acid immersion. The data was analyzed by one-way ANOVA followed by Tukey's HSD post hoc test (p<0.05). PRTA displayed the most weight loss (1.40%) among the zirconia specimens. IPS e.max showed about three times more weight loss (3.05%) than zirconia specimens as an average. SEM examination indicated areas of degradation, bead-like shapes and smoothening of the polishing scratches after acid immersion. EDX displayed ion interactions and possible ion leaching from all specimens. Sa and Sq values for PRTA, ZEN and IPS e.max were significantly lower (p<0.05) after acid immersion. TP values increased significantly for PRT, ZEN and IPS e.max (p<0.05), while the surface gloss of ZEN, PRTA and IPS e.max increased (p<0.05). Monolithic zirconia materials show some surface alterations in an acidic environment with minimum effect on their optical properties. Whether a smoother surface is in fact a sign of true corrosion resistance or is purely the result of an evenly progressive corrosive process is yet to be confirmed by further research. Copyright © 2015 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

How a Fully Automated eHealth Program Simulates Three Therapeutic Processes: A Case Study.

PubMed

Holter, Marianne T S; Johansen, Ayna; Brendryen, Håvar

2016-06-28

eHealth programs may be better understood by breaking down the components of one particular program and discussing its potential for interactivity and tailoring in regard to concepts from face-to-face counseling. In the search for the efficacious elements within eHealth programs, it is important to understand how a program using lapse management may simultaneously support working alliance, internalization of motivation, and behavior maintenance. These processes have been applied to fully automated eHealth programs individually. However, given their significance in face-to-face counseling, it may be important to simulate the processes simultaneously in interactive, tailored programs. We propose a theoretical model for how fully automated behavior change eHealth programs may be more effective by simulating a therapist's support of a working alliance, internalization of motivation, and managing lapses. We show how the model is derived from theory and its application to Endre, a fully automated smoking cessation program that engages the user in several "counseling sessions" about quitting. A descriptive case study based on tools from the intervention mapping protocol shows how each therapeutic process is simulated. The program supports the user's working alliance through alliance factors, the nonembodied relational agent Endre and computerized motivational interviewing. Computerized motivational interviewing also supports internalized motivation to quit, whereas a lapse management component responds to lapses. The description operationalizes working alliance, internalization of motivation, and managing lapses, in terms of eHealth support of smoking cessation. A program may simulate working alliance, internalization of motivation, and lapse management through interactivity and individual tailoring, potentially making fully automated eHealth behavior change programs more effective.

How a Fully Automated eHealth Program Simulates Three Therapeutic Processes: A Case Study

PubMed Central

Johansen, Ayna; Brendryen, Håvar

2016-01-01

Background eHealth programs may be better understood by breaking down the components of one particular program and discussing its potential for interactivity and tailoring in regard to concepts from face-to-face counseling. In the search for the efficacious elements within eHealth programs, it is important to understand how a program using lapse management may simultaneously support working alliance, internalization of motivation, and behavior maintenance. These processes have been applied to fully automated eHealth programs individually. However, given their significance in face-to-face counseling, it may be important to simulate the processes simultaneously in interactive, tailored programs. Objective We propose a theoretical model for how fully automated behavior change eHealth programs may be more effective by simulating a therapist’s support of a working alliance, internalization of motivation, and managing lapses. Methods We show how the model is derived from theory and its application to Endre, a fully automated smoking cessation program that engages the user in several “counseling sessions” about quitting. A descriptive case study based on tools from the intervention mapping protocol shows how each therapeutic process is simulated. Results The program supports the user’s working alliance through alliance factors, the nonembodied relational agent Endre and computerized motivational interviewing. Computerized motivational interviewing also supports internalized motivation to quit, whereas a lapse management component responds to lapses. The description operationalizes working alliance, internalization of motivation, and managing lapses, in terms of eHealth support of smoking cessation. Conclusions A program may simulate working alliance, internalization of motivation, and lapse management through interactivity and individual tailoring, potentially making fully automated eHealth behavior change programs more effective. PMID:27354373

A frameless stereotaxic operating microscope for neurosurgery.

PubMed

Friets, E M; Strohbehn, J W; Hatch, J F; Roberts, D W

1989-06-01

A new system, which we call the frameless stereotaxic operating microscope, is discussed. Its purpose is to display CT or other image data in the operating microscope in the correct scale, orientation, and position without the use of a stereotaxic frame. A nonimaging ultrasonic rangefinder allows the position of the operating microscope and the position of the patient to be determined. Discrete fiducial points on the patient's external anatomy are located in both image space and operating room space, linking the image data and the operating room. Physician-selected image information, e.g., tumor contours or guidance to predetermined targets, is projected through the optics of the operating microscope using a miniature cathode ray tube and a beam splitter. Projected images superpose the surgical field, reconstructed from image data to match the focal plane of the operating microscope. The algorithms on which the system is based are described, and the sources and effects of errors are discussed. The system's performance is simulated, providing an estimate of accuracy. Two phantoms are used to measure accuracy experimentally. Clinical results and observations are given.

Optimal resolution in Fresnel incoherent correlation holographic fluorescence microscopy

PubMed Central

Brooker, Gary; Siegel, Nisan; Wang, Victor; Rosen, Joseph

2011-01-01

Fresnel Incoherent Correlation Holography (FINCH) enables holograms and 3D images to be created from incoherent light with just a camera and spatial light modulator (SLM). We previously described its application to microscopic incoherent fluorescence wherein one complex hologram contains all the 3D information in the microscope field, obviating the need for scanning or serial sectioning. We now report experiments which have led to the optimal optical, electro-optic, and computational conditions necessary to produce holograms which yield high quality 3D images from fluorescent microscopic specimens. An important improvement from our previous FINCH configurations capitalizes on the polarization sensitivity of the SLM so that the same SLM pixels which create the spherical wave simulating the microscope tube lens, also pass the plane waves from the infinity corrected microscope objective, so that interference between the two wave types at the camera creates a hologram. This advance dramatically improves the resolution of the FINCH system. Results from imaging a fluorescent USAF pattern and a pollen grain slide reveal resolution which approaches the Rayleigh limit by this simple method for 3D fluorescent microscopic imaging. PMID:21445140

Advanced EUV mask and imaging modeling

NASA Astrophysics Data System (ADS)

Evanschitzky, Peter; Erdmann, Andreas

2017-10-01

The exploration and optimization of image formation in partially coherent EUV projection systems with complex source shapes requires flexible, accurate, and efficient simulation models. This paper reviews advanced mask diffraction and imaging models for the highly accurate and fast simulation of EUV lithography systems, addressing important aspects of the current technical developments. The simulation of light diffraction from the mask employs an extended rigorous coupled wave analysis (RCWA) approach, which is optimized for EUV applications. In order to be able to deal with current EUV simulation requirements, several additional models are included in the extended RCWA approach: a field decomposition and a field stitching technique enable the simulation of larger complex structured mask areas. An EUV multilayer defect model including a database approach makes the fast and fully rigorous defect simulation and defect repair simulation possible. A hybrid mask simulation approach combining real and ideal mask parts allows the detailed investigation of the origin of different mask 3-D effects. The image computation is done with a fully vectorial Abbe-based approach. Arbitrary illumination and polarization schemes and adapted rigorous mask simulations guarantee a high accuracy. A fully vectorial sampling-free description of the pupil with Zernikes and Jones pupils and an optimized representation of the diffraction spectrum enable the computation of high-resolution images with high accuracy and short simulation times. A new pellicle model supports the simulation of arbitrary membrane stacks, pellicle distortions, and particles/defects on top of the pellicle. Finally, an extension for highly accurate anamorphic imaging simulations is included. The application of the models is demonstrated by typical use cases.

Invited review article: Advanced light microscopy for biological space research.

PubMed

De Vos, Winnok H; Beghuin, Didier; Schwarz, Christian J; Jones, David B; van Loon, Jack J W A; Bereiter-Hahn, Juergen; Stelzer, Ernst H K

2014-10-01

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

High energy proton induced radiation damage of rare earth permanent magnet quadrupoles

NASA Astrophysics Data System (ADS)

Schanz, M.; Endres, M.; Löwe, K.; Lienig, T.; Deppert, O.; Lang, P. M.; Varentsov, D.; Hoffmann, D. H. H.; Gutfleisch, O.

2017-12-01

Permanent magnet quadrupoles (PMQs) are an alternative to common electromagnetic quadrupoles especially for fixed rigidity beam transport scenarios at particle accelerators. Using those magnets for experimental setups can result in certain scenarios, in which a PMQ itself may be exposed to a large amount of primary and secondary particles with a broad energy spectrum, interacting with the magnetic material and affecting its magnetic properties. One specific scenario is proton microscopy, where a proton beam traverses an object and a collimator in which a part of the beam is scattered and deflected into PMQs used as part of a diagnostic system. During the commissioning of the PRIOR (Proton Microscope for Facility for Antiproton and Ion Research) high energy proton microscope facility prototype at Gesellschaft für Schwerionenforschung in 2014, a significant reduction of the image quality was observed which was partially attributed to the demagnetization of the used PMQ lenses and the corresponding decrease of the field quality. In order to study this phenomenon, Monte Carlo simulations were carried out and spare units manufactured from the same magnetic material—single wedges and a fully assembled PMQ module—were deliberately irradiated by a 3.6 GeV intense proton beam. The performed investigations have shown that in proton radiography applications the above described scattering may result in a high irradiation dose in the PMQ magnets. This did not only decrease the overall magnetic strength of the PMQs but also caused a significant degradation of the field quality of an assembled PMQ module by increasing the parasitic multipole field harmonics which effectively makes PMQs impractical for proton radiography applications or similar scenarios.

High energy proton induced radiation damage of rare earth permanent magnet quadrupoles.

PubMed

Schanz, M; Endres, M; Löwe, K; Lienig, T; Deppert, O; Lang, P M; Varentsov, D; Hoffmann, D H H; Gutfleisch, O

2017-12-01

Permanent magnet quadrupoles (PMQs) are an alternative to common electromagnetic quadrupoles especially for fixed rigidity beam transport scenarios at particle accelerators. Using those magnets for experimental setups can result in certain scenarios, in which a PMQ itself may be exposed to a large amount of primary and secondary particles with a broad energy spectrum, interacting with the magnetic material and affecting its magnetic properties. One specific scenario is proton microscopy, where a proton beam traverses an object and a collimator in which a part of the beam is scattered and deflected into PMQs used as part of a diagnostic system. During the commissioning of the PRIOR (Proton Microscope for Facility for Antiproton and Ion Research) high energy proton microscope facility prototype at Gesellschaft für Schwerionenforschung in 2014, a significant reduction of the image quality was observed which was partially attributed to the demagnetization of the used PMQ lenses and the corresponding decrease of the field quality. In order to study this phenomenon, Monte Carlo simulations were carried out and spare units manufactured from the same magnetic material-single wedges and a fully assembled PMQ module-were deliberately irradiated by a 3.6 GeV intense proton beam. The performed investigations have shown that in proton radiography applications the above described scattering may result in a high irradiation dose in the PMQ magnets. This did not only decrease the overall magnetic strength of the PMQs but also caused a significant degradation of the field quality of an assembled PMQ module by increasing the parasitic multipole field harmonics which effectively makes PMQs impractical for proton radiography applications or similar scenarios.

Invited Review Article: Advanced light microscopy for biological space research

NASA Astrophysics Data System (ADS)

De Vos, Winnok H.; Beghuin, Didier; Schwarz, Christian J.; Jones, David B.; van Loon, Jack J. W. A.; Bereiter-Hahn, Juergen; Stelzer, Ernst H. K.

2014-10-01

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

Implicit unified gas-kinetic scheme for steady state solutions in all flow regimes

NASA Astrophysics Data System (ADS)

Zhu, Yajun; Zhong, Chengwen; Xu, Kun

2016-06-01

This paper presents an implicit unified gas-kinetic scheme (UGKS) for non-equilibrium steady state flow computation. The UGKS is a direct modeling method for flow simulation in all regimes with the updates of both macroscopic flow variables and microscopic gas distribution function. By solving the macroscopic equations implicitly, a predicted equilibrium state can be obtained first through iterations. With the newly predicted equilibrium state, the evolution equation of the gas distribution function and the corresponding collision term can be discretized in a fully implicit way for fast convergence through iterations as well. The lower-upper symmetric Gauss-Seidel (LU-SGS) factorization method is implemented to solve both macroscopic and microscopic equations, which improves the efficiency of the scheme. Since the UGKS is a direct modeling method and its physical solution depends on the mesh resolution and the local time step, a physical time step needs to be fixed before using an implicit iterative technique with a pseudo-time marching step. Therefore, the physical time step in the current implicit scheme is determined by the same way as that in the explicit UGKS for capturing the physical solution in all flow regimes, but the convergence to a steady state speeds up through the adoption of a numerical time step with large CFL number. Many numerical test cases in different flow regimes from low speed to hypersonic ones, such as the Couette flow, cavity flow, and the flow passing over a cylinder, are computed to validate the current implicit method. The overall efficiency of the implicit UGKS can be improved by one or two orders of magnitude in comparison with the explicit one.

Attenuation of sonic waves in water-saturated alluvial sediments due to wave-induced fluid flow at microscopic, mesoscopic and macroscopic scales

NASA Astrophysics Data System (ADS)

Milani, Marco; Rubino, J. Germán; Baron, Ludovic; Sidler, Rolf; Holliger, Klaus

2015-10-01

The attenuation and velocity dispersion of sonic waves contain valuable information on the mechanical and hydraulic properties of the probed medium. An inherent complication arising in the interpretation of corresponding measurements is, however, that there are multiple physical mechanisms contributing to the energy dissipation and that the relative importance of the various contributions is difficult to unravel. To address this problem for the practically relevant case of terrestrial alluvial sediments, we analyse the attenuation and velocity dispersion characteristics of broad-band multifrequency sonic logs with dominant source frequencies ranging between 1 and 30 kHz. To adequately compensate for the effects of geometrical spreading, which is critical for reliable attenuation estimates, we simulate our experimental setup using a correspondingly targeted numerical solution of the poroelastic equations. After having applied the thus inferred corrections, the broad-band sonic log data set, in conjunction with a comprehensive suite of complementary logging data, allows for assessing the relative importance of a range of pertinent attenuation mechanisms. In doing so, we focus on the effects of wave-induced fluid flow over a wide range of scales. Our results indicate that the levels of attenuation due to the presence of mesoscopic heterogeneities in unconsolidated clastic sediments fully saturated with water are expected to be largely negligible. Conversely, Monte-Carlo-type inversions indicate that Biot's classical model permits to explain most of the considered data. Refinements with regard to the fitting of the observed attenuation and velocity dispersion characteristics are locally provided by accounting for energy dissipation at the microscopic scale, although the nature of the underlying physical mechanism remains speculative.

Measurement with microscopic MRI and simulation of flow in different aneurysm models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edelhoff, Daniel, E-mail: daniel.edelhoff@tu-dortmund.de; Frank, Frauke; Heil, Marvin

2015-10-15

Purpose: The impact and the development of aneurysms depend to a significant degree on the exchange of liquid between the regular vessel and the pathological extension. A better understanding of this process will lead to improved prediction capabilities. The aim of the current study was to investigate fluid-exchange in aneurysm models of different complexities by combining microscopic magnetic resonance measurements with numerical simulations. In order to evaluate the accuracy and applicability of these methods, the fluid-exchange process between the unaltered vessel lumen and the aneurysm phantoms was analyzed quantitatively using high spatial resolution. Methods: Magnetic resonance flow imaging was usedmore » to visualize fluid-exchange in two different models produced with a 3D printer. One model of an aneurysm was based on histological findings. The flow distribution in the different models was measured on a microscopic scale using time of flight magnetic resonance imaging. The whole experiment was simulated using fast graphics processing unit-based numerical simulations. The obtained simulation results were compared qualitatively and quantitatively with the magnetic resonance imaging measurements, taking into account flow and spin–lattice relaxation. Results: The results of both presented methods compared well for the used aneurysm models and the chosen flow distributions. The results from the fluid-exchange analysis showed comparable characteristics concerning measurement and simulation. Similar symmetry behavior was observed. Based on these results, the amount of fluid-exchange was calculated. Depending on the geometry of the models, 7% to 45% of the liquid was exchanged per second. Conclusions: The result of the numerical simulations coincides well with the experimentally determined velocity field. The rate of fluid-exchange between vessel and aneurysm was well-predicted. Hence, the results obtained by simulation could be validated by the experiment. The observed deviations can be caused by the noise in the measurement and by the limited resolution of the simulation. The resulting differences are small enough to allow reliable predictions of the flow distribution in vessels with stents and for pulsed blood flow.« less

A new route for the synthesis of submicron-sized LaB{sub 6}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lihong, Bao; Wurentuya,; Wei, Wei

Submicron crystalline LaB{sub 6} has been successfully synthesized by a solid-state reaction of La{sub 2}O{sub 3} with NaBH{sub 4} at 1200 °C. The effects of reaction temperature on the crystal structure, grain size and morphology were investigated by X-ray diffraction, scanning electron microscope and transmission electron microscope. It is found that when the reaction temperature is in the range of 1000–1100 °C, there are ultrafine nanoparticles and nanocrystals that coexist. When the reaction temperature elevated to 1200 °C, the grain morphology transformed from ultrafine nanoparticle to submicron crystals completely. High resolution transmission electron microscope images fully confirm the formation ofmore » LaB{sub 6} cubic structure. - Highlights: • Single-phased LaB{sub 6} have been synthesized by a solid-state reaction in a continuous evacuating process. • The reaction temperature has a important effect on the phase composition. • The grain size increase from nano-size to submicron with increasing reaction temperature.« less

Dynamics of basaltic glass dissolution - Capturing microscopic effects in continuum scale models

NASA Astrophysics Data System (ADS)

Aradóttir, E. S. P.; Sigfússon, B.; Sonnenthal, E. L.; Björnsson, G.; Jónsson, H.

2013-11-01

The method of 'multiple interacting continua' (MINC) was applied to include microscopic rate-limiting processes in continuum scale reactive transport models of basaltic glass dissolution. The MINC method involves dividing the system up to ambient fluid and grains, using a specific surface area to describe the interface between the two. The various grains and regions within grains can then be described by dividing them into continua separated by dividing surfaces. Millions of grains can thus be considered within the method without the need to explicity discretizing them. Four continua were used for describing a dissolving basaltic glass grain; the first one describes the ambient fluid around the grain, while the second, third and fourth continuum refer to a diffusive leached layer, the dissolving part of the grain and the inert part of the grain, respectively. The model was validated using the TOUGHREACT simulator and data from column flow through experiments of basaltic glass dissolution at low, neutral and high pH values. Successful reactive transport simulations of the experiments and overall adequate agreement between measured and simulated values provides validation that the MINC approach can be applied for incorporating microscopic effects in continuum scale basaltic glass dissolution models. Equivalent models can be used when simulating dissolution and alteration of other minerals. The study provides an example of how numerical modeling and experimental work can be combined to enhance understanding of mechanisms associated with basaltic glass dissolution. Column outlet concentrations indicated basaltic glass to dissolve stoichiometrically at pH 3. Predictive simulations with the developed MINC model indicated significant precipitation of secondary minerals within the column at neutral and high pH, explaining observed non-stoichiometric outlet concentrations at these pH levels. Clay, zeolite and hydroxide precipitation was predicted to be most abundant within the column.

A study on high NA and evanescent imaging with polarized illumination

NASA Astrophysics Data System (ADS)

Yang, Seung-Hune

Simulation techniques are developed for high NA polarized microscopy with Babinet's principle, partial coherence and vector diffraction for non-periodic geometries. A mathematical model for the Babinet approach is developed and interpreted. Simulation results of the Babinet's principle approach are compared with those of Rigorous Coupled Wave Theory (RCWT) for periodic structures to investigate the accuracy of this approach and its limitations. A microscope system using a special solid immersion lens (SIL) is introduced to image Blu-Ray (BD) optical disc samples without removing the protective cover layer. Aberration caused by the cover layer is minimized with a truncated SIL. Sub-surface imaging simulation is achieved by RCWT, partial coherence, vector diffraction and Babinet's Principle. Simulated results are compared with experimental images and atomic force microscopy (AFM) measurement. A technique for obtaining native and induced using a significant amount of evanescent energy is described for a solid immersion lens (SIL) microscope. Characteristics of native and induced polarization images for different object structures and materials are studied in detail. Experiments are conducted with a NA = 1.48 at lambda = 550nm microscope. Near-field images are simulated and analyzed with an RCWT approach. Contrast curve versus object spatial frequency calculations are compared with experimental measurements. Dependencies of contrast versus source polarization angles and air gap for native and induced polarization image profiles are evaluated. By using the relationship between induced polarization and topographical structure, an induced polarization image of an alternating phase shift mask (PSM) is converted into a topographical image, which shows very good agreement with AFM measurement. Images of other material structures include a dielectric grating, chrome-on-glass grating, silicon CPU structure, BD-R and BD-ROM.

MAGNETIC CYCLES IN A DYNAMO SIMULATION OF FULLY CONVECTIVE M-STAR PROXIMA CENTAURI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yadav, Rakesh K.; Wolk, Scott J.; Christensen, Ulrich R.

2016-12-20

The recent discovery of an Earth-like exoplanet around Proxima Centauri has shined a spot light on slowly rotating fully convective M-stars. When such stars rotate rapidly (period ≲20 days), they are known to generate very high levels of activity that is powered by a magnetic field much stronger than the solar magnetic field. Recent theoretical efforts are beginning to understand the dynamo process that generates such strong magnetic fields. However, the observational and theoretical landscape remains relatively uncharted for fully convective M-stars that rotate slowly. Here, we present an anelastic dynamo simulation designed to mimic some of the physical characteristicsmore » of Proxima Centauri, a representative case for slowly rotating fully convective M-stars. The rotating convection spontaneously generates differential rotation in the convection zone that drives coherent magnetic cycles where the axisymmetric magnetic field repeatedly changes polarity at all latitudes as time progress. The typical length of the “activity” cycle in the simulation is about nine years, in good agreement with the recently proposed activity cycle length of about seven years for Proxima Centauri. Comparing our results with earlier work, we hypothesis that the dynamo mechanism undergoes a fundamental change in nature as fully convective stars spin down with age.« less

3D geometric phase analysis and its application in 3D microscopic morphology measurement

NASA Astrophysics Data System (ADS)

Zhu, Ronghua; Shi, Wenxiong; Cao, Quankun; Liu, Zhanwei; Guo, Baoqiao; Xie, Huimin

2018-04-01

Although three-dimensional (3D) morphology measurement has been widely applied on the macro-scale, there is still a lack of 3D measurement technology on the microscopic scale. In this paper, a microscopic 3D measurement technique based on the 3D-geometric phase analysis (GPA) method is proposed. In this method, with machine vision and phase matching, the traditional GPA method is extended to three dimensions. Using this method, 3D deformation measurement on the micro-scale can be realized using a light microscope. Simulation experiments were conducted in this study, and the results demonstrate that the proposed method has a good anti-noise ability. In addition, the 3D morphology of the necking zone in a tensile specimen was measured, and the results demonstrate that this method is feasible.

Differential phase microscope and micro-tomography with a Foucault knife-edge scanning filter

NASA Astrophysics Data System (ADS)

Watanabe, N.; Hashizume, J.; Goto, M.; Yamaguchi, M.; Tsujimura, T.; Aoki, S.

2013-10-01

An x-ray differential phase microscope with a Foucault knife-edge scanning filter was set up at the bending magnet source BL3C, Photon Factory. A reconstructed phase profile from the differential phase image of an aluminium wire at 5.36 keV was fairly good agreement with the numerical simulation. Phase tomography of a biological specimen, such as an Artemia cyst, could be successfully demonstrated.

Generating 3D and 3D-like animations of strongly uneven surface microareas of bloodstains from small series of partially out-of-focus digital SEM micrographs.

PubMed

Hortolà, Policarp

2010-01-01

When dealing with microscopic still images of some kinds of samples, the out-of-focus problem represents a particularly serious limiting factor for the subsequent generation of fully sharp 3D animations. In order to produce fully-focused 3D animations of strongly uneven surface microareas, a vertical stack of six digital secondary-electron SEM micrographs of a human bloodstain microarea was acquired. Afterwards, single combined images were generated using a macrophotography and light microscope image post-processing software. Subsequently, 3D animations of texture and topography were obtained in different formats using a combination of software tools. Finally, a 3D-like animation of a texture-topography composite was obtained in different formats using another combination of software tools. By one hand, results indicate that the use of image post-processing software not concerned primarily with electron micrographs allows to obtain, in an easy way, fully-focused images of strongly uneven surface microareas of bloodstains from small series of partially out-of-focus digital SEM micrographs. On the other hand, results also indicate that such small series of electron micrographs can be utilized for generating 3D and 3D-like animations that can subsequently be converted into different formats, by using certain user-friendly software facilities not originally designed for use in SEM, that are easily available from Internet. Although the focus of this study was on bloodstains, the methods used in it well probably are also of relevance for studying the surface microstructures of other organic or inorganic materials whose sharp displaying is difficult of obtaining from a single SEM micrograph.

Direct numerical simulations of magmatic differentiation at the microscopic scale

NASA Astrophysics Data System (ADS)

Sethian, J.; Suckale, J.; Elkins-Tanton, L. T.

2010-12-01

A key question in the context of magmatic differentiation and fractional crystallization is the ability of crystals to decouple from the ambient fluid and sink or rise. Field data indicates a complex spectrum of behavior ranging from rapid sedimentation to continued entrainment. Theoretical and laboratory studies paint a similarly rich picture. The goal of this study is to provide a detailed numerical assessment of the competing effects of sedimentation and entrainment at the scale of individual crystals. The decision to simulate magmatic differentiation at the grain scale comes at the price of not being able to simultaneously solve for the convective velocity field at the macroscopic scale, but has the crucial advantage of enabling us to fully resolve the dynamics of the systems from first principles without requiring any simplifying assumptions. The numerical approach used in this study is a customized computational methodology developed specifically for simulations of solid-fluid coupling in geophysical systems. The algorithm relies on a two-step projection scheme: In the first step, we solve the multiple-phase Navier-Stokes or Stokes equation in both domains. In the second step, we project the velocity field in the solid domain onto a rigid-body motion by enforcing that the deformation tensor in the respective domain is zero. This procedure is also used to enforce the no-slip boundary-condition on the solid-fluid interface. We have extensively validated and benchmarked the method. Our preliminary results indicate that, not unexpectedly, the competing effects of sedimentation and entrainment depend sensitively on the size distribution of the crystals, the aspect ratio of individual crystals and the vigor of the ambient flow field. We provide a detailed scaling analysis and quantify our results in terms of the relevant non-dimensional numbers.

Integrated optimisation technique based on computer-aided capacity and safety evaluation for managing downstream lane-drop merging area of signalised junctions

NASA Astrophysics Data System (ADS)

Chen, CHAI; Yiik Diew, WONG

2017-02-01

This study provides an integrated strategy, encompassing microscopic simulation, safety assessment, and multi-attribute decision-making, to optimize traffic performance at downstream merging area of signalized intersections. A Fuzzy Cellular Automata (FCA) model is developed to replicate microscopic movement and merging behavior. Based on simulation experiment, the proposed FCA approach is able to provide capacity and safety evaluation of different traffic scenarios. The results are then evaluated through data envelopment analysis (DEA) and analytic hierarchy process (AHP). Optimized geometric layout and control strategies are then suggested for various traffic conditions. An optimal lane-drop distance that is dependent on traffic volume and speed limit can thus be established at the downstream merging area.

TH-CD-201-07: Experimentally Investigating Proton Energy Deposition On the Microscopic Scale Using Fluorescence Nuclear Track Detectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Underwood, T; University College London, London; McFadden, C

Purpose: In order to further understand the interplay between proton physics and radiobiology it is necessary to consider proton energy deposition on the microscopic scale. In this work we used Fluorescent Nuclear Track Detectors (FNTDs) to experimentally investigate proton energy deposition, track-by-track. Methods: We irradiated 8×4×0.5mm{sup 3} FNTD chips (Landauer Inc) at seven water depths along a pristine proton Bragg peak with range=12cm. After irradiation, the FNTDs were scanned using a confocal microscope (FV1200, Olympus) with a high-power red laser and an oil-immersion objective lens (UPLSAPO60XO, NA=1.35). 10 slice image stacks were acquired with a slice-thickness of 2µm at multiplemore » positions across each FNTD. Image-based analyses of track radius and track “mass” (integrated signal intensity) were performed using trackpy. For comparison, Monte Carlo simulated data were obtained using TOPAS and TOPAS-nBio. Results: Excellent correlation was observed between median track mass and TOPAS dose-averaged linear energy transfer. The resolution of the imaging system was determined insufficient to detect a relationship between track radius and exposure depth. Histograms of track mass (i) displayed strong repeatability across positions within an FNTD and (ii) varied in peak position and shape as a function of depth. TOPAS-nBio simulations implemented on the nanometer scale using physics lists from GEANT4-DNA yielded energy deposition distributions for individual protons and electrons scored within a virtual FNTD. Good agreement was found between these simulated datasets and the FNTD track mass distributions. Conclusion: Robust experimental measurements of the integral energy deposited by individual proton tracks can be performed using FNTDs. Monte Carlo simulations offer an exceedingly powerful approach to the quantification of proton energy deposition on the microscopic scale, but whilst they have been well validated at the macroscopic level, their microscopic validation is far from complete. Our results demonstrate that FNTD-based study can play an important role in addressing this deficit. Tracy Underwood gratefully acknowledges the support of the European Commission under an FP7 Marie Curie International Outgoing Fellowship for Career Development (#630064).« less

A Cellular Automata Model of Bone Formation

PubMed Central

Van Scoy, Gabrielle K.; George, Estee L.; Asantewaa, Flora Opoku; Kerns, Lucy; Saunders, Marnie M.; Prieto-Langarica, Alicia

2017-01-01

Bone remodeling is an elegantly orchestrated process by which osteocytes, osteoblasts and osteoclasts function as a syncytium to maintain or modify bone. On the microscopic level, bone consists of cells that create, destroy and monitor the bone matrix. These cells interact in a coordinated manner to maintain a tightly regulated homeostasis. It is this regulation that is responsible for the observed increase in bone gain in the dominant arm of a tennis player and the observed increase in bone loss associated with spaceflight and osteoporosis. The manner in which these cells interact to bring about a change in bone quality and quantity has yet to be fully elucidated. But efforts to understand the multicellular complexity can ultimately lead to eradication of metabolic bone diseases such as osteoporosis and improved implant longevity. Experimentally validated mathematical models that simulate functional activity and offer eventual predictive capabilities offer tremendous potential in understanding multicellular bone remodeling. Here we undertake the initial challenge to develop a mathematical model of bone formation validated with in vitro data obtained from osteoblastic bone cells induced to mineralize and quantified at 26 days of culture. A cellular automata model was constructed to simulate the in vitro characterization. Permutation tests were performed to compare the distribution of the mineralization in the cultures and the distribution of the mineralization in the mathematical models. The results of the permutation test show the distribution of mineralization from the characterization and mathematical model come from the same probability distribution, therefore validating the cellular automata model. PMID:28189632

Stokes-Einstein relation of the liquid metal rubidium and its relationship to changes in the microscopic dynamics with increasing temperature

NASA Astrophysics Data System (ADS)

Demmel, F.; Tani, A.

2018-06-01

For liquid rubidium the Stokes-Einstein (SE) relation is well fulfilled near the melting point with an effective hydrodynamic diameter, which agrees well with a value from structural investigations. A wealth of thermodynamic and microscopic data exists for a wide range of temperatures for liquid rubidium and hence it represents a good test bed to challenge the SE relation with rising temperature from an experimental point of view. We performed classical molecular dynamics simulations to complement the existing experimental data using a pseudopotential, which describes perfectly the structure and dynamics of liquid rubidium. The derived SE relation from combining experimental shear viscosity data with simulated diffusion coefficients reveals a weak violation at about 1.3 Tmelting≈400 K. The microscopic relaxation dynamics on nearest neighbor distances from neutron spectroscopy demonstrate distinct changes in the amplitude with rising temperature. The derived average relaxation time for density fluctuations on this length scale shows a non-Arrhenius behavior, with a slope change around 1.5 Tmelting≈450 K. Combining the simulated macroscopic self-diffusion coefficient with that microscopic average relaxation time, a distinct violation of the SE relation in the same temperature range can be demonstrated. One can conclude that the changes in the collective dynamics, a mirror of the correlated movements of the particles, are at the origin for the violation of the SE relation. The changes in the dynamics can be understood as a transition from a more viscous liquid metal to a more fluid-like liquid above the crossover temperature range of 1.3-1.5 Tmelting. The decay of the amplitude of density fluctuations in liquid aluminium, lead, and rubidium demonstrates a remarkable agreement and points to a universal thermal crossover in the dynamics of liquid metals.

Variable-Size Bead Layer as Standard Reference for Endothelial Microscopes.

PubMed

Tufo, Simona; Prazzoli, Erica; Ferraro, Lorenzo; Cozza, Federica; Borghesi, Alessandro; Tavazzi, Silvia

2017-02-01

For morphometric analysis of the cell mosaic of corneal endothelium, checking accuracy and precision of instrumentation is a key step. In this study, a standard reference sample is proposed, developed to reproduce the cornea with its shape and the endothelium with its intrinsic variability in the cell size. A polystyrene bead layer (representing the endothelium) was deposited on a lens (representing the cornea). Bead diameters were 20, 25, and 30 μm (fractions in number 55%, 30%, and 15%, respectively). Bead density and hexagonality were simulated to obtain the expected true values and measured using a slit-lamp endothelial microscope applied to 1) a Takagi 700GL slit lamp at 40× magnification (recommended standard setup) and 2) a Takagi 2ZL slit lamp at 25× magnification. The simulation provided the expected bead density 2001 mm and hexagonality 47%. At 40×, density and hexagonality were measured to be 2009 mm (SD 93 mm) and 45% (SD 3%). At 25× on a different slit lamp, the comparison between measured and expected densities provided the factor 1.526 to resize the image and to use the current algorithms of the slit-lamp endothelial microscope for cell recognition. A variable-size polystyrene bead layer on a lens is proposed as a standard sample mimicking the real shape of the cornea and the variability of cell size and cell arrangement of corneal endothelium. The sample is suggested to evaluate accuracy and precision of cell density and hexagonality obtained by different endothelial microscopes, including a slit-lamp endothelial microscope applied to different slit lamps, also at different magnifications.

Regional impacts of climate change on a temperate mixed forest: species-specific microscopic root water uptake strategies

NASA Astrophysics Data System (ADS)

He, L.; Ivanov, V. Y.; Bisht, G.; Schneider, C.; Kalbacher, T.; Hildebrandt, A.

2013-12-01

The current generation of ecohydrological or land surface models oversimplify fine-scale root water uptake processes and are thus likely to produce errors in estimating regional transpiration flux when soil approaches dry condition. As future climate is likely to result in a drier soil state in many regions around the world, a better understanding and numerical representation of plant root water uptake process is crucial. In this study, a microscopic root water uptake approach is proposed to simulate the three-dimensional radial moisture fluxes from the soil to roots, and water flux transfer processes within the root systems. During dry conditions, this microscopic approach can simulate plant's ability to compensate the suppressed root water uptake in water-stressed regions by increasing uptake density in moister regions. This study incorporated the microscopic root water uptake approach based on 'aRoot' and 'PFLOTRAN' models into a larger-scale ecohydrological model ('tRIBS+VEGGIE'). The ecohydrological model provides boundary conditions for the microscopic module, and the latter feedbacks with actual transpiration rates and profiles of moisture sinks. The study is conducted for a northern temperate mixed forest of Northern Michigan. The study addresses two species (oak and aspen) with different root architectures, the primary and secondary type root systems. The modeling results use historical climate situations, as well as empirical observations suggesting that transpiration was not limited by soil moisture even when the surface soil water content approached the residual value. Climate projection scenarios are used to predict different water stress levels that would be experienced by the studied species.

Fission fragment charge and mass distributions in 239Pu(n, f ) in the adiabatic nuclear energy density functional theory

DOE PAGES

Regnier, D.; Dubray, N.; Schunck, N.; ...

2016-05-13

Here, accurate knowledge of fission fragment yields is an essential ingredient of numerous applications ranging from the formation of elements in the r process to fuel cycle optimization for nuclear energy. The need for a predictive theory applicable where no data are available, together with the variety of potential applications, is an incentive to develop a fully microscopic approach to fission dynamics.

Students' Design of Experiments: An Inquiry Module on the Conduction of Heat

ERIC Educational Resources Information Center

Hatzikraniotis, E.; Kallery, M.; Molohidis, A.; Psillos, D.

2010-01-01

This article examines secondary students' design of experiments after engagement in an innovative and inquiry-oriented module on heat transfer. The module consists of an integration of hands-on experiments, simulated experiments and microscopic model simulations, includes a structured series of guided investigative tasks and was implemented for a…

Simulated Sampling of Estuary Plankton

ERIC Educational Resources Information Center

Fortner, Rosanne W.; Jenkins, Deborah Bainer

2009-01-01

To find out about the microscopic life in the valuable estuary environment, it is usually necessary to be near the water. This dry lab offers an alternative, using authentic data and a simulation of plankton sampling. From the types of organisms found in the sample, middle school students can infer relationships in the biological and physical…

Two-photon laser scanning microscopy with electrowetting-based prism scanning

PubMed Central

Supekar, Omkar D.; Ozbay, Baris N.; Zohrabi, Mo; Nystrom, Philip D.; Futia, Gregory L.; Restrepo, Diego; Gibson, Emily A.; Gopinath, Juliet T.; Bright, Victor M.

2017-01-01

Laser scanners are an integral part of high resolution biomedical imaging systems such as confocal or 2-photon excitation (2PE) microscopes. In this work, we demonstrate the utility of electrowetting on dielectric (EWOD) prisms as a lateral laser-scanning element integrated in a conventional 2PE microscope. To the best of our knowledge, this is the first such demonstration for EWOD prisms. EWOD devices provide a transmissive, low power consuming, and compact alternative to conventional adaptive optics, and hence this technology has tremendous potential. We demonstrate 2PE microscope imaging of cultured mouse hippocampal neurons with a FOV of 130 × 130 μm2 using EWOD prism scanning. In addition, we show simulations of the optical system with the EWOD prism, to evaluate the effect of propagating a Gaussian beam through the EWOD prism on the imaging quality. Based on the simulation results a beam size of 0.91 mm full width half max was chosen to conduct the imaging experiments, resulting in a numerical aperture of 0.17 of the imaging system. PMID:29296477

Congested traffic states in empirical observations and microscopic simulations

NASA Astrophysics Data System (ADS)

Treiber, Martin; Hennecke, Ansgar; Helbing, Dirk

2000-08-01

We present data from several German freeways showing different kinds of congested traffic forming near road inhomogeneities, specifically lane closings, intersections, or uphill gradients. The states are localized or extended, homogeneous or oscillating. Combined states are observed as well, like the coexistence of moving localized clusters and clusters pinned at road inhomogeneities, or regions of oscillating congested traffic upstream of nearly homogeneous congested traffic. The experimental findings are consistent with a recently proposed theoretical phase diagram for traffic near on-ramps [D. Helbing, A. Hennecke, and M. Treiber, Phys. Rev. Lett. 82, 4360 (1999)]. We simulate these situations with a continuous microscopic single-lane model, the ``intelligent driver model,'' using empirical boundary conditions. All observations, including the coexistence of states, are qualitatively reproduced by describing inhomogeneities with local variations of one model parameter. We show that the results of the microscopic model can be understood by formulating the theoretical phase diagram for bottlenecks in a more general way. In particular, a local drop of the road capacity induced by parameter variations has essentially the same effect as an on-ramp.

Three-Dimensional (3D) Nanometrology Based on Scanning Electron Microscope (SEM) Stereophotogrammetry.

PubMed

Tondare, Vipin N; Villarrubia, John S; Vlada R, András E

2017-10-01

Three-dimensional (3D) reconstruction of a sample surface from scanning electron microscope (SEM) images taken at two perspectives has been known for decades. Nowadays, there exist several commercially available stereophotogrammetry software packages. For testing these software packages, in this study we used Monte Carlo simulated SEM images of virtual samples. A virtual sample is a model in a computer, and its true dimensions are known exactly, which is impossible for real SEM samples due to measurement uncertainty. The simulated SEM images can be used for algorithm testing, development, and validation. We tested two stereophotogrammetry software packages and compared their reconstructed 3D models with the known geometry of the virtual samples used to create the simulated SEM images. Both packages performed relatively well with simulated SEM images of a sample with a rough surface. However, in a sample containing nearly uniform and therefore low-contrast zones, the height reconstruction error was ≈46%. The present stereophotogrammetry software packages need further improvement before they can be used reliably with SEM images with uniform zones.

Fractal propagation method enables realistic optical microscopy simulations in biological tissues

PubMed Central

Glaser, Adam K.; Chen, Ye; Liu, Jonathan T.C.

2017-01-01

Current simulation methods for light transport in biological media have limited efficiency and realism when applied to three-dimensional microscopic light transport in biological tissues with refractive heterogeneities. We describe here a technique which combines a beam propagation method valid for modeling light transport in media with weak variations in refractive index, with a fractal model of refractive index turbulence. In contrast to standard simulation methods, this fractal propagation method (FPM) is able to accurately and efficiently simulate the diffraction effects of focused beams, as well as the microscopic heterogeneities present in tissue that result in scattering, refractive beam steering, and the aberration of beam foci. We validate the technique and the relationship between the FPM model parameters and conventional optical parameters used to describe tissues, and also demonstrate the method’s flexibility and robustness by examining the steering and distortion of Gaussian and Bessel beams in tissue with comparison to experimental data. We show that the FPM has utility for the accurate investigation and optimization of optical microscopy methods such as light-sheet, confocal, and nonlinear microscopy. PMID:28983499

Atomistic minimal model for estimating profile of electrodeposited nanopatterns

NASA Astrophysics Data System (ADS)

Asgharpour Hassankiadeh, Somayeh; Sadeghi, Ali

2018-06-01

We develop a computationally efficient and methodologically simple approach to realize molecular dynamics simulations of electrodeposition. Our minimal model takes into account the nontrivial electric field due a sharp electrode tip to perform simulations of the controllable coating of a thin layer on a surface with an atomic precision. On the atomic scale a highly site-selective electrodeposition of ions and charged particles by means of the sharp tip of a scanning probe microscope is possible. A better understanding of the microscopic process, obtained mainly from atomistic simulations, helps us to enhance the quality of this nanopatterning technique and to make it applicable in fabrication of nanowires and nanocontacts. In the limit of screened inter-particle interactions, it is feasible to run very fast simulations of the electrodeposition process within the framework of the proposed model and thus to investigate how the shape of the overlayer depends on the tip-sample geometry and dielectric properties, electrolyte viscosity, etc. Our calculation results reveal that the sharpness of the profile of a nano-scale deposited overlayer is dictated by the normal-to-sample surface component of the electric field underneath the tip.

An imaging-based stochastic model for simulation of tumour vasculature

NASA Astrophysics Data System (ADS)

Adhikarla, Vikram; Jeraj, Robert

2012-10-01

A mathematical model which reconstructs the structure of existing vasculature using patient-specific anatomical, functional and molecular imaging as input was developed. The vessel structure is modelled according to empirical vascular parameters, such as the mean vessel branching angle. The model is calibrated such that the resultant oxygen map modelled from the simulated microvasculature stochastically matches the input oxygen map to a high degree of accuracy (R2 ≈ 1). The calibrated model was successfully applied to preclinical imaging data. Starting from the anatomical vasculature image (obtained from contrast-enhanced computed tomography), a representative map of the complete vasculature was stochastically simulated as determined by the oxygen map (obtained from hypoxia [64Cu]Cu-ATSM positron emission tomography). The simulated microscopic vasculature and the calculated oxygenation map successfully represent the imaged hypoxia distribution (R2 = 0.94). The model elicits the parameters required to simulate vasculature consistent with imaging and provides a key mathematical relationship relating the vessel volume to the tissue oxygen tension. Apart from providing an excellent framework for visualizing the imaging gap between the microscopic and macroscopic imagings, the model has the potential to be extended as a tool to study the dynamics between the tumour and the vasculature in a patient-specific manner and has an application in the simulation of anti-angiogenic therapies.

Investigation of prescribed movement in fluid–structure interaction simulation for the human phonation process☆

PubMed Central

Zörner, S.; Kaltenbacher, M.; Döllinger, M.

2013-01-01

In a partitioned approach for computational fluid–structure interaction (FSI) the coupling between fluid and structure causes substantial computational resources. Therefore, a convenient alternative is to reduce the problem to a pure flow simulation with preset movement and applying appropriate boundary conditions. This work investigates the impact of replacing the fully-coupled interface condition with a one-way coupling. To continue to capture structural movement and its effect onto the flow field, prescribed wall movements from separate simulations and/or measurements are used. As an appropriate test case, we apply the different coupling strategies to the human phonation process, which is a highly complex interaction of airflow through the larynx and structural vibration of the vocal folds (VF). We obtain vocal fold vibrations from a fully-coupled simulation and use them as input data for the simplified simulation, i.e. just solving the fluid flow. All computations are performed with our research code CFS++, which is based on the finite element (FE) method. The presented results show that a pure fluid simulation with prescribed structural movement can substitute the fully-coupled approach. However, caution must be used to ensure accurate boundary conditions on the interface, and we found that only a pressure driven flow correctly responds to the physical effects when using specified motion. PMID:24204083

Fully Implict Magneto-hydrodynamics Simulations of Coaxial Plasma Accelerators

DOE PAGES

Subramaniam, Vivek; Raja, Laxminarayan L.

2017-01-05

The resistive Magneto-Hydrodynamic (MHD) model describes the behavior of a strongly ionized plasma in the presence of external electric and magnetic fields. We developed a fully implicit MHD simulation tool to solve the resistive MHD governing equations in the context of a cell-centered finite-volume scheme. The primary objective of this study is to use the fully-implicit algorithm to obtain insights into the plasma acceleration and jet formation processes in Coaxial Plasma accelerators; electromagnetic acceleration devices that utilize self-induced magnetic fields to accelerate thermal plasmas to large velocities. We also carry out plasma-surface simulations in order to study the impact interactionsmore » when these high velocity plasma jets impinge on target material surfaces. Scaling studies are carried out to establish some basic functional relationships between the target-stagnation conditions and the current discharged between the coaxial electrodes.« less

Microscopic origin of the fast blue-green luminescence of chemically synthesized non-oxidized silicon quantum dots.

PubMed

Dohnalová, Kateřina; Fučíková, Anna; Umesh, Chinnaswamy P; Humpolíčková, Jana; Paulusse, Jos M J; Valenta, Jan; Zuilhof, Han; Hof, Martin; Gregorkiewicz, Tom

2012-10-22

The microscopic origin of the bright nanosecond blue-green photoluminescence (PL), frequently reported for synthesized organically terminated Si quantum dots (Si-QDs), has not been fully resolved, hampering potential applications of this interesting material. Here a comprehensive study of the PL from alkyl-terminated Si-QDs of 2-3 nm size, prepared by wet chemical synthesis is reported. Results obtained on the ensemble and those from the single nano-object level are compared, and they provide conclusive evidence that efficient and tunable emission arises due to radiative recombination of electron-hole pairs confined in the Si-QDs. This understanding paves the way towards applications of chemical synthesis for the development of Si-QDs with tunable sizes and bandgaps. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Imaging sequential dehydrogenation of methanol on Cu(110) with a scanning tunneling microscope.

PubMed

Kitaguchi, Y; Shiotari, A; Okuyama, H; Hatta, S; Aruga, T

2011-05-07

Adsorption of methanol and its dehydrogenation on Cu(110) were studied by using a scanning tunneling microscope (STM). Upon adsorption at 12 K, methanol preferentially forms clusters on the surface. The STM could induce dehydrogenation of methanol sequentially to methoxy and formaldehyde. This enabled us to study the binding structures of these products in a single-molecule limit. Methoxy was imaged as a pair of protrusion and depression along the [001] direction. This feature is fully consistent with the previous result that it adsorbs on the short-bridge site with the C-O axis tilted along the [001] direction. The axis was induced to flip back and forth by vibrational excitations with the STM. Two configurations were observed for formaldehyde, whose structures were proposed based on their characteristic images and motions.

Obtaining macroscopic quantities for the contact line problem from Density Functional Theory using asymptotic methods

NASA Astrophysics Data System (ADS)

Sibley, David; Nold, Andreas; Kalliadasis, Serafim

2015-11-01

Density Functional Theory (DFT), a statistical mechanics of fluids approach, captures microscopic details of the fluid density structure in the vicinity of contact lines, as seen in computations in our recent study. Contact lines describe the location where interfaces between two fluids meet solid substrates, and have stimulated a wealth of research due to both their ubiquity in nature and technological applications and also due to their rich multiscale behaviour. Whilst progress can be made computationally to capture the microscopic to mesoscopic structure from DFT, complete analytical results to fully bridge to the macroscale are lacking. In this work, we describe our efforts to bring asymptotic methods to DFT to obtain results for contact angles and other macroscopic quantities in various parameter regimes. We acknowledge financial support from European Research Council via Advanced Grant No. 247031.

Toward automated denoising of single molecular Förster resonance energy transfer data

NASA Astrophysics Data System (ADS)

Lee, Hao-Chih; Lin, Bo-Lin; Chang, Wei-Hau; Tu, I.-Ping

2012-01-01

A wide-field two-channel fluorescence microscope is a powerful tool as it allows for the study of conformation dynamics of hundreds to thousands of immobilized single molecules by Förster resonance energy transfer (FRET) signals. To date, the data reduction from a movie to a final set containing meaningful single-molecule FRET (smFRET) traces involves human inspection and intervention at several critical steps, greatly hampering the efficiency at the post-imaging stage. To facilitate the data reduction from smFRET movies to smFRET traces and to address the noise-limited issues, we developed a statistical denoising system toward fully automated processing. This data reduction system has embedded several novel approaches. First, as to background subtraction, high-order singular value decomposition (HOSVD) method is employed to extract spatial and temporal features. Second, to register and map the two color channels, the spots representing bleeding through the donor channel to the acceptor channel are used. Finally, correlation analysis and likelihood ratio statistic for the change point detection (CPD) are developed to study the two channels simultaneously, resolve FRET states, and report the dwelling time of each state. The performance of our method has been checked using both simulation and real data.

A mononuclear Cu(II) complex with 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine: Synthesis, crystal structure, DNA- and BSA-binding, molecular modeling, and anticancer activity against MCF-7, A-549, and HT-29 cell lines.

PubMed

Anjomshoa, Marzieh; Hadadzadeh, Hassan; Torkzadeh-Mahani, Masoud; Fatemi, Seyed Jamilaldin; Adeli-Sardou, Mahboubeh; Rudbari, Hadi Amiri; Nardo, Viviana Mollica

2015-01-01

The copper(II) complex of 1,2,4-triazine derivatives, [Cu(dppt)2(H2O)](PF6)2(dppt is 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine), has been synthesized and fully characterized by spectroscopic methods and single crystal X-ray diffraction. The in vitro DNA-binding studies of the complex have been investigated by several methods. The results showed that the complex intercalates into the base pairs of DNA. The complex also indicated good binding propensity to BSA. The results of molecular docking and molecular dynamic simulation methods confirm the experimental results. Finally, the in vitro cytotoxicity indicate that the complex has excellent anticancer activity against the three human carcinoma cell lines, MCF-7, A-549, and HT-29, with IC50 values of 9.8, 7.80, and 4.50 μM, respectively. The microscopic analyses of the cancer cells demonstrate that the Cu(II) complex apparently induced apoptosis. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Comparative evaluation of user interfaces for robot-assisted laser phonomicrosurgery.

PubMed

Dagnino, Giulio; Mattos, Leonardo S; Becattini, Gabriele; Dellepiane, Massimo; Caldwell, Darwin G

2011-01-01

This research investigates the impact of three different control devices and two visualization methods on the precision, safety and ergonomics of a new medical robotic system prototype for assistive laser phonomicrosurgery. This system allows the user to remotely control the surgical laser beam using either a flight simulator type joystick, a joypad, or a pen display system in order to improve the traditional surgical setup composed by a mechanical micromanipulator coupled with a surgical microscope. The experimental setup and protocol followed to obtain quantitative performance data from the control devices tested are fully described here. This includes sets of path following evaluation experiments conducted with ten subjects with different skills, for a total of 700 trials. The data analysis method and experimental results are also presented, demonstrating an average 45% error reduction when using the joypad and up to 60% error reduction when using the pen display system versus the standard phonomicrosurgery setup. These results demonstrate the new system can provide important improvements in terms of surgical precision, ergonomics and safety. In addition, the evaluation method presented here is shown to support an objective selection of control devices for this application.

Kinetic phase evolution of spinel cobalt oxide during lithiation

DOE PAGES

Li, Jing; He, Kai; Meng, Qingping; ...

2016-09-15

Spinel cobalt oxide has been proposed to undergo a multiple-step reaction during the electrochemical lithiation process. Understanding the kinetics of the lithiation process in this compound is crucial to optimize its performance and cyclability. In this work, we have utilized a low-angle annular dark-field scanning transmission electron microscopy method to visualize the dynamic reaction process in real time and study the reaction kinetics at different rates. We show that the particles undergo a two-step reaction at the single-particle level, which includes an initial intercalation reaction followed by a conversion reaction. At low rates, the conversion reaction starts after the intercalationmore » reaction has fully finished, consistent with the prediction of density functional theoretical calculations. At high rates, the intercalation reaction is overwhelmed by the subsequently nucleated conversion reaction, and the reaction speeds of both the intercalation and conversion reactions are increased. Phase-field simulations show the crucial role of surface diffusion rates of lithium ions in controlling this process. Furthermore, this work provides microscopic insights into the reaction dynamics in non-equilibrium conditions and highlights the effect of lithium diffusion rates on the overall reaction homogeneity as well as the performance.« less

Kinetic phase evolution of spinel cobalt oxide during lithiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Jing; He, Kai; Meng, Qingping

Spinel cobalt oxide has been proposed to undergo a multiple-step reaction during the electrochemical lithiation process. Understanding the kinetics of the lithiation process in this compound is crucial to optimize its performance and cyclability. In this work, we have utilized a low-angle annular dark-field scanning transmission electron microscopy method to visualize the dynamic reaction process in real time and study the reaction kinetics at different rates. We show that the particles undergo a two-step reaction at the single-particle level, which includes an initial intercalation reaction followed by a conversion reaction. At low rates, the conversion reaction starts after the intercalationmore » reaction has fully finished, consistent with the prediction of density functional theoretical calculations. At high rates, the intercalation reaction is overwhelmed by the subsequently nucleated conversion reaction, and the reaction speeds of both the intercalation and conversion reactions are increased. Phase-field simulations show the crucial role of surface diffusion rates of lithium ions in controlling this process. Furthermore, this work provides microscopic insights into the reaction dynamics in non-equilibrium conditions and highlights the effect of lithium diffusion rates on the overall reaction homogeneity as well as the performance.« less

Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations

PubMed Central

Baxa, Michael C.; Haddadian, Esmael J.; Jumper, John M.; Freed, Karl F.; Sosnick, Tobin R.

2014-01-01

The loss of conformational entropy is a major contribution in the thermodynamics of protein folding. However, accurate determination of the quantity has proven challenging. We calculate this loss using molecular dynamic simulations of both the native protein and a realistic denatured state ensemble. For ubiquitin, the total change in entropy is TΔSTotal = 1.4 kcal⋅mol−1 per residue at 300 K with only 20% from the loss of side-chain entropy. Our analysis exhibits mixed agreement with prior studies because of the use of more accurate ensembles and contributions from correlated motions. Buried side chains lose only a factor of 1.4 in the number of conformations available per rotamer upon folding (ΩU/ΩN). The entropy loss for helical and sheet residues differs due to the smaller motions of helical residues (TΔShelix−sheet = 0.5 kcal⋅mol−1), a property not fully reflected in the amide N-H and carbonyl C=O bond NMR order parameters. The results have implications for the thermodynamics of folding and binding, including estimates of solvent ordering and microscopic entropies obtained from NMR. PMID:25313044

Determination of aberration center of Ronchigram for automated aberration correctors in scanning transmission electron microscopy.

PubMed

Sannomiya, Takumi; Sawada, Hidetaka; Nakamichi, Tomohiro; Hosokawa, Fumio; Nakamura, Yoshio; Tanishiro, Yasumasa; Takayanagi, Kunio

2013-12-01

A generic method to determine the aberration center is established, which can be utilized for aberration calculation and axis alignment for aberration corrected electron microscopes. In this method, decentering induced secondary aberrations from inherent primary aberrations are minimized to find the appropriate axis center. The fitness function to find the optimal decentering vector for the axis was defined as a sum of decentering induced secondary aberrations with properly distributed weight values according to the aberration order. Since the appropriate decentering vector is determined from the aberration values calculated at an arbitrary center axis, only one aberration measurement is in principle required to find the center, resulting in /very fast center search. This approach was tested for the Ronchigram based aberration calculation method for aberration corrected scanning transmission electron microscopy. Both in simulation and in experiments, the center search was confirmed to work well although the convergence to find the best axis becomes slower with larger primary aberrations. Such aberration center determination is expected to fully automatize the aberration correction procedures, which used to require pre-alignment of experienced users. This approach is also applicable to automated aperture positioning. Copyright © 2013 Elsevier B.V. All rights reserved.

Effect of Glycerol Water Binary Mixtures on the Structure and Dynamics of Protein Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghattyvenkatakrishna, Pavan K; Carri, Gustavo A.

We have performed 20ns of fully atomistic molecular dynamics simulations of Hen Egg-White Lysozyme in 0, 10, 20, 30 and 100% by weight of glycerol in water to better understand the microscopic physics behind the bioprotection offered by glycerol to naturally occuring biological systems. The sovlent exposure of protein surface residues changes when glycerol is introduced. The dynamic behavior of the protein, as quantified by the Incoherent Intermediate Scattering Function, shows a non-monotonic dependence on glycerol content. The fluctuations of the protein residues with respect to each other were found to be similar in all water containing solvents; but differentmore » from the pure glycerol case. The increase in the number of protein glycerol hydrogen bonds in glycerol water binary mixtures explains the slowing down of protein dynamics as the glycerol content increases. We also explored the dynamic behavior of the hydration layer. We show that the short-length scale dynamics of this layer are insenstive to glycerol concentration. However, the long-length scale behavior shows a significant dependence on glycerol content. We also provide insights into the behavior of bound and mobile water molecules.« less

An adaptive extended finite element method for the analysis of agglomeration of colloidal particles in a flowing fluid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choi, Young Joon; Jorshari, Razzi Movassaghi; Djilali, Ned

2015-03-10

Direct numerical simulations of the flow-nanoparticle interaction in a colloidal suspension are presented using an extended finite element method (XFEM) in which the dynamics of the nanoparticles is solved in a fully-coupled manner with the flow. The method is capable of accurately describing solid-fluid interfaces without the need of boundary-fitted meshes to investigate the dynamics of particles in complex flows. In order to accurately compute the high interparticle shear stresses and pressures while minimizing computing costs, an adaptive meshing technique is incorporated with the fluid-structure interaction algorithm. The particle-particle interaction at the microscopic level is modeled using the Lennard-Jones (LJ)more » potential and the corresponding potential parameters are determined by a scaling procedure. The study is relevant to the preparation of inks used in the fabrication of catalyst layers for fuel cells. In this paper, we are particularly interested in investigating agglomeration of the nanoparticles under external shear flow in a sliding bi-periodic Lees-Edwards frame. The results indicate that the external shear has a crucial impact on the structure formation of colloidal particles in a suspension.« less

Earthquake cycle modeling of multi-segmented faults: dynamic rupture and ground motion simulation of the 1992 Mw 7.3 Landers earthquake.

NASA Astrophysics Data System (ADS)

Petukhin, A.; Galvez, P.; Somerville, P.; Ampuero, J. P.

2017-12-01

We perform earthquake cycle simulations to study the characteristics of source scaling relations and strong ground motions and in multi-segmented fault ruptures. For earthquake cycle modeling, a quasi-dynamic solver (QDYN, Luo et al, 2016) is used to nucleate events and the fully dynamic solver (SPECFEM3D, Galvez et al., 2014, 2016) is used to simulate earthquake ruptures. The Mw 7.3 Landers earthquake has been chosen as a target earthquake to validate our methodology. The SCEC fault geometry for the three-segmented Landers rupture is included and extended at both ends to a total length of 200 km. We followed the 2-D spatial correlated Dc distributions based on Hillers et. al. (2007) that associates Dc distribution with different degrees of fault maturity. The fault maturity is related to the variability of Dc on a microscopic scale. Large variations of Dc represents immature faults and lower variations of Dc represents mature faults. Moreover we impose a taper (a-b) at the fault edges and limit the fault depth to 15 km. Using these settings, earthquake cycle simulations are performed to nucleate seismic events on different sections of the fault, and dynamic rupture modeling is used to propagate the ruptures. The fault segmentation brings complexity into the rupture process. For instance, the change of strike between fault segments enhances strong variations of stress. In fact, Oglesby and Mai (2012) show the normal stress varies from positive (clamping) to negative (unclamping) between fault segments, which leads to favorable or unfavorable conditions for rupture growth. To replicate these complexities and the effect of fault segmentation in the rupture process, we perform earthquake cycles with dynamic rupture modeling and generate events similar to the Mw 7.3 Landers earthquake. We extract the asperities of these events and analyze the scaling relations between rupture area, average slip and combined area of asperities versus moment magnitude. Finally, the simulated ground motions will be validated by comparison of simulated response spectra with recorded response spectra and with response spectra from ground motion prediction models. This research is sponsored by the Japan Nuclear Regulation Authority.

In Vivo Near Infrared Virtual Intraoperative Surgical Photoacoustic Optical Coherence Tomography

PubMed Central

Lee, Donghyun; Lee, Changho; Kim, Sehui; Zhou, Qifa; Kim, Jeehyun; Kim, Chulhong

2016-01-01

Since its first implementation in otolaryngological surgery nearly a century ago, the surgical microscope has improved the accuracy and the safety of microsurgeries. However, the microscope shows only a magnified surface view of the surgical region. To overcome this limitation, either optical coherence tomography (OCT) or photoacoustic microscopy (PAM) has been independently combined with conventional surgical microscope. Herein, we present a near-infrared virtual intraoperative photoacoustic optical coherence tomography (NIR-VISPAOCT) system that combines both PAM and OCT with a conventional surgical microscope. Using optical scattering and absorption, the NIR-VISPAOCT system simultaneously provides surgeons with real-time comprehensive biological information such as tumor margins, tissue structure, and a magnified view of the region of interest. Moreover, by utilizing a miniaturized beam projector, it can back-project 2D cross-sectional PAM and OCT images onto the microscopic view plane. In this way, both microscopic and cross-sectional PAM and OCT images are concurrently displayed on the ocular lens of the microscope. To verify the usability of the NIR-VISPAOCT system, we demonstrate simulated surgeries, including in vivo image-guided melanoma resection surgery and in vivo needle injection of carbon particles into a mouse thigh. The proposed NIR-VISPAOCT system has potential applications in neurosurgery, ophthalmological surgery, and other microsurgeries. PMID:27731390

Molecular Model of a Quantum Dot Beyond the Constant Interaction Approximation

NASA Astrophysics Data System (ADS)

Temirov, Ruslan; Green, Matthew F. B.; Friedrich, Niklas; Leinen, Philipp; Esat, Taner; Chmielniak, Pawel; Sarwar, Sidra; Rawson, Jeff; Kögerler, Paul; Wagner, Christian; Rohlfing, Michael; Tautz, F. Stefan

2018-05-01

We present a physically intuitive model of molecular quantum dots beyond the constant interaction approximation. It accurately describes their charging behavior and allows the extraction of important molecular properties that are otherwise experimentally inaccessible. The model is applied to data recorded with a noncontact atomic force microscope on three different molecules that act as a quantum dot when attached to the microscope tip. The results are in excellent agreement with first-principles simulations.

Microscopic Mechanism of Doping-Induced Kinetically Constrained Crystallization in Phase-Change Materials.

PubMed

Lee, Tae Hoon; Loke, Desmond; Elliott, Stephen R

2015-10-07

A comprehensive microscopic mechanism of doping-induced kinetically constrained crystallization in phase-change materials is provided by investigating structural and dynamical dopant characteristics via ab initio molecular dynamics simulations. The information gained from this study may provide a basis for a fast screening of dopant species for electronic memory devices, or for understanding the general physics involved in the crystallization of doped glasses. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stage scoring of liver fibrosis using Mueller matrix microscope

NASA Astrophysics Data System (ADS)

Zhou, Jialing; He, Honghui; Wang, Ye; Ma, Hui

2016-10-01

Liver fibrosis is a common pathological process of varied chronic liver diseases including alcoholic hepatitis, virus hepatitis, and so on. Accurate evaluation of liver fibrosis is necessary for effective therapy and a five-stage grading system was developed. Currently, experienced pathologists use stained liver biopsies to assess the degree of liver fibrosis. But it is difficult to obtain highly reproducible results because of huge discrepancy among different observers. Polarization imaging technique has the potential of scoring liver fibrosis since it is capable of probing the structural and optical properties of samples. Considering that the Mueller matrix measurement can provide comprehensive microstructural information of the tissues, in this paper, we apply the Mueller matrix microscope to human liver fibrosis slices in different fibrosis stages. We extract the valid regions and adopt the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters for quantitative analysis. We also use the Monte Carlo simulation to analyze the relationship between the microscopic Mueller matrix parameters and the characteristic structural changes during the fibrosis process. The experimental and Monte Carlo simulated results show good consistency. We get a positive correlation between the parameters and the stage of liver fibrosis. The results presented in this paper indicate that the Mueller matrix microscope can provide additional information for the detections and fibrosis scorings of liver tissues and has great potential in liver fibrosis diagnosis.

Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions

PubMed Central

Kasson, Peter M.; Hess, Berk; Lindahl, Erik

2013-01-01

Cellular lipid membranes are spatially inhomogeneous soft materials. Materials properties such as pressure and surface tension thus show important microscopic-scale variation that is critical to many biological functions. We present a means to calculate pressure and surface tension in a 3D-resolved manner within molecular-dynamics simulations and show how such measurements can yield important insight. We also present the first corrections to local virial and pressure fields to account for the constraints typically used in lipid simulations that otherwise cause problems in highly oriented systems such as bilayers. Based on simulations of an asymmetric bacterial ion channel in a POPC bilayer, we demonstrate how 3D-resolved pressure can probe for both short-range and long-range effects from the protein on the membrane environment. We also show how surface tension is a sensitive metric for inter-leaflet equilibrium and can be used to detect even subtle imbalances between bilayer leaflets in a membrane-protein simulation. Since surface tension is known to modulate the function of many proteins, this effect is an important consideration for predictions of ion channel function. We outline a strategy by which our local pressure measurements, which we make available within a version of the GROMACS simulation package, may be used to design optimally equilibrated membrane-protein simulations. PMID:23318532

Multi-scale image segmentation and numerical modeling in carbonate rocks

NASA Astrophysics Data System (ADS)

Alves, G. C.; Vanorio, T.

2016-12-01

Numerical methods based on computational simulations can be an important tool in estimating physical properties of rocks. These can complement experimental results, especially when time constraints and sample availability are a problem. However, computational models created at different scales can yield conflicting results with respect to the physical laboratory. This problem is exacerbated in carbonate rocks due to their heterogeneity at all scales. We developed a multi-scale approach performing segmentation of the rock images and numerical modeling across several scales, accounting for those heterogeneities. As a first step, we measured the porosity and the elastic properties of a group of carbonate samples with varying micrite content. Then, samples were imaged by Scanning Electron Microscope (SEM) as well as optical microscope at different magnifications. We applied three different image segmentation techniques to create numerical models from the SEM images and performed numerical simulations of the elastic wave-equation. Our results show that a multi-scale approach can efficiently account for micro-porosities in tight micrite-supported samples, yielding acoustic velocities comparable to those obtained experimentally. Nevertheless, in high-porosity samples characterized by larger grain/micrite ratio, results show that SEM scale images tend to overestimate velocities, mostly due to their inability to capture macro- and/or intragranular- porosity. This suggests that, for high-porosity carbonate samples, optical microscope images would be more suited for numerical simulations.

Computational simulations of supersonic magnetohydrodynamic flow control, power and propulsion systems

NASA Astrophysics Data System (ADS)

Wan, Tian

This work is motivated by the lack of fully coupled computational tool that solves successfully the turbulent chemically reacting Navier-Stokes equation, the electron energy conservation equation and the electric current Poisson equation. In the present work, the abovementioned equations are solved in a fully coupled manner using fully implicit parallel GMRES methods. The system of Navier-Stokes equations are solved using a GMRES method with combined Schwarz and ILU(0) preconditioners. The electron energy equation and the electric current Poisson equation are solved using a GMRES method with combined SOR and Jacobi preconditioners. The fully coupled method has also been implemented successfully in an unstructured solver, US3D, and convergence test results were presented. This new method is shown two to five times faster than the original DPLR method. The Poisson solver is validated with analytic test problems. Then, four problems are selected; two of them are computed to explore the possibility of onboard MHD control and power generation, and the other two are simulation of experiments. First, the possibility of onboard reentry shock control by a magnetic field is explored. As part of a previous project, MHD power generation onboard a re-entry vehicle is also simulated. Then, the MHD acceleration experiments conducted at NASA Ames research center are simulated. Lastly, the MHD power generation experiments known as the HVEPS project are simulated. For code validation, the scramjet experiments at University of Queensland are simulated first. The generator section of the HVEPS test facility is computed then. The main conclusion is that the computational tool is accurate for different types of problems and flow conditions, and its accuracy and efficiency are necessary when the flow complexity increases.

Towards Automated Screening of Two-dimensional Crystals

PubMed Central

Cheng, Anchi; Leung, Albert; Fellmann, Denis; Quispe, Joel; Suloway, Christian; Pulokas, James; Carragher, Bridget; Potter, Clinton S.

2007-01-01

Screening trials to determine the presence of two-dimensional (2D) protein crystals suitable for three-dimensional structure determination using electron crystallography is a very labor-intensive process. Methods compatible with fully automated screening have been developed for the process of crystal production by dialysis and for producing negatively stained grids of the resulting trials. Further automation via robotic handling of the EM grids, and semi-automated transmission electron microscopic imaging and evaluation of the trial grids is also possible. We, and others, have developed working prototypes for several of these tools and tested and evaluated them in a simple screen of 24 crystallization conditions. While further development of these tools is certainly required for a turn-key system, the goal of fully automated screening appears to be within reach. PMID:17977016

Multiscale Imaging of the Mouse Cortex Using Two-Photon Microscopy and Wide-Field Illumination

NASA Astrophysics Data System (ADS)

Bumstead, Jonathan R.

The mouse brain can be studied over vast spatial scales ranging from microscopic imaging of single neurons to macroscopic measurements of hemodynamics acquired over the majority of the mouse cortex. However, most neuroimaging modalities are limited by a fundamental trade-off between the spatial resolution and the field-of-view (FOV) over which the brain can be imaged, making it difficult to fully understand the functional and structural architecture of the healthy mouse brain and its disruption in disease. My dissertation has focused on developing multiscale optical systems capable of imaging the mouse brain at both microscopic and mesoscopic spatial scales, specifically addressing the difference in spatial scales imaged with two-photon microscopy (TPM) and optical intrinsic signal imaging (OISI). Central to this work has been the formulation of a principled design strategy for extending the FOV of the two-photon microscope. Using this design approach, we constructed a TPM system with subcellular resolution and a FOV area 100 times greater than a conventional two-photon microscope. To image the ellipsoidal shape of the mouse cortex, we also developed the microscope to image arbitrary surfaces within a single frame using an electrically tunable lens. Finally, to address the speed limitations of the TPM systems developed during my dissertation, I also conducted research in large-scale neural phenomena occurring in the mouse brain imaged with high-speed OISI. The work conducted during my dissertation addresses some of the fundamental principles in designing and applying optical systems for multiscale imaging of the mouse brain.

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

PubMed Central

Vallenet, David; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Lajus, Aurélie; Josso, Adrien; Mercier, Jonathan; Renaux, Alexandre; Rollin, Johan; Rouy, Zoe; Roche, David; Scarpelli, Claude; Médigue, Claudine

2017-01-01

The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations. PMID:27899624

How Sensitive Are Transdermal Transport Predictions by Microscopic Stratum Corneum Models to Geometric and Transport Parameter Input?

PubMed

Wen, Jessica; Koo, Soh Myoung; Lape, Nancy

2018-02-01

While predictive models of transdermal transport have the potential to reduce human and animal testing, microscopic stratum corneum (SC) model output is highly dependent on idealized SC geometry, transport pathway (transcellular vs. intercellular), and penetrant transport parameters (e.g., compound diffusivity in lipids). Most microscopic models are limited to a simple rectangular brick-and-mortar SC geometry and do not account for variability across delivery sites, hydration levels, and populations. In addition, these models rely on transport parameters obtained from pure theory, parameter fitting to match in vivo experiments, and time-intensive diffusion experiments for each compound. In this work, we develop a microscopic finite element model that allows us to probe model sensitivity to variations in geometry, transport pathway, and hydration level. Given the dearth of experimentally-validated transport data and the wide range in theoretically-predicted transport parameters, we examine the model's response to a variety of transport parameters reported in the literature. Results show that model predictions are strongly dependent on all aforementioned variations, resulting in order-of-magnitude differences in lag times and permeabilities for distinct structure, hydration, and parameter combinations. This work demonstrates that universally predictive models cannot fully succeed without employing experimentally verified transport parameters and individualized SC structures. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Modulus design multiwavelength polarization microscope for transmission Mueller matrix imaging.

PubMed

Zhou, Jialing; He, Honghui; Chen, Zhenhua; Wang, Ye; Ma, Hui

2018-01-01

We have developed a polarization microscope based on a commercial transmission microscope. We replace the halogen light source by a collimated LED light source module of six different colors. We use achromatic polarized optical elements that can cover the six different wavelength ranges in the polarization state generator (PSG) and polarization state analyzer (PSA) modules. The dual-rotating wave plate method is used to measure the Mueller matrix of samples, which requires the simultaneous rotation of the two quarter-wave plates in both PSG and PSA at certain angular steps. A scientific CCD detector is used as the image receiving module. A LabView-based software is developed to control the rotation angels of the wave plates and the exposure time of the detector to allow the system to run fully automatically in preprogrammed schedules. Standard samples, such as air, polarizers, and quarter-wave plates, are used to calibrate the intrinsic Mueller matrix of optical components, such as the objectives, using the eigenvalue calibration method. Errors due to the images walk-off in the PSA are studied. Errors in the Mueller matrices are below 0.01 using air and polarizer as standard samples. Data analysis based on Mueller matrix transformation and Mueller matrix polarization decomposition is used to demonstrate the potential application of this microscope in pathological diagnosis. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Single-photon counting multicolor multiphoton fluorescence microscope.

PubMed

Buehler, Christof; Kim, Ki H; Greuter, Urs; Schlumpf, Nick; So, Peter T C

2005-01-01

We present a multicolor multiphoton fluorescence microscope with single-photon counting sensitivity. The system integrates a standard multiphoton fluorescence microscope, an optical grating spectrograph operating in the UV-Vis wavelength region, and a 16-anode photomultiplier tube (PMT). The major technical innovation is in the development of a multichannel photon counting card (mC-PhCC) for direct signal collection from multi-anode PMTs. The electronic design of the mC-PhCC employs a high-throughput, fully-parallel, single-photon counting scheme along with a high-speed electrical or fiber-optical link interface to the data acquisition computer. There is no electronic crosstalk among the detection channels of the mC-PhCC. The collected signal remains linear up to an incident photon rate of 10(8) counts per second. The high-speed data interface offers ample bandwidth for real-time readout: 2 MByte lambda-stacks composed of 16 spectral channels, 256 x 256 pixel image with 12-bit dynamic range can be transferred at 30 frames per second. The modular design of the mC-PhCC can be readily extended to accommodate PMTs of more anodes. Data acquisition from a 64-anode PMT has been verified. As a demonstration of system performance, spectrally resolved images of fluorescent latex spheres and ex-vivo human skin are reported. The multicolor multiphoton microscope is suitable for highly sensitive, real-time, spectrally-resolved three-dimensional imaging in biomedical applications.

STS/DBS power subsystem end-to-end stability margin

NASA Astrophysics Data System (ADS)

Devaux, R. N.; Vattimo, R. J.; Peck, S. R.; Baker, W. E.

Attention is given to a full-up end-to-end subsystem stability test which was performed with a flight solar array providing power to a fully operational spacecraft. The solar array simulator is described, and a comparison is made between test results obtained with the simulator and those obtained with the actual array. It is concluded that stability testing with a fully integrated spacecraft is necessary to ensure that all elements have been adequately modeled.

Wireless Performance of a Fully Passive Neurorecording Microsystem Embedded in Dispersive Human Head Phantom

NASA Technical Reports Server (NTRS)

Schwerdt, Helen N.; Chae, Junseok; Miranda, Felix A.

2012-01-01

This paper reports the wireless performance of a biocompatible fully passive microsystem implanted in phantom media simulating the dispersive dielectric properties of the human head, for potential application in recording cortical neuropotentials. Fully passive wireless operation is achieved by means of backscattering electromagnetic (EM) waves carrying 3rd order harmonic mixing products (2f(sub 0) plus or minus f(sub m)=4.4-4.9 GHZ) containing targeted neuropotential signals (fm approximately equal to 1-1000 Hz). The microsystem is enclosed in 4 micrometer thick parylene-C for biocompatibility and has a footprint of 4 millimeters x 12 millimeters x 500 micrometers. Preliminary testing of the microsystem implanted in the lossy biological simulating media results in signal-to-noise ratio's (SNR) near 22 (SNR approximately equal to 38 in free space) for millivolt level neuropotentials, demonstrating the potential for fully passive wireless microsystems in implantable medical applications.

Linking a one-dimensional pesticide fate model to a three-dimensional groundwater model to simulate pollution risks of shallow and deep groundwater underlying fractured till.

PubMed

Stenemo, Fredrik; Jørgensen, Peter R; Jarvis, Nicholas

2005-09-01

The one-dimensional pesticide fate model MACRO was loose-linked to the three-dimensional discrete fracture/matrix diffusion model FRAC3DVS to describe transport of the pesticide mecoprop in a fractured moraine till and local sand aquifer (5-5.5 m depth) overlying a regional limestone aquifer (16 m depth) at Havdrup, Denmark. Alternative approaches to describe the upper boundary in the groundwater model were examined. Field-scale simulations were run to compare a uniform upper boundary condition with a spatially variable upper boundary derived from Monte-Carlo simulations with MACRO. Plot-scale simulations were run to investigate the influence of the temporal resolution of the upper boundary conditions for fluxes in the groundwater model and the effects of different assumptions concerning the macropore/fracture connectivity between the two models. The influence of within-field variability of leaching on simulated mecoprop concentrations in the local aquifer was relatively small. A fully transient simulation with FRAC3DVS gave 20 times larger leaching to the regional aquifer compared to the case with steady-state water flow, assuming full connectivity with respect to macropores/fractures across the boundary between the two models. For fully transient simulations 'disconnecting' the macropores/fractures at the interface between the two models reduced leaching by a factor 24. A fully connected, transient simulation with FRAC3DVS, with spatially uniform upper boundary fluxes derived from a MACRO simulation with 'effective' parameters is therefore recommended for assessing leaching risks to the regional aquifer, at this, and similar sites.

Probing the inhibitory potency of epigallocatechin gallate against human γB-crystallin aggregation: Spectroscopic, microscopic and simulation studies

NASA Astrophysics Data System (ADS)

Chaudhury, Susmitnarayan; Dutta, Anirudha; Bag, Sudipta; Biswas, Pranandita; Das, Amit Kumar; Dasgupta, Swagata

2018-03-01

Aggregation of human ocular lens proteins, the crystallins is believed to be one of the key reasons for age-onset cataract. Previous studies have shown that human γD-crystallin forms amyloid like fibres under conditions of low pH and elevated temperature. In this article, we have investigated the aggregation propensity of human γB-crystallin in absence and presence of epigallocatechin gallate (EGCG), in vitro, when exposed to stressful conditions. We have used different spectroscopic and microscopic techniques to elucidate the inhibitory effect of EGCG towards aggregation. The experimental results have been substantiated by molecular dynamics simulation studies. We have shown that EGCG possesses inhibitory potency against the aggregation of human γB-crystallin at low pH and elevated temperature.

Evaluating the Laplace pressure of water nanodroplets from simulations

NASA Astrophysics Data System (ADS)

Malek, Shahrazad M. A.; Sciortino, Francesco; Poole, Peter H.; Saika-Voivod, Ivan

2018-04-01

We calculate the components of the microscopic pressure tensor as a function of radial distance r from the centre of a spherical water droplet, modelled using the TIP4P/2005 potential. To do so, we modify a coarse-graining method for calculating the microscopic pressure (Ikeshoji et al 2003 Mol. Simul. 29 101) in order to apply it to a rigid molecular model of water. As test cases, we study nanodroplets ranging in size from 776 to 2880 molecules at 220 K. Beneath a surface region comprising approximately two molecular layers, the pressure tensor becomes approximately isotropic and constant with r. We find that the dependence of the pressure on droplet radius is that expected from the Young-Laplace equation, despite the small size of the droplets.

Computer Simulation of the Forces Acting on a Submerged Polystyrene Probe as it Approaches the Succinonitrile Melt-Solid Interface

NASA Technical Reports Server (NTRS)

Bune, Andris V.; Kaukler, William; Whitaker, Ann (Technical Monitor)

2001-01-01

A Modeling approach to simulate both mesoscale and microscopic forces acting in a typical AFM experiment is presented. A mesoscale level interaction between the cantilever tip and the sample surface is primarily described by the balance of attractive Van der Waals and repulsive forces. Ultimately, the goal is to measure the forces between a particle and the crystal-melt interface. Two modes of AFM operation are considered in this paper - a stationary and a "tapping" one. The continuous mechanics approach to model tip-surface interaction is presented. At microscopic levels, tip contamination and details of tip-surface interaction are modeled using a molecular dynamics approach for the case of polystyrene - succinonitrile contact. Integration of the mesoscale model with a molecular dynamic model is discussed.

Dynamic x-ray imaging of laser-driven nanoplasmas

NASA Astrophysics Data System (ADS)

Fennel, Thomas

2016-05-01

A major promise of current x-ray science at free electron lasers is the realization of unprecedented imaging capabilities for resolving the structure and ultrafast dynamics of matter with nanometer spatial and femtosecond temporal resolution or even below via single-shot x-ray diffraction. Laser-driven atomic clusters and nanoparticles provide an ideal platform for developing and demonstrating the required technology to extract the ultrafast transient spatiotemporal dynamics from the diffraction images. In this talk, the perspectives and challenges of dynamic x-ray imaging will be discussed using complete self-consistent microscopic electromagnetic simulations of IR pump x-ray probe imaging for the example of clusters. The results of the microscopic particle-in-cell simulations (MicPIC) enable the simulation-assisted reconstruction of corresponding experimental data. This capability is demonstrated by converting recently measured LCLS data into a ultrahigh resolution movie of laser-induced plasma expansion. Finally, routes towards reaching attosecond time resolution in the visualization of complex dynamical processes in matter by x-ray diffraction will be discussed.

Spine surgeon's kinematics during discectomy, part II: operating table height and visualization methods, including microscope.

PubMed

Park, Jeong Yoon; Kim, Kyung Hyun; Kuh, Sung Uk; Chin, Dong Kyu; Kim, Keun Su; Cho, Yong Eun

2014-05-01

Surgeon spine angle during surgery was studied ergonomically and the kinematics of the surgeon's spine was related with musculoskeletal fatigue and pain. Spine angles varied depending on operation table height and visualization method, and in a previous paper we showed that the use of a loupe and a table height at the midpoint between the umbilicus and the sternum are optimal for reducing musculoskeletal loading. However, no studies have previously included a microscope as a possible visualization method. The objective of this study is to assess differences in surgeon spine angles depending on operating table height and visualization method, including microscope. We enrolled 18 experienced spine surgeons for this study, who each performed a discectomy using a spine surgery simulator. Three different methods were used to visualize the surgical field (naked eye, loupe, microscope) and three different operating table heights (anterior superior iliac spine, umbilicus, the midpoint between the umbilicus and the sternum) were studied. Whole spine angles were compared for three different views during the discectomy simulation: midline, ipsilateral, and contralateral. A 16-camera optoelectronic motion analysis system was used, and 16 markers were placed from the head to the pelvis. Lumbar lordosis, thoracic kyphosis, cervical lordosis, and occipital angle were compared between the different operating table heights and visualization methods as well as a natural standing position. Whole spine angles differed significantly depending on visualization method. All parameters were closer to natural standing values when discectomy was performed with a microscope, and there were no differences between the naked eye and the loupe. Whole spine angles were also found to differ from the natural standing position depending on operating table height, and became closer to natural standing position values as the operating table height increased, independent of the visualization method. When using a microscope, lumbar lordosis, thoracic kyphosis, and cervical lordosis showed no differences according to table heights above the umbilicus. This study suggests that the use of a microscope and a table height above the umbilicus are optimal for reducing surgeon musculoskeletal fatigue.

A solid state physics approach to the interaction between organic molecules and interstellar dust grains: (C60) on SiC

NASA Astrophysics Data System (ADS)

Merino, P.; Martin-Gago, J. A.; Cernicharo, J.

2011-05-01

We have modeled the interaction of large organic molecules and dust grains in the interstellar medium by means of conventional surface science techniques such as scanning probe microscopes (SPM) and X-ray photoelectron spectroscopy (XPS) among others. With these surface analysis techniques, no frequently used in astrochemistry, we can recreate model systems where the interstellar environment, in a wide range of conditions of pressure and temperature, can be studied. The accurate control of the species that can be studied enables us to simulate in our laboratory the reactions of important molecules on the surface of dust grains. These new kind of experiments provide new information about the chemical mechanisms of the interaction between dust grains and organic molecules which can be compared with the models and the observations. We use a state of the art ultra high vacuum chamber (UHV) with base pressure of 1× 10-10 mbar (2× 106 ppcm^3) where we can prepare macroscopic single-crystal samples simulating a particular dust grain surface. The clean surfaces are exposed to different molecules. The complete system molecule-substrate can be characterized down to the Armstrong scale with the scanning tunneling microscope (STM) and even single molecule orbitals can be resolved. The combination of this technique with diffraction and spectroscopic tools allows us to fully understand the adsorption configuration and chemistry of a particular molecular species on a modeled dust grain surface. Here we present, as a proof-of-concept, the study of a broadly studied molecule, fullerene, (C60) on a silicon carbide (SiC) surface. The stellar winds of carbon-rich red-giants are rich in SiC grains in the inner hot (1500K) shell. These grains can then be covered with C_2 H_2, C H_4 and other hydrocarbons that could lead to complex organic molecules, even PAHs, when they move apart from the star. In the present study we simulate the reaction of C60 molecules with the Si rich (3x3) 6H α-SiC(0001). Although 6H α-SiC is not one of the most common polytypes of SiC in the interstellar atmospheres (mostly abundant in 2H α-SiC and 3C β-SiC) we will use these first results to compare with our on-going measurements on 3C β-SiC.

A Particle Module for the PLUTO Code. I. An Implementation of the MHD–PIC Equations

NASA Astrophysics Data System (ADS)

Mignone, A.; Bodo, G.; Vaidya, B.; Mattia, G.

2018-05-01

We describe an implementation of a particle physics module available for the PLUTO code appropriate for the dynamical evolution of a plasma consisting of a thermal fluid and a nonthermal component represented by relativistic charged particles or cosmic rays (CRs). While the fluid is approached using standard numerical schemes for magnetohydrodynamics, CR particles are treated kinetically using conventional Particle-In-Cell (PIC) techniques. The module can be used either to describe test-particle motion in the fluid electromagnetic field or to solve the fully coupled magnetohydrodynamics (MHD)–PIC system of equations with particle backreaction on the fluid as originally introduced by Bai et al. Particle backreaction on the fluid is included in the form of momentum–energy feedback and by introducing the CR-induced Hall term in Ohm’s law. The hybrid MHD–PIC module can be employed to study CR kinetic effects on scales larger than the (ion) skin depth provided that the Larmor gyration scale is properly resolved. When applicable, this formulation avoids resolving microscopic scales, offering substantial computational savings with respect to PIC simulations. We present a fully conservative formulation that is second-order accurate in time and space, and extends to either the Runge–Kutta (RK) or the corner transport upwind time-stepping schemes (for the fluid), while a standard Boris integrator is employed for the particles. For highly energetic relativistic CRs and in order to overcome the time-step restriction, a novel subcycling strategy that retains second-order accuracy in time is presented. Numerical benchmarks and applications including Bell instability, diffusive shock acceleration, and test-particle acceleration in reconnecting layers are discussed.

Resonant Cavity Enhanced On-Chip Raman Spectrometer Array with Precisely Positioned Metallic Nano-Gaps for Single Molecule Detection

DTIC Science & Technology

2011-03-22

the nanogaps are engraved on. Simulations show that smaller diameters of the nanowires should provide higher enhancement factors for SERS signal...Inverted Microscope with lasers of wavelengths of 512 to 633 nm as the excitation source. The signal was collected and analyzed by a 50cm Spectrometer...the optical path which can selectively pass the Raman signals and reject the excitation lasers . Figure 2.12 Custom built Raman microscope for the

Spreading dynamics of 2D dipolar Langmuir monolayer phases.

PubMed

Heinig, P; Wurlitzer, S; Fischer, Th M

2004-07-01

We study the spreading of a liquid 2D dipolar droplet in a Langmuir monolayer. Interfacial tensions (line tensions) and microscopic contact angles depend on the scale on which they are probed and obey a scaling law. Assuming rapid equilibration of the microscopic contact angle and ideal slippage of the 2D solid/liquid and solid/gas boundary, the driving force of spreading is merely expressed by the shape-dependent long-range interaction integrals. We obtain good agreement between experiment and numerical simulations using this theory.

Reaction-Infiltration Instabilities in Fractured and Porous Rocks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ladd, Anthony

In this project we are developing a multiscale analysis of the evolution of fracture permeability, using numerical simulations and linear stability analysis. Our simulations include fully three-dimensional simulations of the fracture topography, fluid flow, and reactant transport, two-dimensional simulations based on aperture models, and linear stability analysis.

Computer Simulations as an Integral Part of Intermediate Macroeconomics.

ERIC Educational Resources Information Center

Millerd, Frank W.; Robertson, Alastair R.

1987-01-01

Describes the development of two interactive computer simulations which were fully integrated with other course materials. The simulations illustrate the effects of various real and monetary "demand shocks" on aggregate income, interest rates, and components of spending and economic output. Includes an evaluation of the simulations'…

Abaqus Simulations of Rock Response to Dynamic Loading

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steedman, David W.; Coblentz, David

The LANL Geodynamics Team has been applying Abaqus modeling to achieve increasingly complex simulations. Advancements in Abaqus model building and simulation tools allows this progress. We use Lab-developed constitutive models, the fully coupled CEL Abaqus and general contact to simulate response of realistic sites to explosively driven shock.

The influence of computational strategy on prediction of mechanical stress in carotid atherosclerotic plaques: comparison of 2D structure-only, 3D structure-only, one-way and fully coupled fluid-structure interaction analyses.

PubMed

Huang, Yuan; Teng, Zhongzhao; Sadat, Umar; Graves, Martin J; Bennett, Martin R; Gillard, Jonathan H

2014-04-11

Compositional and morphological features of carotid atherosclerotic plaques provide complementary information to luminal stenosis in predicting clinical presentations. However, they alone cannot predict cerebrovascular risk. Mechanical stress within the plaque induced by cyclical changes in blood pressure has potential to assess plaque vulnerability. Various modeling strategies have been employed to predict stress, including 2D and 3D structure-only, 3D one-way and fully coupled fluid-structure interaction (FSI) simulations. However, differences in stress predictions using different strategies have not been assessed. Maximum principal stress (Stress-P1) within 8 human carotid atherosclerotic plaques was calculated based on geometry reconstructed from in vivo computerized tomography and high resolution, multi-sequence magnetic resonance images. Stress-P1 within the diseased region predicted by 2D and 3D structure-only, and 3D one-way FSI simulations were compared to 3D fully coupled FSI analysis. Compared to 3D fully coupled FSI, 2D structure-only simulation significantly overestimated stress level (94.1 kPa [65.2, 117.3] vs. 85.5 kPa [64.4, 113.6]; median [inter-quartile range], p=0.0004). However, when slices around the bifurcation region were excluded, stresses predicted by 2D structure-only simulations showed a good correlation (R(2)=0.69) with values obtained from 3D fully coupled FSI analysis. 3D structure-only model produced a small yet statistically significant stress overestimation compared to 3D fully coupled FSI (86.8 kPa [66.3, 115.8] vs. 85.5 kPa [64.4, 113.6]; p<0.0001). In contrast, one-way FSI underestimated stress compared to 3D fully coupled FSI (78.8 kPa [61.1, 100.4] vs. 85.5 kPa [64.4, 113.7]; p<0.0001). A 3D structure-only model seems to be a computationally inexpensive yet reasonably accurate approximation for stress within carotid atherosclerotic plaques with mild to moderate luminal stenosis as compared to fully coupled FSI analysis. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

A hybrid method for flood simulation in small catchments combining hydrodynamic and hydrological techniques

NASA Astrophysics Data System (ADS)

Bellos, Vasilis; Tsakiris, George

2016-09-01

The study presents a new hybrid method for the simulation of flood events in small catchments. It combines a physically-based two-dimensional hydrodynamic model and the hydrological unit hydrograph theory. Unit hydrographs are derived using the FLOW-R2D model which is based on the full form of two-dimensional Shallow Water Equations, solved by a modified McCormack numerical scheme. The method is tested at a small catchment in a suburb of Athens-Greece for a storm event which occurred in February 2013. The catchment is divided into three friction zones and unit hydrographs of 15 and 30 min are produced. The infiltration process is simulated by the empirical Kostiakov equation and the Green-Ampt model. The results from the implementation of the proposed hybrid method are compared with recorded data at the hydrometric station at the outlet of the catchment and the results derived from the fully hydrodynamic model FLOW-R2D. It is concluded that for the case studied, the proposed hybrid method produces results close to those of the fully hydrodynamic simulation at substantially shorter computational time. This finding, if further verified in a variety of case studies, can be useful in devising effective hybrid tools for the two-dimensional flood simulations, which are lead to accurate and considerably faster results than those achieved by the fully hydrodynamic simulations.

Mechanical characterization of metallic nanowires by using a customized atomic microscope

NASA Astrophysics Data System (ADS)

Celik, Emrah

A new experimental method to characterize the mechanical properties of metallic nanowires is introduced. An accurate and fast mechanical characterization of nanowires requires simultaneous imaging and testing of nanowires. However, there exists no practical experimental procedure in the literature that provides a quantitative mechanical analysis and imaging of the nanowire specimens during mechanical testing. In this study, a customized atomic force microscope (AFM) is placed inside a scanning electron microscope (SEM) in order to locate the position of the nanowires. The tip of the atomic force microscope cantilever is utilized to bend and break the nanowires. The nanowires are prepared by electroplating of nickel ions into the nanoscale pores of the alumina membranes. Force versus bending displacement responses of these nanowires are measured experimentally and then compared against those of the finite element analysis and peridynamic simulations to extract their mechanical properties through an inverse approach. The average elastic modulus of nickel nanowires, which are extracted using finite element analysis and peridynamic simulations, varies between 220 GPa and 225 GPa. The elastic modulus of bulk nickel published in the literature is comparable to that of nickel nanowires. This observation agrees well with the previous findings on nanowires stating that the elastic modulus of nanowires with diameters over 100nm is similar to that of bulk counterparts. The average yield stress of nickel nanowires, which are extracted using finite element analysis and peridynamic simulations, is found to be between 3.6 GPa to 4.1 GPa. The average value of yield stress of nickel nanowires with 250nm diameter is significantly higher than that of bulk nickel. Higher yield stress of nickel nanowires observed in this study can be explained by the lower defect density of nickel nanowires when compared to their bulk counterparts. Deviation in the extracted mechanical properties is investigated by analyzing the major sources of uncertainty in the experimental procedure. The effects of the nanowire orientation, the loading position and the nanowire diameter on the mechanical test results are quantified using ANSYS simulations. Among all of these three sources of uncertainty investigated, the nanowire diameter has been found to have the most significant effect on the extracted mechanical properties.

The interaction with gold suppresses fiber-like conformations of the amyloid β (16-22) peptide

NASA Astrophysics Data System (ADS)

Bellucci, Luca; Ardèvol, Albert; Parrinello, Michele; Lutz, Helmut; Lu, Hao; Weidner, Tobias; Corni, Stefano

2016-04-01

Inorganic surfaces and nanoparticles can accelerate or inhibit the fibrillation process of proteins and peptides, including the biomedically relevant amyloid β peptide. However, the microscopic mechanisms that determine such an effect are still poorly understood. By means of large-scale, state-of-the-art enhanced sampling molecular dynamics simulations, here we identify an interaction mechanism between the segments 16-22 of the amyloid β peptide, known to be fibrillogenic by itself, and the Au(111) surface in water that leads to the suppression of fiber-like conformations from the peptide conformational ensemble. Moreover, thanks to advanced simulation analysis techniques, we characterize the conformational selection vs. induced fit nature of the gold effect. Our results disclose an inhibition mechanism that is rooted in the details of the microscopic peptide-surface interaction rather than in general phenomena such as peptide sequestration from the solution.Inorganic surfaces and nanoparticles can accelerate or inhibit the fibrillation process of proteins and peptides, including the biomedically relevant amyloid β peptide. However, the microscopic mechanisms that determine such an effect are still poorly understood. By means of large-scale, state-of-the-art enhanced sampling molecular dynamics simulations, here we identify an interaction mechanism between the segments 16-22 of the amyloid β peptide, known to be fibrillogenic by itself, and the Au(111) surface in water that leads to the suppression of fiber-like conformations from the peptide conformational ensemble. Moreover, thanks to advanced simulation analysis techniques, we characterize the conformational selection vs. induced fit nature of the gold effect. Our results disclose an inhibition mechanism that is rooted in the details of the microscopic peptide-surface interaction rather than in general phenomena such as peptide sequestration from the solution. Electronic supplementary information (ESI) available: Representative structures for the most populated conformational structures of Aβ16-22 on bulk and on the metal surface. Normalized distribution of the variable s defined as the sum of internal dihedral angles of the peptide in solution and at the gold/water interface. See DOI: 10.1039/C6NR01539E

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daily, Michael D.; Olsen, Brett N.; Schlesinger, Paul H.

In mammalian cells cholesterol is essential for membrane function, but in excess can be cytototoxic. The cellular response to acute cholesterol loading involves biophysical-based mechanisms that regulate cholesterol levels, through modulation of the “activity” or accessibility of cholesterol to extra-membrane acceptors. Experiments and united atom (UA) simulations show that at high concentrations of cholesterol, lipid bilayers thin significantly and cholesterol availability to external acceptors increases substantially. Such cholesterol activation is critical to its trafficking within cells. Here we aim to reduce the computational cost to enable simulation of large and complex systems involved in cholesterol regulation, such as those includingmore » oxysterols and cholesterol-sensing proteins. To accomplish this, we have modified the published MARTINI coarse-grained force field to improve its predictions of cholesterol-induced changes in both macroscopic and microscopic properties of membranes. Most notably, MARTINI fails to capture both the (macroscopic) area condensation and membrane thickening seen at less than 30% cholesterol and the thinning seen above 40% cholesterol. The thinning at high concentration is critical to cholesterol activation. Microscopic properties of interest include cholesterol-cholesterol radial distribution functions (RDFs), tilt angle, and accessible surface area. First, we develop an “angle-corrected” model wherein we modify the coarse-grained bond angle potentials based on atomistic simulations. This modification significantly improves prediction of macroscopic properties, most notably the thickening/thinning behavior, and also slightly improves microscopic property prediction relative to MARTINI. Second, we add to the angle correction a “volume correction” by also adjusting phospholipid bond lengths to achieve a more accurate volume per molecule. The angle + volume correction substantially further improves the quantitative agreement of the macroscopic properties (area per molecule and thickness) with united atom simulations. However, this improvement also reduces the accuracy of microscopic predictions like radial distribution functions and cholesterol tilt below that of either MARTINI or the angle-corrected model. Thus, while both of our forcefield corrections improve MARTINI, the combined angle and volume correction should be used for problems involving sterol effects on the overall structure of the membrane, while our angle-corrected model should be used in cases where the properties of individual lipid and sterol models are critically important.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Juffmann, Thomas; Koppell, Stewart A.; Klopfer, Brannon B.

Feynman once asked physicists to build better electron microscopes to be able to watch biology at work. While electron microscopes can now provide atomic resolution, electron beam induced specimen damage precludes high resolution imaging of sensitive materials, such as single proteins or polymers. Here, we use simulations to show that an electron microscope based on a multi-pass measurement protocol enables imaging of single proteins, without averaging structures over multiple images. While we demonstrate the method for particular imaging targets, the approach is broadly applicable and is expected to improve resolution and sensitivity for a range of electron microscopy imaging modalities,more » including, for example, scanning and spectroscopic techniques. The approach implements a quantum mechanically optimal strategy which under idealized conditions can be considered interaction-free.« less

Parameters in selective laser melting for processing metallic powders

NASA Astrophysics Data System (ADS)

Kurzynowski, Tomasz; Chlebus, Edward; Kuźnicka, Bogumiła; Reiner, Jacek

2012-03-01

The paper presents results of studies on Selective Laser Melting. SLM is an additive manufacturing technology which may be used to process almost all metallic materials in the form of powder. Types of energy emission sources, mainly fiber lasers and/or Nd:YAG laser with similar characteristics and the wavelength of 1,06 - 1,08 microns, are provided primarily for processing metallic powder materials with high absorption of laser radiation. The paper presents results of selected variable parameters (laser power, scanning time, scanning strategy) and fixed parameters such as the protective atmosphere (argon, nitrogen, helium), temperature, type and shape of the powder material. The thematic scope is very broad, so the work was focused on optimizing the process of selective laser micrometallurgy for producing fully dense parts. The density is closely linked with other two conditions: discontinuity of the microstructure (microcracks) and stability (repeatability) of the process. Materials used for the research were stainless steel 316L (AISI), tool steel H13 (AISI), and titanium alloy Ti6Al7Nb (ISO 5832-11). Studies were performed with a scanning electron microscope, a light microscopes, a confocal microscope and a μCT scanner.

Fabrication and In Situ Transmission Electron Microscope Characterization of Free-Standing Graphene Nanoribbon Devices.

PubMed

Wang, Qing; Kitaura, Ryo; Suzuki, Shoji; Miyauchi, Yuhei; Matsuda, Kazunari; Yamamoto, Yuta; Arai, Shigeo; Shinohara, Hisanori

2016-01-26

Edge-dependent electronic properties of graphene nanoribbons (GNRs) have attracted intense interests. To fully understand the electronic properties of GNRs, the combination of precise structural characterization and electronic property measurement is essential. For this purpose, two experimental techniques using free-standing GNR devices have been developed, which leads to the simultaneous characterization of electronic properties and structures of GNRs. Free-standing graphene has been sculpted by a focused electron beam in transmission electron microscope (TEM) and then purified and narrowed by Joule heating down to several nanometer width. Structure-dependent electronic properties are observed in TEM, and significant increase in sheet resistance and semiconducting behavior become more salient as the width of GNR decreases. The narrowest GNR width we obtained with the present method is about 1.6 nm with a large transport gap of 400 meV.

Study of living single cells in culture: automated recognition of cell behavior.

PubMed

Bodin, P; Papin, S; Meyer, C; Travo, P

1988-07-01

An automated system capable of analyzing the behavior, in real time, of single living cells in culture, in a noninvasive and nondestructive way, has been developed. A large number of cell positions in single culture dishes were recorded using a computer controlled, robotized microscope. During subsequent observations, binary images obtained from video image analysis of the microscope visual field allowed the identification of the recorded cells. These cells could be revisited automatically every few minutes. Long-term studies of the behavior of cells make possible the analysis of cellular locomotary and mitotic activities as well as determination of cell shape (chosen from a defined library) for several hours or days in a fully automated way with observations spaced up to 30 minutes. Short-term studies of the behavior of cells permit the study, in a semiautomatic way, of acute effects of drugs (5 to 15 minutes) on changes of surface area and length of cells.

Microscopic Interpretation and Generalization of the Bloch-Torrey Equation for Diffusion Magnetic Resonance

PubMed Central

Seroussi, Inbar; Grebenkov, Denis S.; Pasternak, Ofer; Sochen, Nir

2017-01-01

In order to bridge microscopic molecular motion with macroscopic diffusion MR signal in complex structures, we propose a general stochastic model for molecular motion in a magnetic field. The Fokker-Planck equation of this model governs the probability density function describing the diffusion-magnetization propagator. From the propagator we derive a generalized version of the Bloch-Torrey equation and the relation to the random phase approach. This derivation does not require assumptions such as a spatially constant diffusion coefficient, or ad-hoc selection of a propagator. In particular, the boundary conditions that implicitly incorporate the microstructure into the diffusion MR signal can now be included explicitly through a spatially varying diffusion coefficient. While our generalization is reduced to the conventional Bloch-Torrey equation for piecewise constant diffusion coefficients, it also predicts scenarios in which an additional term to the equation is required to fully describe the MR signal. PMID:28242566

Microstructural and mechanical properties on friction welding of dissimilar metals used in motor vehicles

NASA Astrophysics Data System (ADS)

Jesudoss Hynes, N. Rajesh; Shenbaga Velu, P.

2018-02-01

In the last two decades, major car manufacturing companies are exploring the possibilities of joining magnesium with aluminium, via friction welding technique for many crucial automotive applications. Our primary objective, is to carry out an experimental investigation in order to study the behaviour of dissimilar joints. The microscopic structure at the welded joint interface was analysed using an optical microscopy and scanning electron microscope. It was found that, by increasing the value of friction time, the value of the tensile strength increases and the result of tensile strength is found to be 120 MPa at a friction time of 10 s. Micro hardness was found to be higher at the interface of the weldment due to the development of a brittle intermetallic compound. Micro structural studies using SEM reveals, distinct zones such as an unaffected parent metal zone, the heat affected zone, a thermo-mechanically affected zone and a fully deformed plasticised zone.

Experimental stress–strain analysis of tapered silica optical fibers with nanofiber waist

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holleis, S.; Hoinkes, T.; Wuttke, C.

2014-04-21

We experimentally determine tensile force–elongation diagrams of tapered optical fibers with a nanofiber waist. The tapered optical fibers are produced from standard silica optical fibers using a heat and pull process. Both, the force–elongation data and scanning electron microscope images of the rupture points indicate a brittle material. Despite the small waist radii of only a few hundred nanometers, our experimental data can be fully explained by a nonlinear stress–strain model that relies on material properties of macroscopic silica optical fibers. This is an important asset when it comes to designing miniaturized optical elements as one can rely on themore » well-founded material characteristics of standard optical fibers. Based on this understanding, we demonstrate a simple and non-destructive technique that allows us to determine the waist radius of the tapered optical fiber. We find excellent agreement with independent scanning electron microscope measurements of the waist radius.« less

Holographic digital microscopy in on-line process control

NASA Astrophysics Data System (ADS)

Osanlou, Ardeshir

2011-09-01

This article investigates the feasibility of real-time three-dimensional imaging of microscopic objects within various emulsions while being produced in specialized production vessels. The study is particularly relevant to on-line process monitoring and control in chemical, pharmaceutical, food, cleaning, and personal hygiene industries. Such processes are often dynamic and the materials cannot be measured once removed from the production vessel. The technique reported here is applicable to three-dimensional characterization analyses on stirred fluids in small reaction vessels. Relatively expensive pulsed lasers have been avoided through the careful control of the speed of the moving fluid in relation to the speed of the camera exposure and the wavelength of the continuous wave laser used. The ultimate aim of the project is to introduce a fully robust and compact digital holographic microscope as a process control tool in a full size specialized production vessel.

Gaussian theory for spatially distributed self-propelled particles

NASA Astrophysics Data System (ADS)

Seyed-Allaei, Hamid; Schimansky-Geier, Lutz; Ejtehadi, Mohammad Reza

2016-12-01

Obtaining a reduced description with particle and momentum flux densities outgoing from the microscopic equations of motion of the particles requires approximations. The usual method, we refer to as truncation method, is to zero Fourier modes of the orientation distribution starting from a given number. Here we propose another method to derive continuum equations for interacting self-propelled particles. The derivation is based on a Gaussian approximation (GA) of the distribution of the direction of particles. First, by means of simulation of the microscopic model, we justify that the distribution of individual directions fits well to a wrapped Gaussian distribution. Second, we numerically integrate the continuum equations derived in the GA in order to compare with results of simulations. We obtain that the global polarization in the GA exhibits a hysteresis in dependence on the noise intensity. It shows qualitatively the same behavior as we find in particles simulations. Moreover, both global polarizations agree perfectly for low noise intensities. The spatiotemporal structures of the GA are also in agreement with simulations. We conclude that the GA shows qualitative agreement for a wide range of noise intensities. In particular, for low noise intensities the agreement with simulations is better as other approximations, making the GA to an acceptable candidates of describing spatially distributed self-propelled particles.

Effect of Self-Assembly of Fullerene Nano-Particles on Lipid Membrane

PubMed Central

Zhang, Saiqun; Mu, Yuguang; Zhang, John Z. H.; Xu, Weixin

2013-01-01

Carbon nanoparticles can penetrate the cell membrane and cause cytotoxicity. The diffusion feature and translocation free energy of fullerene through lipid membranes is well reported. However, the knowledge on self-assembly of fullerenes and resulting effects on lipid membrane is poorly addressed. In this work, the self-assembly of fullerene nanoparticles and the resulting influence on the dioleoylphosphtidylcholine (DOPC) model membrane were studied by using all-atom molecular dynamics simulations with explicit solvents. Our simulation results confirm that gathered small fullerene cluster can invade lipid membrane. Simulations show two pathways: 1) assembly process is completely finished before penetration; 2) assembly process coincides with penetration. Simulation results also demonstrate that in the membrane interior, fullerene clusters tend to stay at the position which is 1.0 nm away from the membrane center. In addition, the diverse microscopic stacking mode (i.e., equilateral triangle, tetrahedral pentahedral, trigonal bipyramid and octahedron) of these small fullerene clusters are well characterized. Thus our simulations provide a detailed high-resolution characterization of the microscopic structures of the small fullerene clusters. Further, we found the gathered small fullerene clusters have significant adverse disturbances to the local structure of the membrane, but no great influence on the global integrity of the lipid membrane, which suggests the prerequisite of high-content fullerene for cytotoxicity. PMID:24204827

Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks.

PubMed

Cazade, Pierre-André; Berezovska, Ganna; Meuwly, Markus

2015-05-01

The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled. All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics. Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites. Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion. Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

Numerical simulation of dendrite growth in nickel-based superalloy and validated by in-situ observation using high temperature confocal laser scanning microscopy

NASA Astrophysics Data System (ADS)

Yan, Xuewei; Xu, Qingyan; Liu, Baicheng

2017-12-01

Dendritic structures are the predominant microstructural constituents of nickel-based superalloys, an understanding of the dendrite growth is required in order to obtain the desirable microstructure and improve the performance of castings. For this reason, numerical simulation method and an in-situ observation technology by employing high temperature confocal laser scanning microscopy (HT-CLSM) were used to investigate dendrite growth during solidification process. A combined cellular automaton-finite difference (CA-FD) model allowing for the prediction of dendrite growth of binary alloys was developed. The algorithm of cells capture was modified, and a deterministic cellular automaton (DCA) model was proposed to describe neighborhood tracking. The dendrite and detail morphology, especially hundreds of dendrites distribution at a large scale and three-dimensional (3-D) polycrystalline growth, were successfully simulated based on this model. The dendritic morphologies of samples before and after HT-CLSM were both observed by optical microscope (OM) and scanning electron microscope (SEM). The experimental observations presented a reasonable agreement with the simulation results. It was also found that primary or secondary dendrite arm spacing, and segregation pattern were significantly influenced by dendrite growth. Furthermore, the directional solidification (DS) dendritic evolution behavior and detail morphology were also simulated based on the proposed model, and the simulation results also agree well with experimental results.

Cosmic reionization on computers. Ultraviolet continuum slopes and dust opacities in high redshift galaxies

DOE PAGES

Khakhaleva-Li, Zimu; Gnedin, Nickolay Y.

2016-03-30

In this study, we compare the properties of stellar populations of model galaxies from the Cosmic Reionization On Computers (CROC) project with the exiting UV and IR data. Since CROC simulations do not follow cosmic dust directly, we adopt two variants of the dust-follows-metals ansatz to populate model galaxies with dust. Using the dust radiative transfer code Hyperion, we compute synthetic stellar spectra, UV continuum slopes, and IR fluxes for simulated galaxies. We find that the simulation results generally match observational measurements, but, perhaps, not in full detail. The differences seem to indicate that our adopted dust-follows-metals ansatzes are notmore » fully sufficient. While the discrepancies with the exiting data are marginal, the future JWST data will be of much higher precision, rendering highly significant any tentative difference between theory and observations. It is, therefore, likely, that in order to fully utilize the precision of JWST observations, fully dynamical modeling of dust formation, evolution, and destruction may be required.« less

Compressive Spectral Method for the Simulation of the Nonlinear Gravity Waves

PubMed Central

Bayındır, Cihan

2016-01-01

In this paper an approach for decreasing the computational effort required for the spectral simulations of the fully nonlinear ocean waves is introduced. The proposed approach utilizes the compressive sampling algorithm and depends on the idea of using a smaller number of spectral components compared to the classical spectral method. After performing the time integration with a smaller number of spectral components and using the compressive sampling technique, it is shown that the ocean wave field can be reconstructed with a significantly better efficiency compared to the classical spectral method. For the sparse ocean wave model in the frequency domain the fully nonlinear ocean waves with Jonswap spectrum is considered. By implementation of a high-order spectral method it is shown that the proposed methodology can simulate the linear and the fully nonlinear ocean waves with negligible difference in the accuracy and with a great efficiency by reducing the computation time significantly especially for large time evolutions. PMID:26911357

Cosmic reionization on computers. Ultraviolet continuum slopes and dust opacities in high redshift galaxies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khakhaleva-Li, Zimu; Gnedin, Nickolay Y.

In this study, we compare the properties of stellar populations of model galaxies from the Cosmic Reionization On Computers (CROC) project with the exiting UV and IR data. Since CROC simulations do not follow cosmic dust directly, we adopt two variants of the dust-follows-metals ansatz to populate model galaxies with dust. Using the dust radiative transfer code Hyperion, we compute synthetic stellar spectra, UV continuum slopes, and IR fluxes for simulated galaxies. We find that the simulation results generally match observational measurements, but, perhaps, not in full detail. The differences seem to indicate that our adopted dust-follows-metals ansatzes are notmore » fully sufficient. While the discrepancies with the exiting data are marginal, the future JWST data will be of much higher precision, rendering highly significant any tentative difference between theory and observations. It is, therefore, likely, that in order to fully utilize the precision of JWST observations, fully dynamical modeling of dust formation, evolution, and destruction may be required.« less

5D Tempest simulations of kinetic edge turbulence

NASA Astrophysics Data System (ADS)

Xu, X. Q.; Xiong, Z.; Cohen, B. I.; Cohen, R. H.; Dorr, M. R.; Hittinger, J. A.; Kerbel, G. D.; Nevins, W. M.; Rognlien, T. D.; Umansky, M. V.; Qin, H.

2006-10-01

Results are presented from the development and application of TEMPEST, a nonlinear five dimensional (3d2v) gyrokinetic continuum code. The simulation results and theoretical analysis include studies of H-mode edge plasma neoclassical transport and turbulence in real divertor geometry and its relationship to plasma flow generation with zero external momentum input, including the important orbit-squeezing effect due to the large electric field flow-shear in the edge. In order to extend the code to 5D, we have formulated a set of fully nonlinear electrostatic gyrokinetic equations and a fully nonlinear gyrokinetic Poisson's equation which is valid for both neoclassical and turbulence simulations. Our 5D gyrokinetic code is built on 4D version of Tempest neoclassical code with extension to a fifth dimension in binormal direction. The code is able to simulate either a full torus or a toroidal segment. Progress on performing 5D turbulence simulations will be reported.

Use of single scatter electron monte carlo transport for medical radiation sciences

DOEpatents

Svatos, Michelle M.

2001-01-01

The single scatter Monte Carlo code CREEP models precise microscopic interactions of electrons with matter to enhance physical understanding of radiation sciences. It is designed to simulate electrons in any medium, including materials important for biological studies. It simulates each interaction individually by sampling from a library which contains accurate information over a broad range of energies.

Increasing the Transfer of Simulation Technology from R&D into School Settings: An Approach to Evaluation from Overarching Vision to Individual Artifact in Education

ERIC Educational Resources Information Center

Blasi, Laura; Alfonso, Berta

2006-01-01

Building and evaluating artifacts specifically for K-12 education, technologists committed to design sciences are needed along with an approach to evaluation increasing the systemic transfer from research and development into school settings. The authors describe THE VIRTUAL LAB scanning electronic microscope simulation, including (a) its…

A fully automated calibration method for an optical see-through head-mounted operating microscope with variable zoom and focus.

PubMed

Figl, Michael; Ede, Christopher; Hummel, Johann; Wanschitz, Felix; Ewers, Rolf; Bergmann, Helmar; Birkfellner, Wolfgang

2005-11-01

Ever since the development of the first applications in image-guided therapy (IGT), the use of head-mounted displays (HMDs) was considered an important extension of existing IGT technologies. Several approaches to utilizing HMDs and modified medical devices for augmented reality (AR) visualization were implemented. These approaches include video-see through systems, semitransparent mirrors, modified endoscopes, and modified operating microscopes. Common to all these devices is the fact that a precise calibration between the display and three-dimensional coordinates in the patient's frame of reference is compulsory. In optical see-through devices based on complex optical systems such as operating microscopes or operating binoculars-as in the case of the system presented in this paper-this procedure can become increasingly difficult since precise camera calibration for every focus and zoom position is required. We present a method for fully automatic calibration of the operating binocular Varioscope M5 AR for the full range of zoom and focus settings available. Our method uses a special calibration pattern, a linear guide driven by a stepping motor, and special calibration software. The overlay error in the calibration plane was found to be 0.14-0.91 mm, which is less than 1% of the field of view. Using the motorized calibration rig as presented in the paper, we were also able to assess the dynamic latency when viewing augmentation graphics on a mobile target; spatial displacement due to latency was found to be in the range of 1.1-2.8 mm maximum, the disparity between the true object and its computed overlay represented latency of 0.1 s. We conclude that the automatic calibration method presented in this paper is sufficient in terms of accuracy and time requirements for standard uses of optical see-through systems in a clinical environment.

Directed polymers versus directed percolation

NASA Astrophysics Data System (ADS)

Halpin-Healy, Timothy

1998-10-01

Universality plays a central role within the rubric of modern statistical mechanics, wherein an insightful continuum formulation rises above irrelevant microscopic details, capturing essential scaling behaviors. Nevertheless, occasions do arise where the lattice or another discrete aspect can constitute a formidable legacy. Directed polymers in random media, along with its close sibling, directed percolation, provide an intriguing case in point. Indeed, the deep blood relation between these two models may have sabotaged past efforts to fully characterize the Kardar-Parisi-Zhang universality class, to which the directed polymer belongs.

A micro-macro coupling approach of MD-SPH method for reactive energetic materials

NASA Astrophysics Data System (ADS)

Liu, Gui Rong; Wang, Guang Yu; Peng, Qing; De, Suvranu

2017-01-01

The simulation of reactive energetic materials has long been the interest of researchers because of the extensive applications of explosives. Much research has been done on the subject at macro scale in the past and research at micro scale has been initiated recently. Equation of state (EoS) is the relation between physical quantities (pressure, temperature, energy and volume) describing thermodynamic states of materials under a given set of conditions. It plays a significant role in determining the characteristics of energetic materials, including Chapman-Jouguet point and detonation velocity. Furthermore, EoS is the key to connect microscopic and macroscopic phenomenon when simulating the macro effects of an explosion. For instance, an ignition and growth model for high explosives uses two JWL EoSs, one for solid explosive and the other for gaseous products, which are often obtained from experiments that can be quite expensive and hazardous. Therefore, it is ideal to calculate the EoS of energetic materials through computational means. In this paper, the EoSs for both solid and gaseous products of β-HMX are calculated using molecular dynamics simulation with ReaxFF-d3, a reactive force field obtained from quantum mechanics. The microscopic simulation results are then compared with experiments and the continuum ignition and growth model. Good agreement is observed. Then, the EoSs obtained through micro-scale simulation is applied in a smoothed particle hydrodynamics (SPH) code to simulate the macro effects of explosions. Simulation results are compared with experiments.

The impact of loupes and microscopes on vision in endodontics.

PubMed

Perrin, P; Neuhaus, K W; Lussi, A

2014-05-01

To report on an intraradicular visual test in a simulated clinical setting under different optical conditions. Miniaturized visual tests with E-optotypes (bar distance from 0.01 to 0.05 mm) were fixed inside the root canal system of an extracted maxillary molar at different locations: at the orifice, a depth of 5 mm and the apex. The tooth was mounted in a phantom head for a simulated clinical setting. Unaided vision was compared with Galilean loupes (2.5× magnification) with integrated light source and an operating microscope (6× magnification). The influence of the dentists' age within two groups was evaluated: <40 years (n = 9) and ≥40 years (n = 15). Some younger dentists were able to identify the E-optotypes at the orifice, but otherwise, natural vision did not reveal any measurable result. With Galilean loupes, the younger dentists <40 years could see a 0.05 mm structure at the root canal orifice, in contrast to the older group ≥40 years. Only the microscope allowed the observation of structures inside the root canal, independent of age. Unaided vision and Galilean loupes with an integrated light source could not provide any measurable vision inside the root canal, but younger dentists <40 years could detect with Galilean loupes a canal orifice corresponding to the tip of the smallest endodontic instruments. Dentists over 40 years of age were dependent on the microscope to inspect the root canal system. © 2013 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Microscopy and microanalysis of complex nanosized strengthening precipitates in new generation commercial Al-Cu-Li alloys.

PubMed

Guinel, M J-F; Brodusch, N; Sha, G; Shandiz, M A; Demers, H; Trudeau, M; Ringer, S P; Gauvin, R

2014-09-01

Precipitates (ppts) in new generation aluminum-lithium alloys (AA2099 and AA2199) were characterised using scanning and transmission electron microscopy and atom probe tomography. Results obtained on the following ppts are reported: Guinier-Preston zones, T1 (Al2 CuLi), β' (Al3 Zr) and δ' (Al3 Li). The focus was placed on their composition and the presence of minor elements. X-ray energy-dispersive spectrometry in the electron microscopes and mass spectrometry in the atom probe microscope showed that T1 ppts were enriched in zinc (Zn) and magnesium up to about 1.9 and 3.5 at.%, respectively. A concentration of 2.5 at.% Zn in the δ' ppts was also measured. Unlike Li and copper, Zn in the T1 ppts could not be detected using electron energy-loss spectroscopy in the transmission electron microscope because of its too low concentration and the small sizes of these ppts. Indeed, Monte Carlo simulations of EEL spectra for the Zn L2,3 edge showed that the signal-to-noise ratio was not high enough and that the detection limit was at least 2.5 at.%, depending on the probe current. Also, the simulation of X-ray spectra confirmed that the detection limit was exceeded for the Zn Kα X-ray line because the signal-to-noise ratio was high enough in that case, which is in agreement with our observations. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

A fully-automated multiscale kernel graph cuts based particle localization scheme for temporal focusing two-photon microscopy

NASA Astrophysics Data System (ADS)

Huang, Xia; Li, Chunqiang; Xiao, Chuan; Sun, Wenqing; Qian, Wei

2017-03-01

The temporal focusing two-photon microscope (TFM) is developed to perform depth resolved wide field fluorescence imaging by capturing frames sequentially. However, due to strong nonignorable noises and diffraction rings surrounding particles, further researches are extremely formidable without a precise particle localization technique. In this paper, we developed a fully-automated scheme to locate particles positions with high noise tolerance. Our scheme includes the following procedures: noise reduction using a hybrid Kalman filter method, particle segmentation based on a multiscale kernel graph cuts global and local segmentation algorithm, and a kinematic estimation based particle tracking method. Both isolated and partial-overlapped particles can be accurately identified with removal of unrelated pixels. Based on our quantitative analysis, 96.22% isolated particles and 84.19% partial-overlapped particles were successfully detected.

U.S. Highway 280 alternatives analysis and visualization

DOT National Transportation Integrated Search

2005-06-01

The Regional Planning Commission of Greater Birmingham (RPCGB), with coordination from Progress 280 and : the Alabama Department of Transportation (ALDOT), initiated the current study to utilize microscopic traffic : simulation to examine the effects...

Modeling cooperative driving behavior in freeway merges.

DOT National Transportation Integrated Search

2011-11-01

Merging locations are major sources of freeway bottlenecks and are therefore important for freeway operations analysis. Microscopic simulation tools have been successfully used to analyze merging bottlenecks and to design optimum geometric configurat...

New approaches in agent-based modeling of complex financial systems

NASA Astrophysics Data System (ADS)

Chen, Ting-Ting; Zheng, Bo; Li, Yan; Jiang, Xiong-Fei

2017-12-01

Agent-based modeling is a powerful simulation technique to understand the collective behavior and microscopic interaction in complex financial systems. Recently, the concept for determining the key parameters of agent-based models from empirical data instead of setting them artificially was suggested. We first review several agent-based models and the new approaches to determine the key model parameters from historical market data. Based on the agents' behaviors with heterogeneous personal preferences and interactions, these models are successful in explaining the microscopic origination of the temporal and spatial correlations of financial markets. We then present a novel paradigm combining big-data analysis with agent-based modeling. Specifically, from internet query and stock market data, we extract the information driving forces and develop an agent-based model to simulate the dynamic behaviors of complex financial systems.

Limit of validity of Ostwald's rule of stages in a statistical mechanical model of crystallization.

PubMed

Hedges, Lester O; Whitelam, Stephen

2011-10-28

We have only rules of thumb with which to predict how a material will crystallize, chief among which is Ostwald's rule of stages. It states that the first phase to appear upon transformation of a parent phase is the one closest to it in free energy. Although sometimes upheld, the rule is without theoretical foundation and is not universally obeyed, highlighting the need for microscopic understanding of crystallization controls. Here we study in detail the crystallization pathways of a prototypical model of patchy particles. The range of crystallization pathways it exhibits is richer than can be predicted by Ostwald's rule, but a combination of simulation and analytic theory reveals clearly how these pathways are selected by microscopic parameters. Our results suggest strategies for controlling self-assembly pathways in simulation and experiment.

Simulation study on compressive laminar optical tomography for cardiac action potential propagation

PubMed Central

Harada, Takumi; Tomii, Naoki; Manago, Shota; Kobayashi, Etsuko; Sakuma, Ichiro

2017-01-01

To measure the activity of tissue at the microscopic level, laminar optical tomography (LOT), which is a microscopic form of diffuse optical tomography, has been developed. However, obtaining sufficient recording speed to determine rapidly changing dynamic activity remains major challenges. For a high frame rate of the reconstructed data, we here propose a new LOT method using compressed sensing theory, called compressive laminar optical tomography (CLOT), in which novel digital micromirror device-based illumination and data reduction in a single reconstruction are applied. In the simulation experiments, the reconstructed volumetric images of the action potentials that were acquired from 5 measured images with random pattern featured a wave border at least to a depth of 2.5 mm. Consequently, it was shown that CLOT has potential for over 200 fps required for the cardiac electrophysiological phenomena. PMID:28736675

Capturing microscopic features of bone remodeling into a macroscopic model based on biological rationales of bone adaptation.

PubMed

Kim, Young Kwan; Kameo, Yoshitaka; Tanaka, Sakae; Adachi, Taiji

2017-10-01

To understand Wolff's law, bone adaptation by remodeling at the cellular and tissue levels has been discussed extensively through experimental and simulation studies. For the clinical application of a bone remodeling simulation, it is significant to establish a macroscopic model that incorporates clarified microscopic mechanisms. In this study, we proposed novel macroscopic models based on the microscopic mechanism of osteocytic mechanosensing, in which the flow of fluid in the lacuno-canalicular porosity generated by fluid pressure gradients plays an important role, and theoretically evaluated the proposed models, taking biological rationales of bone adaptation into account. The proposed models were categorized into two groups according to whether the remodeling equilibrium state was defined globally or locally, i.e., the global or local uniformity models. Each remodeling stimulus in the proposed models was quantitatively evaluated through image-based finite element analyses of a swine cancellous bone, according to two introduced criteria associated with the trabecular volume and orientation at remodeling equilibrium based on biological rationales. The evaluation suggested that nonuniformity of the mean stress gradient in the local uniformity model, one of the proposed stimuli, has high validity. Furthermore, the adaptive potential of each stimulus was discussed based on spatial distribution of a remodeling stimulus on the trabecular surface. The theoretical consideration of a remodeling stimulus based on biological rationales of bone adaptation would contribute to the establishment of a clinically applicable and reliable simulation model of bone remodeling.

Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations

NASA Astrophysics Data System (ADS)

Flegg, Mark B.; Hellander, Stefan; Erban, Radek

2015-05-01

In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is called the ghost cell method (GCM), since it works by constructing a "ghost cell" in which molecules can disappear and jump into the compartment-based simulation. Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step Δt (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter h, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered: Δt → 0 and h is fixed; Δt → 0 and h → 0 such that √{ Δt } / h is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model.

Stereovision-based integrated system for point cloud reconstruction and simulated brain shift validation.

PubMed

Yang, Xiaochen; Clements, Logan W; Luo, Ma; Narasimhan, Saramati; Thompson, Reid C; Dawant, Benoit M; Miga, Michael I

2017-07-01

Intraoperative soft tissue deformation, referred to as brain shift, compromises the application of current image-guided surgery navigation systems in neurosurgery. A computational model driven by sparse data has been proposed as a cost-effective method to compensate for cortical surface and volumetric displacements. We present a mock environment developed to acquire stereoimages from a tracked operating microscope and to reconstruct three-dimensional point clouds from these images. A reconstruction error of 1 mm is estimated by using a phantom with a known geometry and independently measured deformation extent. The microscope is tracked via an attached tracking rigid body that facilitates the recording of the position of the microscope via a commercial optical tracking system as it moves during the procedure. Point clouds, reconstructed under different microscope positions, are registered into the same space to compute the feature displacements. Using our mock craniotomy device, realistic cortical deformations are generated. When comparing our tracked microscope stereo-pair measure of mock vessel displacements to that of the measurement determined by the independent optically tracked stylus marking, the displacement error was [Formula: see text] on average. These results demonstrate the practicality of using tracked stereoscopic microscope as an alternative to laser range scanners to collect sufficient intraoperative information for brain shift correction.

Portable telepathology: methods and tools.

PubMed

Alfaro, Luis; Roca, Ma José

2008-07-15

Telepathology is becoming easier to implement in most pathology departments. In fact e-mail image transmit can be done from almost any pathologist as a simplistic telepathology system. We tried to develop a way to improve capabilities of communication among pathologists with the idea that the system should be affordable for everybody. We took the premise that any pathology department would have microscopes and computers with Internet connection, and selected a few elements to convert them into a telepathology station. Needs were reduced to a camera to collect images, a universal microscope adapter for the camera, a device to connect the camera to the computer, and a software for the remote image transmit. We found out a microscope adapter (MaxView Plus) that allowed us connect almost any domestic digital camera to any microscope. The video out signal from the camera was sent to the computer through an Aver Media USB connector. At last, we selected a group of portable applications that were assembled into a USB memory device. Portable applications are computer programs that can be carried generally on USB flash drives, but also in any other portable device, and used on any (Windows) computer without installation. Besides, when unplugging the device, none of personal data is left behind. We selected open-source applications, and based the pathology image transmission to VLC Media Player due to its functionality as streaming server, portability and ease of use and configuration. Audio transmission was usually done through normal phone lines. We also employed alternative videoconferencing software, SightSpeed for bi-directional image transmission from microscopes, and conventional cameras allowing visual communication and also image transmit from gross pathology specimens. All these elements allowed us to install and use a telepathology system in a few minutes, fully prepared for real time image broadcast.

Portable telepathology: methods and tools

PubMed Central

Alfaro, Luis; Roca, Ma José

2008-01-01

Telepathology is becoming easier to implement in most pathology departments. In fact e-mail image transmit can be done from almost any pathologist as a simplistic telepathology system. We tried to develop a way to improve capabilities of communication among pathologists with the idea that the system should be affordable for everybody. We took the premise that any pathology department would have microscopes and computers with Internet connection, and selected a few elements to convert them into a telepathology station. Needs were reduced to a camera to collect images, a universal microscope adapter for the camera, a device to connect the camera to the computer, and a software for the remote image transmit. We found out a microscope adapter (MaxView Plus) that allowed us connect almost any domestic digital camera to any microscope. The video out signal from the camera was sent to the computer through an Aver Media USB connector. At last, we selected a group of portable applications that were assembled into a USB memory device. Portable applications are computer programs that can be carried generally on USB flash drives, but also in any other portable device, and used on any (Windows) computer without installation. Besides when unplugging the device, none of personal data is left behind. We selected open-source applications, and based the pathology image transmission to VLC Media Player due to its functionality as streaming server, portability and ease of use and configuration. Audio transmission was usually done through normal phone lines. We also employed alternative videoconferencing software, SightSpeed for bi-directional image transmission from microscopes, and conventional cameras allowing visual communication and also image transmit from gross pathology specimens. All these elements allowed us to install and use a telepathology system in a few minutes, fully prepared for real time image broadcast. PMID:18673507

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.

PubMed

Vallenet, David; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Lajus, Aurélie; Josso, Adrien; Mercier, Jonathan; Renaux, Alexandre; Rollin, Johan; Rouy, Zoe; Roche, David; Scarpelli, Claude; Médigue, Claudine

2017-01-04

The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Spectral-element simulation of two-dimensional elastic wave propagation in fully heterogeneous media on a GPU cluster

NASA Astrophysics Data System (ADS)

Rudianto, Indra; Sudarmaji

2018-04-01

We present an implementation of the spectral-element method for simulation of two-dimensional elastic wave propagation in fully heterogeneous media. We have incorporated most of realistic geological features in the model, including surface topography, curved layer interfaces, and 2-D wave-speed heterogeneity. To accommodate such complexity, we use an unstructured quadrilateral meshing technique. Simulation was performed on a GPU cluster, which consists of 24 core processors Intel Xeon CPU and 4 NVIDIA Quadro graphics cards using CUDA and MPI implementation. We speed up the computation by a factor of about 5 compared to MPI only, and by a factor of about 40 compared to Serial implementation.

Development of a fully implicit particle-in-cell scheme for gyrokinetic electromagnetic turbulence simulation in XGC1

NASA Astrophysics Data System (ADS)

Ku, Seung-Hoe; Hager, R.; Chang, C. S.; Chacon, L.; Chen, G.; EPSI Team

2016-10-01

The cancelation problem has been a long-standing issue for long wavelengths modes in electromagnetic gyrokinetic PIC simulations in toroidal geometry. As an attempt of resolving this issue, we implemented a fully implicit time integration scheme in the full-f, gyrokinetic PIC code XGC1. The new scheme - based on the implicit Vlasov-Darwin PIC algorithm by G. Chen and L. Chacon - can potentially resolve cancelation problem. The time advance for the field and the particle equations is space-time-centered, with particle sub-cycling. The resulting system of equations is solved by a Picard iteration solver with fixed-point accelerator. The algorithm is implemented in the parallel velocity formalism instead of the canonical parallel momentum formalism. XGC1 specializes in simulating the tokamak edge plasma with magnetic separatrix geometry. A fully implicit scheme could be a way to accurate and efficient gyrokinetic simulations. We will test if this numerical scheme overcomes the cancelation problem, and reproduces the dispersion relation of Alfven waves and tearing modes in cylindrical geometry. Funded by US DOE FES and ASCR, and computing resources provided by OLCF through ALCC.

Multiple imputation for handling missing outcome data when estimating the relative risk.

PubMed

Sullivan, Thomas R; Lee, Katherine J; Ryan, Philip; Salter, Amy B

2017-09-06

Multiple imputation is a popular approach to handling missing data in medical research, yet little is known about its applicability for estimating the relative risk. Standard methods for imputing incomplete binary outcomes involve logistic regression or an assumption of multivariate normality, whereas relative risks are typically estimated using log binomial models. It is unclear whether misspecification of the imputation model in this setting could lead to biased parameter estimates. Using simulated data, we evaluated the performance of multiple imputation for handling missing data prior to estimating adjusted relative risks from a correctly specified multivariable log binomial model. We considered an arbitrary pattern of missing data in both outcome and exposure variables, with missing data induced under missing at random mechanisms. Focusing on standard model-based methods of multiple imputation, missing data were imputed using multivariate normal imputation or fully conditional specification with a logistic imputation model for the outcome. Multivariate normal imputation performed poorly in the simulation study, consistently producing estimates of the relative risk that were biased towards the null. Despite outperforming multivariate normal imputation, fully conditional specification also produced somewhat biased estimates, with greater bias observed for higher outcome prevalences and larger relative risks. Deleting imputed outcomes from analysis datasets did not improve the performance of fully conditional specification. Both multivariate normal imputation and fully conditional specification produced biased estimates of the relative risk, presumably since both use a misspecified imputation model. Based on simulation results, we recommend researchers use fully conditional specification rather than multivariate normal imputation and retain imputed outcomes in the analysis when estimating relative risks. However fully conditional specification is not without its shortcomings, and so further research is needed to identify optimal approaches for relative risk estimation within the multiple imputation framework.

A simulator study of the combined effects of alcohol and marihuana on driving behavior--phase II

DOT National Transportation Integrated Search

1983-02-01

Author's abstract: The study described in this report investigated the effects of alcohol and marihuana, alone and in combination, on driver performance and behavior in a fully interactive driving simulator. The simulator provided the driver a comple...

A fully-implicit Particle-In-Cell Monte Carlo Collision code for the simulation of inductively coupled plasmas

NASA Astrophysics Data System (ADS)

Mattei, S.; Nishida, K.; Onai, M.; Lettry, J.; Tran, M. Q.; Hatayama, A.

2017-12-01

We present a fully-implicit electromagnetic Particle-In-Cell Monte Carlo collision code, called NINJA, written for the simulation of inductively coupled plasmas. NINJA employs a kinetic enslaved Jacobian-Free Newton Krylov method to solve self-consistently the interaction between the electromagnetic field generated by the radio-frequency coil and the plasma response. The simulated plasma includes a kinetic description of charged and neutral species as well as the collision processes between them. The algorithm allows simulations with cell sizes much larger than the Debye length and time steps in excess of the Courant-Friedrichs-Lewy condition whilst preserving the conservation of the total energy. The code is applied to the simulation of the plasma discharge of the Linac4 H- ion source at CERN. Simulation results of plasma density, temperature and EEDF are discussed and compared with optical emission spectroscopy measurements. A systematic study of the energy conservation as a function of the numerical parameters is presented.

A cellular automata model of bone formation.

PubMed

Van Scoy, Gabrielle K; George, Estee L; Opoku Asantewaa, Flora; Kerns, Lucy; Saunders, Marnie M; Prieto-Langarica, Alicia

2017-04-01

Bone remodeling is an elegantly orchestrated process by which osteocytes, osteoblasts and osteoclasts function as a syncytium to maintain or modify bone. On the microscopic level, bone consists of cells that create, destroy and monitor the bone matrix. These cells interact in a coordinated manner to maintain a tightly regulated homeostasis. It is this regulation that is responsible for the observed increase in bone gain in the dominant arm of a tennis player and the observed increase in bone loss associated with spaceflight and osteoporosis. The manner in which these cells interact to bring about a change in bone quality and quantity has yet to be fully elucidated. But efforts to understand the multicellular complexity can ultimately lead to eradication of metabolic bone diseases such as osteoporosis and improved implant longevity. Experimentally validated mathematical models that simulate functional activity and offer eventual predictive capabilities offer tremendous potential in understanding multicellular bone remodeling. Here we undertake the initial challenge to develop a mathematical model of bone formation validated with in vitro data obtained from osteoblastic bone cells induced to mineralize and quantified at 26 days of culture. A cellular automata model was constructed to simulate the in vitro characterization. Permutation tests were performed to compare the distribution of the mineralization in the cultures and the distribution of the mineralization in the mathematical models. The results of the permutation test show the distribution of mineralization from the characterization and mathematical model come from the same probability distribution, therefore validating the cellular automata model. Copyright © 2017 Elsevier Inc. All rights reserved.

Experimental and simulation-based investigation of He, Ne and Ar irradiation of polymers for ion microscopy

PubMed Central

Rzeznik, Lukasz; Fleming, Yves; Wirtz, Tom

2016-01-01

Summary Secondary ion mass spectrometry (SIMS) on the helium ion microscope (HIM) promises higher lateral resolution than on classical SIMS instruments. However, full advantage of this new technique can only be obtained when the interaction of He+ or Ne+ primary ions with the sample is fully controlled. In this work we investigate how He+ and Ne+ bombardment influences roughness formation and preferential sputtering for polymer samples and how they compare to Ar+ primary ions used in classical SIMS by combining experimental techniques with Molecular Dynamics (MD) simulations and SD_TRIM_SP modelling. The results show that diffusion coefficients for He, Ne and Ar in polymers are sufficiently high to prevent any accumulation of rare gas atoms in the polymers which could lead to some swelling and bubble formation. Roughness formation was also not observed. Preferential sputtering is more of a problem, with enrichment of carbon up to surface concentrations above 80%. In general, the preferential sputtering is largely depending on the primary ion species and the impact energies. For He+ bombardment, it is more of an issue for low keV impact energies and for the heavier primary ion species the preferential sputtering is sample dependent. For He+ steady state conditions are reached for fluences much higher than 1018 ions/cm2. For Ne+ and Ar+, the transient regime extends up to fluences of 1017–1018 ions/cm2. Hence, preferential sputtering needs to be taken into account when interpreting images recorded under He+ or Ne+ bombardment on the HIM. PMID:27547629

Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy

PubMed Central

Weigert, Martin; Bundschuh, Sebastian T.

2018-01-01

Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy. Here we present biobeam, an open-source software package that enables simulation of operational light-sheet microscopes by combining data from 105–106 multiplexed and GPU-accelerated point-spread-function calculations. The wave-optical nature of these simulations leads to the faithful reproduction of spatially varying aberrations, diffraction artifacts, geometric image distortions, adaptive optics, and emergent wave-optical phenomena, and renders image-formation in light-sheet microscopy computationally tractable. PMID:29652879

[Detection of marginal leakage of Class V restorations in vitro by micro-CT].

PubMed

Gu, Lin-juan; Zhao, Xin-yi; Li, Shi-bao

2012-09-01

To evaluate the reliability and superiority of micro-CT in marginal leakage assessment of Class V restorations. Class V preparations with gingival margins in dentin and occlusal in enamel were made in sixteen extracted non-carious human molars and restored with dental bonding agents and composite resin. All teeth were then immersed in 50% ammonia-silver nitrate solution for 12 hours, followed by developing solution for 8 hours. Each restoration was scanned by a micro-CT and silver leakage was measured and three-dimensional image of the silver leakage alone cavity wall were reconstructed. Afterward, all restorations were sectioned and examined for leakage depth using a microscope. The silver leakage depth of each restoration obtained by micro-CT and microscope were compared for equivalency. The silver leakage depths in gingival wall obtained with micro-CT (0.78 mm) and microscope (0.74 mm) showed no significant difference (P > 0.05), while the judgment of leakage depths in occlusal wall in micro-CT image (0.40 mm) was affected by adjacent enamel structure, giving less leakage depths compared to microscope (0.72 mm)(P < 0.01). The three-dimensional shapes of the microleakages displayed clearly by micro-CT alone wall of Class V restorations were multiform and some leakages showed channels on their way to spreading. Micro-CT can detect precisely the silver leakage in the dentin wall of a restoration and display its three-dimensional shape fully. Enamel structure affects the detection of the silver leakage next to it.

Energy density functional on a microscopic basis

NASA Astrophysics Data System (ADS)

Baldo, M.; Robledo, L.; Schuck, P.; Viñas, X.

2010-06-01

In recent years impressive progress has been made in the development of highly accurate energy density functionals, which allow us to treat medium-heavy nuclei. In this approach one tries to describe not only the ground state but also the first relevant excited states. In general, higher accuracy requires a larger set of parameters, which must be carefully chosen to avoid redundancy. Following this line of development, it is unavoidable that the connection of the functional with the bare nucleon-nucleon interaction becomes more and more elusive. In principle, the construction of a density functional from a density matrix expansion based on the effective nucleon-nucleon interaction is possible, and indeed the approach has been followed by few authors. However, to what extent a density functional based on such a microscopic approach can reach the accuracy of the fully phenomenological ones remains an open question. A related question is to establish which part of a functional can be actually derived by a microscopic approach and which part, in contrast, must be left as purely phenomenological. In this paper we discuss the main problems that are encountered when the microscopic approach is followed. To this purpose we will use the method we have recently introduced to illustrate the different aspects of these problems. In particular we will discuss the possible connection of the density functional with the nuclear matter equation of state and the distinct features of finite-size effect typical of nuclei.

Efficient uncertainty quantification in fully-integrated surface and subsurface hydrologic simulations

NASA Astrophysics Data System (ADS)

Miller, K. L.; Berg, S. J.; Davison, J. H.; Sudicky, E. A.; Forsyth, P. A.

2018-01-01

Although high performance computers and advanced numerical methods have made the application of fully-integrated surface and subsurface flow and transport models such as HydroGeoSphere common place, run times for large complex basin models can still be on the order of days to weeks, thus, limiting the usefulness of traditional workhorse algorithms for uncertainty quantification (UQ) such as Latin Hypercube simulation (LHS) or Monte Carlo simulation (MCS), which generally require thousands of simulations to achieve an acceptable level of accuracy. In this paper we investigate non-intrusive polynomial chaos for uncertainty quantification, which in contrast to random sampling methods (e.g., LHS and MCS), represents a model response of interest as a weighted sum of polynomials over the random inputs. Once a chaos expansion has been constructed, approximating the mean, covariance, probability density function, cumulative distribution function, and other common statistics as well as local and global sensitivity measures is straightforward and computationally inexpensive, thus making PCE an attractive UQ method for hydrologic models with long run times. Our polynomial chaos implementation was validated through comparison with analytical solutions as well as solutions obtained via LHS for simple numerical problems. It was then used to quantify parametric uncertainty in a series of numerical problems with increasing complexity, including a two-dimensional fully-saturated, steady flow and transient transport problem with six uncertain parameters and one quantity of interest; a one-dimensional variably-saturated column test involving transient flow and transport, four uncertain parameters, and two quantities of interest at 101 spatial locations and five different times each (1010 total); and a three-dimensional fully-integrated surface and subsurface flow and transport problem for a small test catchment involving seven uncertain parameters and three quantities of interest at 241 different times each. Numerical experiments show that polynomial chaos is an effective and robust method for quantifying uncertainty in fully-integrated hydrologic simulations, which provides a rich set of features and is computationally efficient. Our approach has the potential for significant speedup over existing sampling based methods when the number of uncertain model parameters is modest ( ≤ 20). To our knowledge, this is the first implementation of the algorithm in a comprehensive, fully-integrated, physically-based three-dimensional hydrosystem model.

Macular photostress and visual experience between microscope and intracameral illumination during cataract surgery.

PubMed

Seo, Hyejin; Nam, Dong Heun; Lee, Jong Yeon; Park, Su Jin; Kim, Yu Jeong; Kim, Seong-Woo; Chung, Tae-Young; Inoue, Makoto; Kim, Terry

2018-02-01

To evaluate macular photostress and visual experience between coaxial microscope illumination versus oblique intracameral illumination during cataract surgery. Gachon University Gil Hospital, Incheon, South Korea. Prospective case series. Consecutive patients who had cataract surgery using microscope illumination and intracameral illumination were included. The patients were asked to complete a questionnaire (seeing strong lights, feeling photophobia, feeling startled (fright) when seeing lights, seeing any colors, seeing any instruments or surgical procedures, and estimating intraoperative visual function) designed to describe their cataract surgery experience. The images projected on the retina of the model eye (rear view) with artificial opaque fragments in the anterior chamber during simulating cataract surgery were compared between the 2 illumination types. Sixty patients completed the questionnaire. Scores for strong lights, photophobia, fright, and color perception were significantly higher with microscope illumination than with intracameral illumination (all P < .001). More patients preferred the intracameral illumination (45 [75.0%]) to the microscope illumination (13 [21.7%]). In the rear-view images created in a model eye, only the bright microscope light in the center was seen without any lens image in the microscope illumination. However, in the intracameral illumination, the less bright light from the light pipe in the periphery and the lens fragments were seen more clearly. In a view of the patients' visual experience, oblique intracameral illumination caused less subjective photostress and was preferred over coaxial microscope illumination. Objective findings from the model-eye experiment correlated to the result of visual experience. Copyright © 2018 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

Asymptotic Normality of the Maximum Pseudolikelihood Estimator for Fully Visible Boltzmann Machines.

PubMed

Nguyen, Hien D; Wood, Ian A

2016-04-01

Boltzmann machines (BMs) are a class of binary neural networks for which there have been numerous proposed methods of estimation. Recently, it has been shown that in the fully visible case of the BM, the method of maximum pseudolikelihood estimation (MPLE) results in parameter estimates, which are consistent in the probabilistic sense. In this brief, we investigate the properties of MPLE for the fully visible BMs further, and prove that MPLE also yields an asymptotically normal parameter estimator. These results can be used to construct confidence intervals and to test statistical hypotheses. These constructions provide a closed-form alternative to the current methods that require Monte Carlo simulation or resampling. We support our theoretical results by showing that the estimator behaves as expected in simulation studies.

Large Eddy Simulation in a Channel with Exit Boundary Conditions

NASA Technical Reports Server (NTRS)

Cziesla, T.; Braun, H.; Biswas, G.; Mitra, N. K.

1996-01-01

The influence of the exit boundary conditions (vanishing first derivative of the velocity components and constant pressure) on the large eddy simulation of the fully developed turbulent channel flow has been investigated for equidistant and stretched grids at the channel exit. Results show that the chosen exit boundary conditions introduce some small disturbance which is mostly damped by the grid stretching. The difference between the fully developed turbulent channel flow obtained with LES with periodicity condition and the inlet and exit and the LES with fully developed flow at the inlet and the exit boundary condition is less than 10% for equidistant grids and less than 5% for the case grid stretching. The chosen boundary condition is of interest because it may be used in complex flows with backflow at exit.

Temperature fluctuations in fully-developed turbulent channel flow with heated upper wall

NASA Astrophysics Data System (ADS)

Bahri, Carla; Mueller, Michael; Hultmark, Marcus

2013-11-01

The interactions and scaling differences between the velocity field and temperature field in a wall-bounded turbulent flow are investigated. In particular, a fully developed turbulent channel flow perturbed by a step change in the wall temperature is considered with a focus on the details of the developing thermal boundary layer. For this specific study, temperature acts as a passive scalar, having no dynamical effect on the flow. A combination of experimental investigation and direct numerical simulation (DNS) is presented. Velocity and temperature data are acquired with high accuracy where, the flow is allowed to reach a fully-developed state before encountering a heated upper wall at constant temperature. The experimental data is compared with DNS data where simulations of the same configuration are conducted.

Traffic operations modeling of Connecticut roundabouts : final report.

DOT National Transportation Integrated Search

2015-12-30

The Connecticut Department of Transportation (ConnDOT) has constructed four roundabouts in : the State of Connecticut within the past ten years. VISSIM, a microscopic traffic simulation software : program was utilized to analyze roundabout during the...

Calibration of microsimulation models for multimodal freight networks.

DOT National Transportation Integrated Search

2012-06-01

This research presents a framework for incorporating the unique operating characteristics of multi-modal freight networks : into the calibration process for microscopic traffic simulation models. Because of the nature of heavy freight movements : in ...

Calibration of CORSIM models under saturated traffic flow conditions.

DOT National Transportation Integrated Search

2013-09-01

This study proposes a methodology to calibrate microscopic traffic flow simulation models. : The proposed methodology has the capability to calibrate simultaneously all the calibration : parameters as well as demand patterns for any network topology....

Microscope-integrated optical coherence tomography for image-aided positioning of glaucoma surgery

NASA Astrophysics Data System (ADS)

Li, Xiqi; Wei, Ling; Dong, Xuechuan; Huang, Ping; Zhang, Chun; He, Yi; Shi, Guohua; Zhang, Yudong

2015-07-01

Most glaucoma surgeries involve creating new aqueous outflow pathways with the use of a small surgical instrument. This article reported a microscope-integrated, real-time, high-speed, swept-source optical coherence tomography system (SS-OCT) with a 1310-nm light source for glaucoma surgery. A special mechanism was designed to produce an adjustable system suitable for use in surgery. A two-graphic processing unit architecture was used to speed up the data processing and real-time volumetric rendering. The position of the surgical instrument can be monitored and measured using the microscope and a grid-inserted image of the SS-OCT. Finally, experiments were simulated to assess the effectiveness of this integrated system. Experimental results show that this system is a suitable positioning tool for glaucoma surgery.

Multi-pass transmission electron microscopy

DOE PAGES

Juffmann, Thomas; Koppell, Stewart A.; Klopfer, Brannon B.; ...

2017-05-10

Feynman once asked physicists to build better electron microscopes to be able to watch biology at work. While electron microscopes can now provide atomic resolution, electron beam induced specimen damage precludes high resolution imaging of sensitive materials, such as single proteins or polymers. Here, we use simulations to show that an electron microscope based on a multi-pass measurement protocol enables imaging of single proteins, without averaging structures over multiple images. While we demonstrate the method for particular imaging targets, the approach is broadly applicable and is expected to improve resolution and sensitivity for a range of electron microscopy imaging modalities,more » including, for example, scanning and spectroscopic techniques. The approach implements a quantum mechanically optimal strategy which under idealized conditions can be considered interaction-free.« less

Fully compressible solutions for early stage Richtmyer–Meshkov instability

DOE PAGES

Margolin, Len G.; Reisner, Jon Michael

2016-10-27

Here, we will consider the effects of compressibility and viscosity on the early dynamics of the Richtmyer–Meshkov instability (RMI). In particular, we will combine theory, scaling, and high resolution simulation of RMI to probe the details of the initial compression and the subsequent viscous damping as a shock interacts with a density discontinuity. We will propose a refinement of the classic 1D model for the linear regime of RMI that, for small initial perturbation wavelengths, more accurately reproduces the 2D dynamics of a fully resolved numerical simulation.

Studying aerosol light scattering based on aspect ratio distribution observed by fluorescence microscope.

PubMed

Li, Li; Zheng, Xu; Li, Zhengqiang; Li, Zhanhua; Dubovik, Oleg; Chen, Xingfeng; Wendisch, Manfred

2017-08-07

Particle shape is crucial to the properties of light scattered by atmospheric aerosol particles. A method of fluorescence microscopy direct observation was introduced to determine the aspect ratio distribution of aerosol particles. The result is comparable with that of the electron microscopic analysis. The measured aspect ratio distribution has been successfully applied in modeling light scattering and further in simulation of polarization measurements of the sun/sky radiometer. These efforts are expected to improve shape retrieval from skylight polarization by using directly measured aspect ratio distribution.

Artificial testing targets with controllable blur for adaptive optics microscopes

NASA Astrophysics Data System (ADS)

Hattori, Masayuki; Tamada, Yosuke; Murata, Takashi; Oya, Shin; Hasebe, Mitsuyasu; Hayano, Yutaka; Kamei, Yasuhiro

2017-08-01

This letter proposes a method of configuring a testing target to evaluate the performance of adaptive optics microscopes. In this method, a testing slide with fluorescent beads is used to simultaneously determine the point spread function and the field of view. The point spread function is reproduced to simulate actual biological samples by etching a microstructure on the cover glass. The fabrication process is simplified to facilitate an onsite preparation. The artificial tissue consists of solid materials and silicone oil and is stable for use in repetitive experiments.

Microscopic theory of cation exchange in CdSe nanocrystals.

PubMed

Ott, Florian D; Spiegel, Leo L; Norris, David J; Erwin, Steven C

2014-10-10

Although poorly understood, cation-exchange reactions are increasingly used to dope or transform colloidal semiconductor nanocrystals (quantum dots). We use density-functional theory and kinetic Monte Carlo simulations to develop a microscopic theory that explains structural, optical, and electronic changes observed experimentally in Ag-cation-exchanged CdSe nanocrystals. We find that Coulomb interactions, both between ionized impurities and with the polarized nanocrystal surface, play a key role in cation exchange. Our theory also resolves several experimental puzzles related to photoluminescence and electrical behavior in CdSe nanocrystals doped with Ag.

Microscopic analysis of Hopper flow with ellipsoidal particles

NASA Astrophysics Data System (ADS)

Liu, Sida; Zhou, Zongyan; Zou, Ruiping; Pinson, David; Yu, Aibing

2013-06-01

Hoppers are widely used in process industries. With such widespread application, difficulties in achieving desired operational behaviors have led to extensive experimental and mathematical studies in the past decades. Particularly, the discrete element method has become one of the most important simulation tools for design and analysis. So far, most studies are on spherical particles for computational convenience. In this work, ellipsoidal particles are used as they can represent a large variation of particle shapes. Hopper flow with ellipsoidal particles is presented highlighting the effect of particle shape on the microscopic properties.

Transformation of the θ-phase in Mg-Li-Al alloys: a density functional theory study.

PubMed

Zhang, Caili; Han, Peide; Zhang, Zhuxia; Dong, Minghui; Zhang, Lili; Gu, Xiangyang; Yang, Yanqing; Xu, Bingshe

2012-03-01

In Mg-Li-Al alloys, θ-phase MgAlLi(2) is a strengthening and metastable phase which is liable to be transformed to the equilibrium phase AlLi on overaging. While the structural details of the θ-phase MgAlLi(2) and the microscopic transformation are still unknown. In this paper, the structure of MgAlLi(2) unit cell was determined through X-ray powder diffraction simulation. Microscopic transformation process of θ-phase MgAlLi(2) was discussed in detail using first principles method.

Kinetic particle simulation of discharge and wall erosion of a Hall thruster

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cho, Shinatora; Komurasaki, Kimiya; Arakawa, Yoshihiro

2013-06-15

The primary lifetime limiting factor of Hall thrusters is the wall erosion caused by the ion induced sputtering, which is predominated by dielectric wall sheath and pre-sheath. However, so far only fluid or hybrid simulation models were applied to wall erosion and lifetime studies in which this non-quasi-neutral and non-equilibrium area cannot be treated directly. Thus, in this study, a 2D fully kinetic particle-in-cell model was presented for Hall thruster discharge and lifetime simulation. Because the fully kinetic lifetime simulation was yet to be achieved so far due to the high computational cost, the semi-implicit field solver and the techniquemore » of mass ratio manipulation was employed to accelerate the computation. However, other artificial manipulations like permittivity or geometry scaling were not used in order to avoid unrecoverable change of physics. Additionally, a new physics recovering model for the mass ratio was presented for better preservation of electron mobility at the weakly magnetically confined plasma region. The validity of the presented model was examined by various parametric studies, and the thrust performance and wall erosion rate of a laboratory model magnetic layer type Hall thruster was modeled for different operation conditions. The simulation results successfully reproduced the measurement results with typically less than 10% discrepancy without tuning any numerical parameters. It is also shown that the computational cost was reduced to the level that the Hall thruster fully kinetic lifetime simulation is feasible.« less

JPRS Report, Science & Technology, China

DTIC Science & Technology

1991-09-12

original Sanyo 183-cm television projector; its perfor- air-cushion seat; the hydraulic action tube and the air mance has been improved in terms of...is amplified to control the motion of the hydraulic action tube and the air cushion to simulate the sensation of Simulator Cockpit overload motion...Academy has detected face science, measurement science, microscope tech- obvious neutrons in a vacuum using a palladium elec- nology, ultra- microfine

LES-based filter-matrix lattice Boltzmann model for simulating fully developed turbulent channel flow

NASA Astrophysics Data System (ADS)

Zhuo, Congshan; Zhong, Chengwen

2016-11-01

In this paper, a three-dimensional filter-matrix lattice Boltzmann (FMLB) model based on large eddy simulation (LES) was verified for simulating wall-bounded turbulent flows. The Vreman subgrid-scale model was employed in the present FMLB-LES framework, which had been proved to be capable of predicting turbulent near-wall region accurately. The fully developed turbulent channel flows were performed at a friction Reynolds number Reτ of 180. The turbulence statistics computed from the present FMLB-LES simulations, including mean stream velocity profile, Reynolds stress profile and root-mean-square velocity fluctuations greed well with the LES results of multiple-relaxation-time (MRT) LB model, and some discrepancies in comparison with those direct numerical simulation (DNS) data of Kim et al. was also observed due to the relatively low grid resolution. Moreover, to investigate the influence of grid resolution on the present LES simulation, a DNS simulation on a finer gird was also implemented by present FMLB-D3Q19 model. Comparisons of detailed computed various turbulence statistics with available benchmark data of DNS showed quite well agreement.

Microscopic Structure and Solubility Predictions of Multifunctional Solids in Supercritical Carbon Dioxide: A Molecular Simulation Study.

PubMed

Noroozi, Javad; Paluch, Andrew S

2017-02-23

Molecular dynamics simulations were employed to both estimate the solubility of nonelectrolyte solids, such as acetanilide, acetaminophen, phenacetin, methylparaben, and lidocaine, in supercritical carbon dioxide and understand the underlying molecular-level driving forces. The solubility calculations involve the estimation of the solute's limiting activity coefficient, which may be computed using conventional staged free-energy calculations. For the case of lidocaine, wherein the infinite dilution approximation is not appropriate, we demonstrate how the activity coefficient at finite concentrations may be estimated without additional effort using the dilute solution approximation and how this may be used to further understand the solvation process. Combining with experimental pure-solid properties, namely, the normal melting point and enthalpy of fusion, solubilities were estimated. The results are in good quantitative agreement with available experimental data, suggesting that molecular simulations may be a powerful tool for understanding supercritical processes and the design of carbon dioxide-philic molecular systems. Structural analyses were performed to shed light on the microscopic details of the solvation of different functional groups by carbon dioxide and the observed solubility trends.

Finite element analysis of heat load of tungsten relevant to ITER conditions

NASA Astrophysics Data System (ADS)

Zinovev, A.; Terentyev, D.; Delannay, L.

2017-12-01

A computational procedure is proposed in order to predict the initiation of intergranular cracks in tungsten with ITER specification microstructure (i.e. characterised by elongated micrometre-sized grains). Damage is caused by a cyclic heat load, which emerges from plasma instabilities during operation of thermonuclear devices. First, a macroscopic thermo-mechanical simulation is performed in order to obtain temperature- and strain field in the material. The strain path is recorded at a selected point of interest of the macroscopic specimen, and is then applied at the microscopic level to a finite element mesh of a polycrystal. In the microscopic simulation, the stress state at the grain boundaries serves as the marker of cracking initiation. The simulated heat load cycle is a representative of edge-localized modes, which are anticipated during normal operations of ITER. Normal stresses at the grain boundary interfaces were shown to strongly depend on the direction of grain orientation with respect to the heat flux direction and to attain higher values if the flux is perpendicular to the elongated grains, where it apparently promotes crack initiation.

Dehydrogenation of aromatic molecules under a scanning tunneling microscope: pathways and inelastic spectroscopy simulations.

PubMed

Lesnard, Hervé; Bocquet, Marie-Laure; Lorente, Nicolas

2007-04-11

We have performed a theoretical study on the dehydrogenation of benzene and pyridine molecules on Cu(100) induced by a scanning tunneling microscope (STM). Density functional theory calculations have been used to characterize benzene, pyridine, and different dehydrogenation products. The adiabatic pathways for single and double dehydrogenation have been evaluated with the nudge elastic band method. After identification of the transition states, the analysis of the electronic structure along the reaction pathway yields interesting information on the electronic process that leads to H-scission. The adiabatic barriers show that the formation of double dehydrogenated fragments is difficult and probably beyond reach under the actual experimental conditions. However, nonadiabatic processes cannot be ruled out. Hence, in order to identify the final dehydrogenation products, the inelastic spectra are simulated and compared with the experimental ones. We can then assign phenyl (C6H5) and alpha-pyridil (alpha-C5H4N) as the STM-induced dehydrogenation products of benzene and pyridine, respectively. Our simulations permit us to understand why phenyl, pyridine, and alpha-pyridil present tunneling-active C-H stretch modes in opposition to benzene.

Enhancing the performance of the light field microscope using wavefront coding.

PubMed

Cohen, Noy; Yang, Samuel; Andalman, Aaron; Broxton, Michael; Grosenick, Logan; Deisseroth, Karl; Horowitz, Mark; Levoy, Marc

2014-10-06

Light field microscopy has been proposed as a new high-speed volumetric computational imaging method that enables reconstruction of 3-D volumes from captured projections of the 4-D light field. Recently, a detailed physical optics model of the light field microscope has been derived, which led to the development of a deconvolution algorithm that reconstructs 3-D volumes with high spatial resolution. However, the spatial resolution of the reconstructions has been shown to be non-uniform across depth, with some z planes showing high resolution and others, particularly at the center of the imaged volume, showing very low resolution. In this paper, we enhance the performance of the light field microscope using wavefront coding techniques. By including phase masks in the optical path of the microscope we are able to address this non-uniform resolution limitation. We have also found that superior control over the performance of the light field microscope can be achieved by using two phase masks rather than one, placed at the objective's back focal plane and at the microscope's native image plane. We present an extended optical model for our wavefront coded light field microscope and develop a performance metric based on Fisher information, which we use to choose adequate phase masks parameters. We validate our approach using both simulated data and experimental resolution measurements of a USAF 1951 resolution target; and demonstrate the utility for biological applications with in vivo volumetric calcium imaging of larval zebrafish brain.

Integrated system for point cloud reconstruction and simulated brain shift validation using tracked surgical microscope

NASA Astrophysics Data System (ADS)

Yang, Xiaochen; Clements, Logan W.; Luo, Ma; Narasimhan, Saramati; Thompson, Reid C.; Dawant, Benoit M.; Miga, Michael I.

2017-03-01

Intra-operative soft tissue deformation, referred to as brain shift, compromises the application of current imageguided surgery (IGS) navigation systems in neurosurgery. A computational model driven by sparse data has been used as a cost effective method to compensate for cortical surface and volumetric displacements. Stereoscopic microscopes and laser range scanners (LRS) are the two most investigated sparse intra-operative imaging modalities for driving these systems. However, integrating these devices in the clinical workflow to facilitate development and evaluation requires developing systems that easily permit data acquisition and processing. In this work we present a mock environment developed to acquire stereo images from a tracked operating microscope and to reconstruct 3D point clouds from these images. A reconstruction error of 1 mm is estimated by using a phantom with a known geometry and independently measured deformation extent. The microscope is tracked via an attached tracking rigid body that facilitates the recording of the position of the microscope via a commercial optical tracking system as it moves during the procedure. Point clouds, reconstructed under different microscope positions, are registered into the same space in order to compute the feature displacements. Using our mock craniotomy device, realistic cortical deformations are generated. Our experimental results report approximately 2mm average displacement error compared with the optical tracking system. These results demonstrate the practicality of using tracked stereoscopic microscope as an alternative to LRS to collect sufficient intraoperative information for brain shift correction.

Comparison of Middle Ear Visualization With Endoscopy and Microscopy.

PubMed

Bennett, Marc L; Zhang, Dongqing; Labadie, Robert F; Noble, Jack H

2016-04-01

The primary goal of chronic ear surgery is the creation of a safe, clean dry ear. For cholesteatomas, complete removal of disease is dependent on visualization. Conventional microscopy is adequate for most dissection, but various subregions of the middle ear are better visualized with endoscopy. The purpose of the present study was to quantitatively assess the improved visualization that endoscopes afford as compared with operating microscopes. Microscopic and endoscopic views were simulated using a three-dimensional model developed from temporal bone scans. Surface renderings of the ear canal and middle ear subsegments were defined and the percentage of visualization of each middle ear subsegment, both with and without ossicles, was then determined for the microscope as well as for 0-, 30-, and 45-degree endoscopes. Using this information, we analyzed which mode of visualization is best suited for dissection within a particular anatomical region. Using a 0-degree scope provides significantly more visualization of every subregion, except the antrum, compared with a microscope. In addition, angled scopes permit visualizing significantly more surface area of every subregion of the middle ear than straight scopes or microscopes. Endoscopes offer advantages for cholesteatoma dissection in difficult-to-visualize areas including the sinus tympani and epitympanum.

Dynamic evaluation of two decades of WRF-CMAQ ozone simulations over the contiguous United States

EPA Science Inventory

Dynamic evaluation of the fully coupled Weather Research and Forecasting (WRF)– Community Multi-scale Air Quality (CMAQ) model ozone simulations over the contiguous United States (CONUS) using two decades of simulations covering the period from 1990 to 2010 is conducted to ...

Dynamic evaluation of two decades of WRF-CMAQ ozone simulations over the contiguous United States

EPA Science Inventory

Dynamic evaluation of the fully coupled Weather Research and Forecasting (WRF)– Community Multi-scale Air Quality (CMAQ) model ozone simulations over the contiguous United States (CONUS) using two decades of simulations covering the period from 1990 to 2010 is conducted to assess...

Drama in Dynamics: Boom, Splash, and Speed

DOE Office of Scientific and Technical Information (OSTI.GOV)

Netzloff, Heather Marie

2004-12-19

The full nature of chemistry and physics cannot be captured by static calculations alone. Dynamics calculations allow the simulation of time-dependent phenomena. This facilitates both comparisons with experimental data and the prediction and interpretation of details not easily obtainable from experiments. Simulations thus provide a direct link between theory and experiment, between microscopic details of a system and macroscopic observed properties. Many types of dynamics calculations exist. The most important distinction between the methods and the decision of which method to use can be described in terms of the size and type of molecule/reaction under consideration and the type andmore » level of accuracy required in the final properties of interest. These considerations must be balanced with available computational codes and resources as simulations to mimic ''real-life'' may require many time steps. As indicated in the title, the theme of this thesis is dynamics. The goal is to utilize the best type of dynamics for the system under study while trying to perform dynamics in the most accurate way possible. As a quantum chemist, this involves some level of first principles calculations by default. Very accurate calculations of small molecules and molecular systems are now possible with relatively high-level ab initio quantum chemistry. For example, a quantum chemical potential energy surface (PES) can be developed ''on-the-fly'' with dynamic reaction path (DRP) methods. In this way a classical trajectory is developed without prior knowledge of the PES. In order to treat solvation processes and the condensed phase, large numbers of molecules are required, especially in predicting bulk behavior. The Effective Fragment Potential (EFP) method for solvation decreases the cost of a fully quantum mechanical calculation by dividing a chemical system into an ab initio region that contains the solute and an ''effective fragment'' region that contains the remaining solvent molecules. But, despite the reduced cost relative to fully QM calculations, the EFP method, due to its complex, QM-based potential, does require more computation time than simple interaction potentials, especially when the method is used for large scale molecular dynamics simulations. Thus, the EFP method was parallelized to facilitate these calculations within the quantum chemistry program GAMESS. The EFP method provides relative energies and structures that are in excellent agreement with the analogous fully quantum results for small water clusters. The ability of the method to predict bulk water properties with a comparable accuracy is assessed by performing EFP molecular dynamics simulations. Molecular dynamics simulations can provide properties that are directly comparable with experimental results, for example radial distribution functions. The molecular PES is a fundamental starting point for chemical reaction dynamics. Many methods can be used to obtain a PES; for example, assuming a global functional form for the PES or, as mentioned above, performing ''on-the-fly'' dynamics with Al or semi-empirical calculations at every molecular configuration. But as the size of the system grows, using electronic structure theory to build a PES and, therefore, study reaction dynamics becomes virtually impossible. The program Grow builds a PES as an interpolation of Al data; the goal is to attempt to produce an accurate PES with the smallest number of Al calculations. The Grow-GAMESS interface was developed to obtain the Al data from GAMESS. Classical or quantum dynamics can be performed on the resulting surface. The interface includes the novel capability to build multi-reference PESs; these types of calculations are applicable to problems ranging from atmospheric chemistry to photochemical reaction mechanisms in organic and inorganic chemistry to fundamental biological phenomena such as photosynthesis.« less

Evidence of weak land-atmosphere coupling under varying bare soil conditions: Are fully coupled Darcy/Navier-Stokes models necessary for simulating soil moisture dynamics?

NASA Astrophysics Data System (ADS)

Illangasekare, T. H.; Trautz, A. C.; Howington, S. E.; Cihan, A.

2017-12-01

It is a well-established fact that the land and atmosphere form a continuum in which the individual domains are coupled by heat and mass transfer processes such as bare-soil evaporation. Soil moisture dynamics can be simulated at the representative elementary volume (REV) scale using decoupled and fully coupled Darcy/Navier-Stokes models. Decoupled modeling is an asynchronous approach in which flow and transport in the soil and atmosphere is simulated independently; the two domains are coupled out of time-step via prescribed flux parameterizations. Fully coupled modeling in contrast, solves the governing equations for flow and transport in both domains simultaneously with the use of coupling interface boundary conditions. This latter approach, while being able to provide real-time two-dimensional feedbacks, is considerably more complex and computationally intensive. In this study, we investigate whether fully coupled models are necessary, or if the simpler decoupled models can sufficiently capture soil moisture dynamics under varying land preparations. A series of intermediate-scale physical and numerical experiments were conducted in which soil moisture distributions and evaporation estimates were monitored at high spatiotemporal resolutions for different heterogeneous packing and soil roughness scenarios. All experimentation was conducted at the newly developed Center for Experimental Study of Subsurface Environmental Processes (CESEP) wind tunnel-porous media user test-facility at the Colorado School of. Near-surface atmospheric measurements made during the experiments demonstrate that the land-atmosphere coupling was relatively weak and insensitive to the applied edaphic and surface conditions. Simulations with a decoupled multiphase heat and mass transfer model similarly show little sensitivity to local variations in atmospheric forcing; a single, simple flux parameterization can sufficiently capture the soil moisture dynamics (evaporation and redistribution) as long as the subsurface conditions (i.e., heterogeneity) are properly described. These findings suggest that significant improvements to simulations results should not be expected if fully coupled modeling were adopted in scenarios of weak land-atmosphere coupling in the context of bare soil evaporation.

Microscopic models for uphill diffusion

NASA Astrophysics Data System (ADS)

Colangeli, Matteo; De Masi, Anna; Presutti, Errico

2017-10-01

We study a system of particles which jump on the sites of the interval [1, L] of { Z} . The density at the boundaries is kept fixed to simulate the action of mass reservoirs. The evolution depends on two parameters \

Software Reviews.

ERIC Educational Resources Information Center

Science and Children, 1988

1988-01-01

Reviews six software packages for use with school age children ranging from grade 3 to grade 12. Includes "The Microcomputer Based Lab Project: Motion, Sound"; "Genetics"; "Geologic History"; "The Microscope Simulator"; and "Wiz Works" all for Apple II and "Reading for Information: Level…

Life cycle assessment framework of traffic systems based on microscopic simulation.

DOT National Transportation Integrated Search

2014-03-01

Transportation is an important infrastructure process needed in many steps of the supply chain of any product. Transportation-associated global impacts are therefore important factor influencing the sustainability of any product cycle. Moreover, traf...

Advanced Traffic Management Systems (ATMS) research analysis database system

DOT National Transportation Integrated Search

2001-06-01

The ATMS Research Analysis Database Systems (ARADS) consists of a Traffic Software Data Dictionary (TSDD) and a Traffic Software Object Model (TSOM) for application to microscopic traffic simulation and signal optimization domains. The purpose of thi...

Simulating electron wave dynamics in graphene superlattices exploiting parallel processing advantages

NASA Astrophysics Data System (ADS)

Rodrigues, Manuel J.; Fernandes, David E.; Silveirinha, Mário G.; Falcão, Gabriel

2018-01-01

This work introduces a parallel computing framework to characterize the propagation of electron waves in graphene-based nanostructures. The electron wave dynamics is modeled using both "microscopic" and effective medium formalisms and the numerical solution of the two-dimensional massless Dirac equation is determined using a Finite-Difference Time-Domain scheme. The propagation of electron waves in graphene superlattices with localized scattering centers is studied, and the role of the symmetry of the microscopic potential in the electron velocity is discussed. The computational methodologies target the parallel capabilities of heterogeneous multi-core CPU and multi-GPU environments and are built with the OpenCL parallel programming framework which provides a portable, vendor agnostic and high throughput-performance solution. The proposed heterogeneous multi-GPU implementation achieves speedup ratios up to 75x when compared to multi-thread and multi-core CPU execution, reducing simulation times from several hours to a couple of minutes.

Connecting macroscopic dynamics with microscopic properties in active microtubule network contraction

NASA Astrophysics Data System (ADS)

Foster, Peter J.; Yan, Wen; Fürthauer, Sebastian; Shelley, Michael J.; Needleman, Daniel J.

2017-12-01

The cellular cytoskeleton is an active material, driven out of equilibrium by molecular motor proteins. It is not understood how the collective behaviors of cytoskeletal networks emerge from the properties of the network’s constituent motor proteins and filaments. Here we present experimental results on networks of stabilized microtubules in Xenopus oocyte extracts, which undergo spontaneous bulk contraction driven by the motor protein dynein, and investigate the effects of varying the initial microtubule density and length distribution. We find that networks contract to a similar final density, irrespective of the length of microtubules or their initial density, but that the contraction timescale varies with the average microtubule length. To gain insight into why this microscopic property influences the macroscopic network contraction time, we developed simulations where microtubules and motors are explicitly represented. The simulations qualitatively recapitulate the variation of contraction timescale with microtubule length, and allowed stress contributions from different sources to be estimated and decoupled.

Electron-excited energy dispersive x-ray spectrometry in the variable pressure scanning electron microscope (EDS/VPSEM): it's not microanalysis anymore!

NASA Astrophysics Data System (ADS)

Newbury, Dale E.; Ritchie, Nicholas W. M.

2015-10-01

X-ray spectra suffer significantly degraded spatial resolution when measured in the variable-pressure scanning electron microscope (VPSEM, chamber pressure 1 Pa to 2500 Pa) as compared to highvacuum SEM (operating pressure < 10 mPa). Depending on the gas path length, electrons that are scattered hundreds of micrometers outside the focused beam can contribute 90% or more of the measured spectrum. Monte Carlo electron trajectory simulation, available in NIST DTSA-II, models the gas scattering and simulates mixed composition targets, e.g., particle on substrate. The impact of gas scattering at the major (C > 0.1 mass fraction), minor (0.01 <= C <= 0.1), and trace (C < 0.01) constituent levels can be estimated. NIST DTSA-II for Java-platforms is available free at: http://www.cstl.nist.gov/div837/837.02/epq/dtsa2/index.html).

Equation-free multiscale computation: algorithms and applications.

PubMed

Kevrekidis, Ioannis G; Samaey, Giovanni

2009-01-01

In traditional physicochemical modeling, one derives evolution equations at the (macroscopic, coarse) scale of interest; these are used to perform a variety of tasks (simulation, bifurcation analysis, optimization) using an arsenal of analytical and numerical techniques. For many complex systems, however, although one observes evolution at a macroscopic scale of interest, accurate models are only given at a more detailed (fine-scale, microscopic) level of description (e.g., lattice Boltzmann, kinetic Monte Carlo, molecular dynamics). Here, we review a framework for computer-aided multiscale analysis, which enables macroscopic computational tasks (over extended spatiotemporal scales) using only appropriately initialized microscopic simulation on short time and length scales. The methodology bypasses the derivation of macroscopic evolution equations when these equations conceptually exist but are not available in closed form-hence the term equation-free. We selectively discuss basic algorithms and underlying principles and illustrate the approach through representative applications. We also discuss potential difficulties and outline areas for future research.

Bright-field scanning confocal electron microscopy using a double aberration-corrected transmission electron microscope.

PubMed

Wang, Peng; Behan, Gavin; Kirkland, Angus I; Nellist, Peter D; Cosgriff, Eireann C; D'Alfonso, Adrian J; Morgan, Andrew J; Allen, Leslie J; Hashimoto, Ayako; Takeguchi, Masaki; Mitsuishi, Kazutaka; Shimojo, Masayuki

2011-06-01

Scanning confocal electron microscopy (SCEM) offers a mechanism for three-dimensional imaging of materials, which makes use of the reduced depth of field in an aberration-corrected transmission electron microscope. The simplest configuration of SCEM is the bright-field mode. In this paper we present experimental data and simulations showing the form of bright-field SCEM images. We show that the depth dependence of the three-dimensional image can be explained in terms of two-dimensional images formed in the detector plane. For a crystalline sample, this so-called probe image is shown to be similar to a conventional diffraction pattern. Experimental results and simulations show how the diffracted probes in this image are elongated in thicker crystals and the use of this elongation to estimate sample thickness is explored. Copyright © 2010 Elsevier B.V. All rights reserved.

Microscopic Scale Simulation of the Ablation of Fibrous Materials

NASA Technical Reports Server (NTRS)

Lachaud, Jean Romain; Mansour, Nagi N.

2010-01-01

Ablation by oxidation of carbon-fiber preforms impregnated in carbonized phenolic matrix is modeled at microscopic scale. Direct numerical simulations show that the carbonized phenolic matrix ablates in volume leaving the carbon fibers exposed. This is due to the fact that the reactivity of carbonized phenolic is higher than the reactivity of carbon fibers. After the matrix is depleted, the fibers ablate showing progressive reduction of their diameter. The overall material recession occurs when the fibers are consumed. Two materials with the same carbon-fiber preform, density and chemical composition, but with different matrix distributions are studied. These studies show that at moderate temperatures (< 1000 K) the microstructure of the material influences its recession rate; a fact that is not captured by current models that are based on chemical composition only. Surprisingly, the response of these impregnated-fiber materials is weakly dependent on the microstructure at very high temperatures (e.g., Stardust peak heating conditions: 3360K).

Self-Repairing Mechanism of MUF/Epoxy Microcapsules for Epoxy Material

NASA Astrophysics Data System (ADS)

Ni, Zhuo; Lin, Yuhao; Zhou, Xiaobo

2017-12-01

In this paper, a post curing reaction for the microcapsule/epoxy composite material and the conditions of thermal treatment for self-healing process were studied by differential scanning calorimetry (DSC). The condition of thermal treatment for post curing (60°C, 2 hours) was employed to fully cure the epoxy composite. Damage mechanism for the epoxy material was demonstrated via data simulation and three-point bending experiment for the stress distribution reveals that micro-cracks are more likely to be generated on the central region in stress concentration area of two constrained boundaries and the numbers of micro-cracks are reduced from the central area to the two ends of the material. Self-repairing performances of MUF microcapsule/epoxy composite materials were characterized using both destructive bending tests and non-destructive DMA measurements. Self-healing efficiencies of the composites embedded 2% and 5% microcapsule content measured by DMA are 101% and 104% respectively which are close to those results of 104% and 113% correspondingly measured by bending tests. Crack formation and development, core material releasing for MUF microcapsules and physiochemical process of the self-repairing were investigated by using OM, fluorescent technique and infrared microscope. These provide detailed evidences and important information on self-healing mechanism of the microcapsule/epoxy self-repairing material.

Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation

PubMed Central

Vaikuntanathan, Suriyanarayanan; Rotskoff, Grant; Hudson, Alexander; Geissler, Phillip L.

2016-01-01

Modern theories of the hydrophobic effect highlight its dependence on length scale, emphasizing the importance of interfaces in the vicinity of sizable hydrophobes. We recently showed that a faithful treatment of such nanoscale interfaces requires careful attention to the statistics of capillary waves, with significant quantitative implications for the calculation of solvation thermodynamics. Here, we show that a coarse-grained lattice model like that of Chandler [Chandler D (2005) Nature 437(7059):640–647], when informed by this understanding, can capture a broad range of hydrophobic behaviors with striking accuracy. Specifically, we calculate probability distributions for microscopic density fluctuations that agree very well with results of atomistic simulations, even many SDs from the mean and even for probe volumes in highly heterogeneous environments. This accuracy is achieved without adjustment of free parameters, because the model is fully specified by well-known properties of liquid water. As examples of its utility, we compute the free-energy profile for a solute crossing the air–water interface, as well as the thermodynamic cost of evacuating the space between extended nanoscale surfaces. These calculations suggest that a highly reduced model for aqueous solvation can enable efficient multiscale modeling of spatial organization driven by hydrophobic and interfacial forces. PMID:26957607

Testing and Analysis of Composite Skin/Stringer Debonding Under Multi-Axial Loading

NASA Technical Reports Server (NTRS)

Krueger, Ronald; Cvitkovich, Michael K.; OBrien, T. Kevin; Minguet, Pierre J.

1999-01-01

Damage mechanisms in composite bonded skin/stringer constructions under uniaxial and biaxial (in-plane/out- of-plane) loading conditions were examined. Specimens consisted of a tapered composite flange bonded onto a composite skin. Tests were performed under monotonic loading conditions in tension, three-point bending, and combined tension/bending . For combined tension/bending testing, a unique servohydraulic load frame was used that was capable of applying both in-plane tension and out-of-plane bending loads simultaneously. Specimen edges were examined on the microscope to document the damage occurrence and to identify typical damage patterns. The observations showed that, for all three load cases, failure initiated in the flange, near the flange tip, causing the flange to almost fully debond from the skin. A two-dimensional plane-strain finite element model was developed to analyze the different test cases using a geometrically nonlinear solution. For all three loading conditions, principal stresses exceeded the transverse strength of the material in the flange area. Additionally, delaminations of various lengths were simulated in two locations where delaminations were observed. The analyses showed that unstable delamination propagation is likely to occur in one location at the loads corresponding to matrix ply crack initiation for all three load cases.

Biofilm formation and design features of indwelling silicone rubber tracheoesophageal voice prostheses--an electron microscopical study.

PubMed

Leunisse, C; van Weissenbruch, R; Busscher, H J; van der Mei, H C; Dijk, F; Albers, F W

2001-01-01

After total laryngectomy, voice can be restored with a silicone rubber tracheoesophageal voice prosthesis. However, biofilm formation and subsequent deterioration of the silicone material of the prosthesis will limit device life by impairing valve function. To simulate the natural process of biofilm development under dynamic nutrient conditions, a modified Robbins device was used to evaluate the biofilm-related valve dysfunction of the Groningen, Provox2, Blom-Singer indwelling, and VoiceMaster voice prostheses. Obstruction of the semicircular slit-valved Groningen prosthesis leading to increased airway resistance was caused not only by a buildup of deposits on the esophageal flange and valve hat, but also by accumulation of deposits on the semicircular valve seating. The hinged flap valved Provox2 and indwelling Blom-Singer prostheses failed to close sufficiently because of biofilm formation on the valve seating. The esophageal flange of the VoiceMaster prosthesis was affected, but the tripod structure of the ball valve was fully colonized up to the titanium sleeve, which interfered with proper valve opening and closure. These findings on biofilm formation could be used for the further development and modification of critical design features of voice prostheses to facilitate tracheoesophageal speech. Copyright 2001 John Wiley & Sons, Inc.

The local strength of individual alumina particles

NASA Astrophysics Data System (ADS)

Pejchal, Václav; Fornabaio, Marta; Žagar, Goran; Mortensen, Andreas

2017-12-01

We implement the C-shaped sample test method and micro-cantilever beam testing to measure the local strength of microscopic, low-aspect-ratio ceramic particles, namely high-purity vapor grown α-alumina Sumicorundum® particles 15-30 μm in diameter, known to be attractive reinforcing particles for aluminum. Individual particles are shaped by focused ion beam micromachining so as to probe in tension a portion of the particle surface that is left unaffected by ion-milling. Mechanical testing of C-shaped specimens is done ex-situ using a nanoindentation apparatus, and in the SEM using an in-situ nanomechanical testing system for micro-cantilever beams. The strength is evaluated for each individual specimen using bespoke finite element simulation. Results show that, provided the particle surface is free of readily observable defects such as pores, twins or grain boundaries and their associated grooves, the particles can achieve local strength values that approach those of high-perfection single-crystal alumina whiskers, on the order of 10 GPa, outperforming high-strength nanocrystalline alumina fibers and nano-thick alumina platelets used in bio-inspired composites. It is also shown that by far the most harmful defects are grain boundaries, leading to the general conclusion that alumina particles must be single-crystalline or alternatively nanocrystalline to fully develop their potential as a strong reinforcing phase in composite materials.

Direct numerical simulations of agglomeration of circular colloidal particles in two-dimensional shear flow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choi, Young Joon, E-mail: yjchoi@uvic.ca; Djilali, Ned, E-mail: ndjilali@uvic.ca

2016-01-15

Colloidal agglomeration of nanoparticles in shear flow is investigated by solving the fluid-particle and particle-particle interactions in a 2D system. We use an extended finite element method in which the dynamics of the particles is solved in a fully coupled manner with the flow, allowing an accurate description of the fluid-particle interfaces without the need of boundary-fitted meshes or of empirical correlations to account for the hydrodynamic interactions between the particles. Adaptive local mesh refinement using a grid deformation method is incorporated with the fluid-structure interaction algorithm, and the particle-particle interaction at the microscopic level is modeled using the Lennard-Jonesmore » potential. Motivated by the process used in fabricating fuel cell catalysts from a colloidal ink, the model is applied to investigate agglomeration of colloidal particles under external shear flow in a sliding bi-periodic Lees-Edwards frame with varying shear rates and particle fraction ratios. Both external shear and particle fraction are found to have a crucial impact on the structure formation of colloidal particles in a suspension. Segregation intensity and graph theory are used to analyze the underlying agglomeration patterns and structures, and three agglomeration regimes are identified.« less

Lattice Boltzmann simulations of heat transfer in fully developed periodic incompressible flows

NASA Astrophysics Data System (ADS)

Wang, Zimeng; Shang, Helen; Zhang, Junfeng

2017-06-01

Flow and heat transfer in periodic structures are of great interest for many applications. In this paper, we carefully examine the periodic features of fully developed periodic incompressible thermal flows, and incorporate them in the lattice Boltzmann method (LBM) for flow and heat transfer simulations. Two numerical approaches, the distribution modification (DM) approach and the source term (ST) approach, are proposed; and they can both be used for periodic thermal flows with constant wall temperature (CWT) and surface heat flux boundary conditions. However, the DM approach might be more efficient, especially for CWT systems since the ST approach requires calculations of the streamwise temperature gradient at all lattice nodes. Several example simulations are conducted, including flows through flat and wavy channels and flows through a square array with circular cylinders. Results are compared to analytical solutions, previous studies, and our own LBM calculations using different simulation techniques (i.e., the one-module simulation vs. the two-module simulation, and the DM approach vs. the ST approach) with good agreement. These simple, however, representative simulations demonstrate the accuracy and usefulness of our proposed LBM methods for future thermal periodic flow simulations.

Investigation of Influence of Surface Nanoparticle on Emission Properties of Scandia-Doped Dispenser Cathodes

NASA Astrophysics Data System (ADS)

Zhang, Xizhu; Wang, Jinshu; Wang, Yiman; Liu, Wei; Zhou, Meiling; Gao, Zhiyuan

2013-06-01

The microstructure of a fully activated scandia doped dispenser (SDD) cathode has been studied by scanning electron microscope (SEM). The observation results display that nanoparticles appear at the growth steps and the surface of tungsten grains of the fully activated SDD cathode. To study the influence of the nanoparticles on the emission, the local electric field strengths around the nanoparticles have been calculated by Maxwell 2D code and Comsol. The calculation results show that the local electric field strengths are enhanced by 1.1 to 3.8 times to average value based on different model conditions. The highest field strength is about 1.54 × 105 V/cm at an average field strength of 40 KV/cm, which is related to a space-charge limited (SCL) current density of 100 A/cm2 in the experimental configuration. This implies the field strength is not high enough to cause field emission.

COSMIC REIONIZATION ON COMPUTERS. ULTRAVIOLET CONTINUUM SLOPES AND DUST OPACITIES IN HIGH REDSHIFT GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khakhaleva-Li, Zimu; Gnedin, Nickolay Y., E-mail: zimu@uchicago.edu, E-mail: gnedin@fnal.gov

We compare the properties of stellar populations of model galaxies from the Cosmic Reionization On Computers (CROC) project with the exiting ultraviolet (UV) and IR data. Since CROC simulations do not follow cosmic dust directly, we adopt two variants of the dust-follows-metals ansatz to populate model galaxies with dust. Using the dust radiative transfer code Hyperion, we compute synthetic stellar spectra, UV continuum slopes, and IR fluxes for simulated galaxies. We find that the simulation results generally match observational measurements, but, perhaps, not in full detail. The differences seem to indicate that our adopted dust-follows-metals ansatzes are not fully sufficient.more » While the discrepancies with the exiting data are marginal, the future James Webb Space Telescope (JWST) data will be of much higher precision, rendering highly significant any tentative difference between theory and observations. It is, therefore, likely, that in order to fully utilize the precision of JWST observations, fully dynamical modeling of dust formation, evolution, and destruction may be required.« less

Near real-time digital holographic microscope based on GPU parallel computing

NASA Astrophysics Data System (ADS)

Zhu, Gang; Zhao, Zhixiong; Wang, Huarui; Yang, Yan

2018-01-01

A transmission near real-time digital holographic microscope with in-line and off-axis light path is presented, in which the parallel computing technology based on compute unified device architecture (CUDA) and digital holographic microscopy are combined. Compared to other holographic microscopes, which have to implement reconstruction in multiple focal planes and are time-consuming the reconstruction speed of the near real-time digital holographic microscope can be greatly improved with the parallel computing technology based on CUDA, so it is especially suitable for measurements of particle field in micrometer and nanometer scale. Simulations and experiments show that the proposed transmission digital holographic microscope can accurately measure and display the velocity of particle field in micrometer scale, and the average velocity error is lower than 10%.With the graphic processing units(GPU), the computing time of the 100 reconstruction planes(512×512 grids) is lower than 120ms, while it is 4.9s using traditional reconstruction method by CPU. The reconstruction speed has been raised by 40 times. In other words, it can handle holograms at 8.3 frames per second and the near real-time measurement and display of particle velocity field are realized. The real-time three-dimensional reconstruction of particle velocity field is expected to achieve by further optimization of software and hardware. Keywords: digital holographic microscope,

Toward textbook multigrid efficiency for fully implicit resistive magnetohydrodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams, Mark F.; Samtaney, Ravi, E-mail: samtaney@pppl.go; Brandt, Achi

2010-09-01

Multigrid methods can solve some classes of elliptic and parabolic equations to accuracy below the truncation error with a work-cost equivalent to a few residual calculations - so-called 'textbook' multigrid efficiency. We investigate methods to solve the system of equations that arise in time dependent magnetohydrodynamics (MHD) simulations with textbook multigrid efficiency. We apply multigrid techniques such as geometric interpolation, full approximate storage, Gauss-Seidel smoothers, and defect correction for fully implicit, nonlinear, second-order finite volume discretizations of MHD. We apply these methods to a standard resistive MHD benchmark problem, the GEM reconnection problem, and add a strong magnetic guide field,more » which is a critical characteristic of magnetically confined fusion plasmas. We show that our multigrid methods can achieve near textbook efficiency on fully implicit resistive MHD simulations.« less

Toward textbook multigrid efficiency for fully implicit resistive magnetohydrodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams, Mark F.; Samtaney, Ravi; Brandt, Achi

2010-09-01

Multigrid methods can solve some classes of elliptic and parabolic equations to accuracy below the truncation error with a work-cost equivalent to a few residual calculations – so-called ‘‘textbook” multigrid efficiency. We investigate methods to solve the system of equations that arise in time dependent magnetohydrodynamics (MHD) simulations with textbook multigrid efficiency. We apply multigrid techniques such as geometric interpolation, full approximate storage, Gauss–Seidel smoothers, and defect correction for fully implicit, nonlinear, second-order finite volume discretizations of MHD. We apply these methods to a standard resistive MHD benchmark problem, the GEM reconnection problem, and add a strong magnetic guide field,more » which is a critical characteristic of magnetically confined fusion plasmas. We show that our multigrid methods can achieve near textbook efficiency on fully implicit resistive MHD simulations.« less

Toward textbook multigrid efficiency for fully implicit resistive magnetohydrodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams, Mark F.; Samtaney, Ravi; Brandt, Achi

2013-12-14

Multigrid methods can solve some classes of elliptic and parabolic equations to accuracy below the truncation error with a work-cost equivalent to a few residual calculations – so-called “textbook” multigrid efficiency. We investigate methods to solve the system of equations that arise in time dependent magnetohydrodynamics (MHD) simulations with textbook multigrid efficiency. We apply multigrid techniques such as geometric interpolation, full approximate storage, Gauss-Seidel smoothers, and defect correction for fully implicit, nonlinear, second-order finite volume discretizations of MHD. We apply these methods to a standard resistive MHD benchmark problem, the GEM reconnection problem, and add a strong magnetic guide field,more » which is a critical characteristic of magnetically confined fusion plasmas. We show that our multigrid methods can achieve near textbook efficiency on fully implicit resistive MHD simulations.« less

Multi-dimensional, fully implicit, exactly conserving electromagnetic particle-in-cell simulations in curvilinear geometry

NASA Astrophysics Data System (ADS)

Chen, Guangye; Chacon, Luis

2015-11-01

We discuss a new, conservative, fully implicit 2D3V Vlasov-Darwin particle-in-cell algorithm in curvilinear geometry for non-radiative, electromagnetic kinetic plasma simulations. Unlike standard explicit PIC schemes, fully implicit PIC algorithms are unconditionally stable and allow exact discrete energy and charge conservation. Here, we extend these algorithms to curvilinear geometry. The algorithm retains its exact conservation properties in curvilinear grids. The nonlinear iteration is effectively accelerated with a fluid preconditioner for weakly to modestly magnetized plasmas, which allows efficient use of large timesteps, O (√{mi/me}c/veT) larger than the explicit CFL. In this presentation, we will introduce the main algorithmic components of the approach, and demonstrate the accuracy and efficiency properties of the algorithm with various numerical experiments in 1D (slow shock) and 2D (island coalescense).

Scaling of Guide-Field Magnetic Reconnection using Anisotropic Fluid Closure

NASA Astrophysics Data System (ADS)

Ohia, O.; Egedal, J.; Lukin, V. S.; Daughton, W.; Le, A.

2012-10-01

Collisionless magnetic reconnection, a process linked to solar flares, coronal mass ejections, and magnetic substorms, has been widely studied through fluid models and fully kinetic simulations. While fluid models often reproduce the fast reconnection rate of fully kinetic simulations, significant differences are observed in the structure of the reconnection regions [1]. However, guide-field fluid simulations implementing new equations of state that accurately account for the anisotropic electron pressure [2] reproduce the detailed reconnection region observed in kinetic simulations [3]. Implementing this two-fluid simulation using the HiFi framework [4], we study the force balance of the electron layers in guide-field reconnection and derive scaling laws for their characteristics.[1ex] [1] Daughton W et al., Phys. Plasmas 13, 072101 (2006).[0ex] [2] Le A et al., Phys. Rev. Lett. 102, 085001 (2009). [0ex] [3] Ohia O, et al., Phys. Rev. Lett. In Press (2012).[0ex] [4] Lukin VS, Linton MG, Nonlinear Proc. Geoph. 18, 871 (2011)

Multi-Physics Demonstration Problem with the SHARP Reactor Simulation Toolkit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merzari, E.; Shemon, E. R.; Yu, Y. Q.

This report describes to employ SHARP to perform a first-of-a-kind analysis of the core radial expansion phenomenon in an SFR. This effort required significant advances in the framework Multi-Physics Demonstration Problem with the SHARP Reactor Simulation Toolkit used to drive the coupled simulations, manipulate the mesh in response to the deformation of the geometry, and generate the necessary modified mesh files. Furthermore, the model geometry is fairly complex, and consistent mesh generation for the three physics modules required significant effort. Fully-integrated simulations of a 7-assembly mini-core test problem have been performed, and the results are presented here. Physics models ofmore » a full-core model of the Advanced Burner Test Reactor have also been developed for each of the three physics modules. Standalone results of each of the three physics modules for the ABTR are presented here, which provides a demonstration of the feasibility of the fully-integrated simulation.« less

Images created in a model eye during simulated cataract surgery can be the basis for images perceived by patients during cataract surgery

PubMed Central

Inoue, M; Uchida, A; Shinoda, K; Taira, Y; Noda, T; Ohnuma, K; Bissen-Miyajima, H; Hirakata, A

2014-01-01

Purpose To evaluate the images created in a model eye during simulated cataract surgery. Patients and methods This study was conducted as a laboratory investigation and interventional case series. An artificial opaque lens, a clear intraocular lens (IOL), or an irrigation/aspiration (I/A) tip was inserted into the ‘anterior chamber' of a model eye with the frosted posterior surface corresponding to the retina. Video images were recorded of the posterior surface of the model eye from the rear during simulated cataract surgery. The video clips were shown to 20 patients before cataract surgery, and the similarity of their visual perceptions to these images was evaluated postoperatively. Results The images of the moving lens fragments and I/A tip and the insertion of the IOL were seen from the rear. The image through the opaque lens and the IOL without moving objects was the light of the surgical microscope from the rear. However, when the microscope light was turned off after IOL insertion, the images of the microscope and operating room were observed by the room illumination from the rear. Seventy percent of the patients answered that the visual perceptions of moving lens fragments were similar to the video clips and 55% reported similarity with the IOL insertion. Eighty percent of the patients recommended that patients watch the video clip before their scheduled cataract surgery. Conclusions The patients' visual perceptions during cataract surgery can be reproduced in the model eye. Watching the video images preoperatively may help relax the patients during surgery. PMID:24788007

Numerical simulations for active tectonic processes: increasing interoperability and performance

NASA Technical Reports Server (NTRS)

Donnellan, A.; Fox, G.; Rundle, J.; McLeod, D.; Tullis, T.; Grant, L.

2002-01-01

The objective of this project is to produce a system to fully model earthquake-related data. This task develops simulation and analysis tools to study the physics of earthquakes using state-of-the-art modeling.

Distributed microscopic actuation analysis of deformable plate membrane mirrors

NASA Astrophysics Data System (ADS)

Lu, Yifan; Yue, Honghao; Deng, Zongquan; Tzou, Hornsen

2018-02-01

To further reduce the areal density of optical mirrors used in space telescopes and other space-borne optical structures, the concept of flexible membrane deformable mirror has been proposed. Because of their high flexibility, poor stiffness and low damping properties, environmental excitations such as orbital maneuver, path changing, and non-uniform heating may induce unexpected vibrations and thus reduce working performance. Therefore, active vibration control is essential for these membrane mirrors. In this paper, two different mirror models, i.e., the plate membrane model and pure membrane model, are studied respectively. In order to investigate the modal vibration characteristics of the mirror, a piezoelectric layer is fully laminated on its non-reflective side to serve as actuators. Dynamic equations of the mirror laminated with piezoelectric actuators are presented first. Then, the actuator induced modal control force is defined. When the actuator area shrinks to infinitesimal, the expressions of microscopic local modal control force and its two components are obtained to predict the spatial microscopic actuation behavior of the mirror. Different membrane pretension forces are also applied to reveal the tension effects on the actuation of the mirror. Analyses indicate that the spatial distribution of modal micro-control forces is exactly the same with the sensing signals distribution of the mirror, which provides crucial guidelines for optimal actuator placement of membrane deformable mirrors.

Immersion-scanning-tunneling-microscope for long-term variable-temperature experiments at liquid-solid interfaces

NASA Astrophysics Data System (ADS)

Ochs, Oliver; Heckl, Wolfgang M.; Lackinger, Markus

2018-05-01

Fundamental insights into the kinetics and thermodynamics of supramolecular self-assembly on surfaces are uniquely gained by variable-temperature high-resolution Scanning-Tunneling-Microscopy (STM). Conventionally, these experiments are performed with standard ambient microscopes extended with heatable sample stages for local heating. However, unavoidable solvent evaporation sets a technical limit on the duration of these experiments, hence prohibiting long-term experiments. These, however, would be highly desirable to provide enough time for temperature stabilization and settling of drift but also to study processes with inherently slow kinetics. To overcome this dilemma, we propose a STM that can operate fully immersed in solution. The instrument is mounted onto the lid of a hermetically sealed heatable container that is filled with the respective solution. By closing the container, both the sample and microscope are immersed in solution. Thereby solvent evaporation is eliminated and an environment for long-term experiments with utmost stable and controllable temperatures between room-temperature and 100 °C is provided. Important experimental requirements for the immersion-STM and resulting design criteria are discussed, the strategy for protection against corrosive media is described, the temperature stability and drift behavior are thoroughly characterized, and first long-term high resolution experiments at liquid-solid interfaces are presented.

High-Bandwidth Dynamic Full-Field Profilometry for Nano-Scale Characterization of MEMS

NASA Astrophysics Data System (ADS)

Chen, Liang-Chia; Huang, Yao-Ting; Chang, Pi-Bai

2006-10-01

The article describes an innovative optical interferometric methodology to delivery dynamic surface profilometry with a measurement bandwidth up to 10MHz or higher and a vertical resolution up to 1 nm. Previous work using stroboscopic microscopic interferometry for dynamic characterization of micro (opto)electromechanical systems (M(O)EMS) has been limited in measurement bandwidth mainly within a couple of MHz. For high resonant mode analysis, the stroboscopic light pulse is insufficiently short to capture the moving fringes from dynamic motion of the detected structure. In view of this need, a microscopic prototype based on white-light stroboscopic interferometry with an innovative light superposition strategy was developed to achieve dynamic full-field profilometry with a high measurement bandwidth up to 10MHz or higher. The system primarily consists of an optical microscope, on which a Mirau interferometric objective embedded with a piezoelectric vertical translator, a high-power LED light module with dual operation modes and light synchronizing electronics unit are integrated. A micro cantilever beam used in AFM was measured to verify the system capability in accurate characterisation of dynamic behaviours of the device. The full-field seventh-mode vibration at a vibratory frequency of 3.7MHz can be fully characterized and nano-scale vertical measurement resolution as well as tens micrometers of vertical measurement range can be performed.

Stability of DNA Origami Nanoarrays in Cell Lysate

PubMed Central

Mei, Qian; Wei, Xixi; Su, Fengyu; Liu, Yan; Youngbull, Cody; Johnson, Roger; Lindsay, Stuart; Yan, Hao; Meldrum, Deirdre

2012-01-01

Scaffolded DNA origami, a method to create self-assembled nanostructures with spatially addressable features, has recently been used to develop water-soluble molecular chips for label-free RNA detection, platforms for deterministic protein positioning, and single molecule reaction observatories. These applications highlight the possibility of exploiting the unique properties and biocompatibility of DNA nanostructures in live, cellular systems. Herein, we assembled several DNA origami nanostructures of differing shape, size and probes, and investigated their interaction with lysate obtained from various normal and cancerous cell lines. We separated and analyzed the origami–lysate mixtures using agarose gel electrophoresis and recovered the DNA structures for functional assay and subsequent microscopic examination. Our results demonstrate that DNA origami nanostructures are stable in cell lysate and can be easily separated from lysate mixtures, in contrast to natural, single- and double-stranded DNA. Atomic force microscope (AFM) and transmission electron microscope (TEM) images show that the DNA origami structures are fully intact after separation from cell lysates and hybridize to their targets, verifying the superior structural integrity and functionality of self-assembled DNA origami nanostructures relative to conventional oligonucleotides. The stability and functionality of DNA origami structures in cell lysate validate their use for biological applications, for example, as programmable molecular rafts or disease detection platforms. PMID:21366226

Characterization of compression behaviors of fully covered biodegradable polydioxanone biliary stent for human body: A numerical approach by finite element model.

PubMed

Liu, Yanhui; Zhang, Peihua

2016-09-01

This paper presents a study of the compression behaviors of fully covered biodegradable polydioxanone biliary stents (FCBPBs) developed for human body by finite element method. To investigate the relationship between the compression force and structure parameter (monofilament diameter and braid-pin number), nine numerical models based on actual biliary stent were established, the simulation and experimental results are in good agreement with each other when calculating the compression force derived from both experiment and simulation results, indicating that the simulation results can be provided a useful reference to the investigation of biliary stents. The stress distribution on FCBPBSs was studied to optimize the structure of FCBPBSs. In addition, the plastic dissipation analysis and plastic strain of FCBPBSs were obtained via the compression simulation, revealing the structure parameter effect on the tolerance. Copyright © 2016 Elsevier Ltd. All rights reserved.

Testing the Applicability of Nernst-Planck Theory in Ion Channels: Comparisons with Brownian Dynamics Simulations

PubMed Central

Song, Chen; Corry, Ben

2011-01-01

The macroscopic Nernst-Planck (NP) theory has often been used for predicting ion channel currents in recent years, but the validity of this theory at the microscopic scale has not been tested. In this study we systematically tested the ability of the NP theory to accurately predict channel currents by combining and comparing the results with those of Brownian dynamics (BD) simulations. To thoroughly test the theory in a range of situations, calculations were made in a series of simplified cylindrical channels with radii ranging from 3 to 15 Å, in a more complex ‘catenary’ channel, and in a realistic model of the mechanosensitive channel MscS. The extensive tests indicate that the NP equation is applicable in narrow ion channels provided that accurate concentrations and potentials can be input as the currents obtained from the combination of BD and NP match well with those obtained directly from BD simulations, although some discrepancies are seen when the ion concentrations are not radially uniform. This finding opens a door to utilising the results of microscopic simulations in continuum theory, something that is likely to be useful in the investigation of a range of biophysical and nano-scale applications and should stimulate further studies in this direction. PMID:21731672

Testing the applicability of Nernst-Planck theory in ion channels: comparisons with Brownian dynamics simulations.

PubMed

Song, Chen; Corry, Ben

2011-01-01

The macroscopic Nernst-Planck (NP) theory has often been used for predicting ion channel currents in recent years, but the validity of this theory at the microscopic scale has not been tested. In this study we systematically tested the ability of the NP theory to accurately predict channel currents by combining and comparing the results with those of Brownian dynamics (BD) simulations. To thoroughly test the theory in a range of situations, calculations were made in a series of simplified cylindrical channels with radii ranging from 3 to 15 Å, in a more complex 'catenary' channel, and in a realistic model of the mechanosensitive channel MscS. The extensive tests indicate that the NP equation is applicable in narrow ion channels provided that accurate concentrations and potentials can be input as the currents obtained from the combination of BD and NP match well with those obtained directly from BD simulations, although some discrepancies are seen when the ion concentrations are not radially uniform. This finding opens a door to utilising the results of microscopic simulations in continuum theory, something that is likely to be useful in the investigation of a range of biophysical and nano-scale applications and should stimulate further studies in this direction.

Multiscale modeling and simulation of microtubule-motor-protein assemblies

NASA Astrophysics Data System (ADS)

Gao, Tong; Blackwell, Robert; Glaser, Matthew A.; Betterton, M. D.; Shelley, Michael J.

2015-12-01

Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate-consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation.

Multiscale modeling and simulation of microtubule-motor-protein assemblies.

PubMed

Gao, Tong; Blackwell, Robert; Glaser, Matthew A; Betterton, M D; Shelley, Michael J

2015-01-01

Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate-consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation.

Multiscale modeling and simulation of microtubule–motor-protein assemblies

PubMed Central

Gao, Tong; Blackwell, Robert; Glaser, Matthew A.; Betterton, M. D.; Shelley, Michael J.

2016-01-01

Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate–consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation. PMID:26764729

Direct construction of mesoscopic models from microscopic simulations

NASA Astrophysics Data System (ADS)

Lei, Huan; Caswell, Bruce; Karniadakis, George Em

2010-02-01

Starting from microscopic molecular-dynamics (MD) simulations of constrained Lennard-Jones (LJ) clusters (with constant radius of gyration Rg ), we construct two mesoscopic models [Langevin dynamics and dissipative particle dynamics (DPD)] by coarse graining the LJ clusters into single particles. Both static and dynamic properties of the coarse-grained models are investigated and compared with the MD results. The effective mean force field is computed as a function of the intercluster distance, and the corresponding potential scales linearly with the number of particles per cluster and the temperature. We verify that the mean force field can reproduce the equation of state of the atomistic systems within a wide density range but the radial distribution function only within the dilute and the semidilute regime. The friction force coefficients for both models are computed directly from the time-correlation function of the random force field of the microscopic system. For high density or a large cluster size the friction force is overestimated and the diffusivity underestimated due to the omission of many-body effects as a result of the assumed pairwise form of the coarse-grained force field. When the many-body effect is not as pronounced (e.g., smaller Rg or semidilute system), the DPD model can reproduce the dynamic properties of the MD system.

Computational Biochemistry-Enzyme Mechanisms Explored.

PubMed

Culka, Martin; Gisdon, Florian J; Ullmann, G Matthias

2017-01-01

Understanding enzyme mechanisms is a major task to achieve in order to comprehend how living cells work. Recent advances in biomolecular research provide huge amount of data on enzyme kinetics and structure. The analysis of diverse experimental results and their combination into an overall picture is, however, often challenging. Microscopic details of the enzymatic processes are often anticipated based on several hints from macroscopic experimental data. Computational biochemistry aims at creation of a computational model of an enzyme in order to explain microscopic details of the catalytic process and reproduce or predict macroscopic experimental findings. Results of such computations are in part complementary to experimental data and provide an explanation of a biochemical process at the microscopic level. In order to evaluate the mechanism of an enzyme, a structural model is constructed which can be analyzed by several theoretical approaches. Several simulation methods can and should be combined to get a reliable picture of the process of interest. Furthermore, abstract models of biological systems can be constructed combining computational and experimental data. In this review, we discuss structural computational models of enzymatic systems. We first discuss various models to simulate enzyme catalysis. Furthermore, we review various approaches how to characterize the enzyme mechanism both qualitatively and quantitatively using different modeling approaches. © 2017 Elsevier Inc. All rights reserved.

Urban growth simulation from "first principles".

PubMed

Andersson, Claes; Lindgren, Kristian; Rasmussen, Steen; White, Roger

2002-08-01

General and mathematically transparent models of urban growth have so far suffered from a lack in microscopic realism. Physical models that have been used for this purpose, i.e., diffusion-limited aggregation, dielectric breakdown models, and correlated percolation all have microscopic dynamics for which analogies with urban growth appear stretched. Based on a Markov random field formulation we have developed a model that is capable of reproducing a variety of important characteristic urban morphologies and that has realistic microscopic dynamics. The results presented in this paper are particularly important in relation to "urban sprawl," an important aspect of which is aggressively spreading low-density land uses. This type of growth is increasingly causing environmental, social, and economical problems around the world. The microdynamics of our model, or its "first principles," can be mapped to human decisions and motivations and thus potentially also to policies and regulations. We measure statistical properties of macrostates generated by the urban growth mechanism that we propose, and we compare these to empirical measurements as well as to results from other models. To showcase the open-endedness of the model and to thereby relate our work to applied urban planning we have also included a simulated city consisting of a large number of land use classes in which also topographical data have been used.

Images of intravitreal objects projected onto posterior surface of model eye.

PubMed

Kawamura, Ryosuke; Shinoda, Kei; Inoue, Makoto; Noda, Toru; Ohnuma, Kazuhiko; Hirakata, Akito

2013-11-01

To try to recreate the images reported by patients during vitreous surgery in a model eye. A fluid-filled model eye with a posterior frosted translucent surface which corresponded to the retina was used. Three holes were made in the model eye through which an endoillumination pipe and intraocular forceps could be inserted. A thin plastic sheet simulating an epiretinal membrane and an intraocular lens (IOL) simulating a dislocated IOL were placed on the retina. The images falling on the posterior surface were photographed from the rear. The images seen through the surgical microscope were also recorded. The images from the rear were mirror images of those seen through the surgical microscope. Intraocular instruments were seen as black shafts from the rear. When the plastic sheet was picked up, the tip of the forceps was seen more sharply on the posterior surface. The images of the dislocated IOL from the posterior were similar to that seen through the surgical microscope, including the yellow optics and blue haptics. Intravitreal objects can form images on the surface of a model eye. Objects located closer to the surface are seen more sharply, and the colour of the objects can be identified. © 2013 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Measurements and simulations of microscopic damage to DNA in water by 30 keV electrons: A general approach applicable to other radiation sources and biological targets

NASA Astrophysics Data System (ADS)

Hahn, Marc Benjamin; Meyer, Susann; Kunte, Hans-Jörg; Solomun, Tihomir; Sturm, Heinz

2017-05-01

The determination of the microscopic dose-damage relationship for DNA in an aqueous environment is of a fundamental interest for dosimetry and applications in radiation therapy and protection. We combine geant4 particle-scattering simulations in water with calculations concerning the movement of biomolecules to obtain the energy deposit in the biologically relevant nanoscopic volume. We juxtaposition these results to the experimentally determined damage to obtain the dose-damage relationship at a molecular level. This approach is tested for an experimentally challenging system concerning the direct irradiation of plasmid DNA (pUC19) in water with electrons as primary particles. Here a microscopic target model for the plasmid DNA based on the relation of lineal energy and radiation quality is used to calculate the effective target volume. It was found that on average fewer than two ionizations within a 7.5-nm radius around the sugar-phosphate backbone are sufficient to cause a single strand break, with a corresponding median lethal energy deposit being E1 /2=6 ±4 eV. The presented method is applicable for ionizing radiation (e.g., γ rays, x rays, and electrons) and a variety of targets, such as DNA, proteins, or cells.

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes

PubMed Central

Mosaliganti, Kishore R.; Noche, Ramil R.; Xiong, Fengzhu; Swinburne, Ian A.; Megason, Sean G.

2012-01-01

The quantification of cell shape, cell migration, and cell rearrangements is important for addressing classical questions in developmental biology such as patterning and tissue morphogenesis. Time-lapse microscopic imaging of transgenic embryos expressing fluorescent reporters is the method of choice for tracking morphogenetic changes and establishing cell lineages and fate maps in vivo. However, the manual steps involved in curating thousands of putative cell segmentations have been a major bottleneck in the application of these technologies especially for cell membranes. Segmentation of cell membranes while more difficult than nuclear segmentation is necessary for quantifying the relations between changes in cell morphology and morphogenesis. We present a novel and fully automated method to first reconstruct membrane signals and then segment out cells from 3D membrane images even in dense tissues. The approach has three stages: 1) detection of local membrane planes, 2) voting to fill structural gaps, and 3) region segmentation. We demonstrate the superior performance of the algorithms quantitatively on time-lapse confocal and two-photon images of zebrafish neuroectoderm and paraxial mesoderm by comparing its results with those derived from human inspection. We also compared with synthetic microscopic images generated by simulating the process of imaging with fluorescent reporters under varying conditions of noise. Both the over-segmentation and under-segmentation percentages of our method are around 5%. The volume overlap of individual cells, compared to expert manual segmentation, is consistently over 84%. By using our software (ACME) to study somite formation, we were able to segment touching cells with high accuracy and reliably quantify changes in morphogenetic parameters such as cell shape and size, and the arrangement of epithelial and mesenchymal cells. Our software has been developed and tested on Windows, Mac, and Linux platforms and is available publicly under an open source BSD license (https://github.com/krm15/ACME). PMID:23236265

Cellular automata model for use with real freeway data

DOT National Transportation Integrated Search

2002-01-01

The exponential rate of increase in freeway traffic is expanding the need for accurate and : realistic methods to model and predict traffic flow. Traffic modeling and simulation facilitates an : examination of both microscopic and macroscopic views o...

Plasma transport in the Io torus - The importance of microscopic diffusion

NASA Technical Reports Server (NTRS)

Mei, YI; Thorne, Richard M.

1991-01-01

This paper considers the question of whether the distribution of mass in the Io plasma torus is consistent with the concept of interchange eddy transport. Specifically, the flux tube content exhibits a gradual decrease with increasing radial distance from the source near Io without any evidence for substantial density irregularity associated with the plasma source or loss. Using a simple one-dimensional numerical model to simulate macroscopic interchange eddy transport, it is demonstrated that this smooth equilibrium distribution of mass can occur but only with the inclusion of a minimal level of small scale microscopic mixing at a rate approaching Bohm diffusion. Otherwise, the system exhibits a chaotic appearance which never approaches an equilibrium distribution. Various physical mechanisms for the microscopic diffusion process which is required to provide a sufficiently rapid mixing of material between the macroscopic eddies are discussed.

Reliable results from stochastic simulation models

Treesearch

Donald L., Jr. Gochenour; Leonard R. Johnson

1973-01-01

Development of a computer simulation model is usually done without fully considering how long the model should run (e.g. computer time) before the results are reliable. However construction of confidence intervals (CI) about critical output parameters from the simulation model makes it possible to determine the point where model results are reliable. If the results are...

Unpacking Students' Conceptualizations through Haptic Feedback

ERIC Educational Resources Information Center

Magana, A. J.; Balachandran, S.

2017-01-01

While it is clear that the use of computer simulations has a beneficial effect on learning when compared to instruction without computer simulations, there is still room for improvement to fully realize their benefits for learning. Haptic technologies can fulfill the educational potential of computer simulations by adding the sense of touch.…

Partially coherent X-ray wavefront propagation simulations including grazing-incidence focusing optics.

PubMed

Canestrari, Niccolo; Chubar, Oleg; Reininger, Ruben

2014-09-01

X-ray beamlines in modern synchrotron radiation sources make extensive use of grazing-incidence reflective optics, in particular Kirkpatrick-Baez elliptical mirror systems. These systems can focus the incoming X-rays down to nanometer-scale spot sizes while maintaining relatively large acceptance apertures and high flux in the focused radiation spots. In low-emittance storage rings and in free-electron lasers such systems are used with partially or even nearly fully coherent X-ray beams and often target diffraction-limited resolution. Therefore, their accurate simulation and modeling has to be performed within the framework of wave optics. Here the implementation and benchmarking of a wave-optics method for the simulation of grazing-incidence mirrors based on the local stationary-phase approximation or, in other words, the local propagation of the radiation electric field along geometrical rays, is described. The proposed method is CPU-efficient and fully compatible with the numerical methods of Fourier optics. It has been implemented in the Synchrotron Radiation Workshop (SRW) computer code and extensively tested against the geometrical ray-tracing code SHADOW. The test simulations have been performed for cases without and with diffraction at mirror apertures, including cases where the grazing-incidence mirrors can be hardly approximated by ideal lenses. Good agreement between the SRW and SHADOW simulation results is observed in the cases without diffraction. The differences between the simulation results obtained by the two codes in diffraction-dominated cases for illumination with fully or partially coherent radiation are analyzed and interpreted. The application of the new method for the simulation of wavefront propagation through a high-resolution X-ray microspectroscopy beamline at the National Synchrotron Light Source II (Brookhaven National Laboratory, USA) is demonstrated.

Anelastic Models of Fully-Convective Stars: Differential Rotation, Meridional Circulation and Residual Entropy

NASA Astrophysics Data System (ADS)

Sainsbury-Martinez, Felix; Browning, Matthew; Miesch, Mark; Featherstone, Nicholas A.

2018-01-01

Low-Mass stars are typically fully convective, and as such their dynamics may differ significantly from sun-like stars. Here we present a series of 3D anelastic HD and MHD simulations of fully convective stars, designed to investigate how the meridional circulation, the differential rotation, and residual entropy are affected by both varying stellar parameters, such as the luminosity or the rotation rate, and by the presence of a magnetic field. We also investigate, more specifically, a theoretical model in which isorotation contours and residual entropy (σ‧ = σ ‑ σ(r)) are intrinsically linked via the thermal wind equation (as proposed in the Solar context by Balbus in 2009). We have selected our simulation parameters in such as way as to span the transition between Solar-like differential rotation (fast equator + slow poles) and ‘anti-Solar’ differential rotation (slow equator + fast poles), as characterised by the convective Rossby number and △Ω. We illustrate the transition from single-celled to multi-celled MC profiles, and from positive to negative latitudinal entropy gradients. We show that an extrapolation involving both TWB and the σ‧/Ω link provides a reasonable estimate for the interior profile of our fully convective stars. Finally, we also present a selection of MHD simulations which exhibit an almost unsuppressed differential rotation profile, with energy balances remaining dominated by kinetic components.

On determination of charge transfer efficiency of thick, fully depleted CCDs with 55 Fe x-rays

DOE PAGES

Yates, D.; Kotov, I.; Nomerotski, A.

2017-07-01

Charge transfer efficiency (CTE) is one of the most important CCD characteristics. Our paper examines ways to optimize the algorithms used to analyze 55Fe x-ray data on the CCDs, as well as explores new types of observables for CTE determination that can be used for testing LSST CCDs. Furthermore, the observables are modeled employing simple Monte Carlo simulations to determine how the charge diffusion in thick, fully depleted silicon affects the measurement. The data is compared to the simulations for one of the observables, integral flux of the x-ray hit.

Tempest Simulations of Collisionless Damping of the Geodesic-Acoustic Mode in Edge-Plasma Pedestals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, X. Q.; Xiong, Z.; Nevins, W. M.

The fully nonlinear (full-f) four-dimensional TEMPEST gyrokinetic continuum code correctly produces the frequency and collisionless damping of geodesic-acoustic modes (GAMs) and zonal flow, with fully nonlinear Boltzmann electrons for the inverse aspect ratio {epsilon} scan and the tokamak safety factor q scan in homogeneous plasmas. TEMPEST simulations show that the GAMs exist in the edge pedestal for steep density and temperature gradients in the form of outgoing waves. The enhanced GAM damping may explain experimental beam emission spectroscopy measurements on the edge q scaling of the GAM amplitude.

Tempest Simulations of Collisionless Damping of the Geodesic-Acoustic Mode in Edge-Plasma Pedestals

NASA Astrophysics Data System (ADS)

Xu, X. Q.; Xiong, Z.; Gao, Z.; Nevins, W. M.; McKee, G. R.

2008-05-01

The fully nonlinear (full-f) four-dimensional TEMPEST gyrokinetic continuum code correctly produces the frequency and collisionless damping of geodesic-acoustic modes (GAMs) and zonal flow, with fully nonlinear Boltzmann electrons for the inverse aspect ratio γ scan and the tokamak safety factor q scan in homogeneous plasmas. TEMPEST simulations show that the GAMs exist in the edge pedestal for steep density and temperature gradients in the form of outgoing waves. The enhanced GAM damping may explain experimental beam emission spectroscopy measurements on the edge q scaling of the GAM amplitude.

TEMPEST simulations of collisionless damping of the geodesic-acoustic mode in edge-plasma pedestals.

PubMed

Xu, X Q; Xiong, Z; Gao, Z; Nevins, W M; McKee, G R

2008-05-30

The fully nonlinear (full-f) four-dimensional TEMPEST gyrokinetic continuum code correctly produces the frequency and collisionless damping of geodesic-acoustic modes (GAMs) and zonal flow, with fully nonlinear Boltzmann electrons for the inverse aspect ratio scan and the tokamak safety factor q scan in homogeneous plasmas. TEMPEST simulations show that the GAMs exist in the edge pedestal for steep density and temperature gradients in the form of outgoing waves. The enhanced GAM damping may explain experimental beam emission spectroscopy measurements on the edge q scaling of the GAM amplitude.

A Novel Solid State Ultracapacitor

NASA Technical Reports Server (NTRS)

Cortes-Pena, A. Y.; Rolin, T. D.; Hill, C. W.

2017-01-01

Novel dielectric materials were researched to develop an internal barrier layer capacitor that is fully solid state. These materials included reduced nanoparticles of barium titanate that were coated with various atomic layer deposited oxides. The nanoparticle powders were then densified into pellets and characterized using a dielectric test fixture over a frequency range of 20 Hz to 2 MHz. Densification and sintering were evaluated using scanning electron microscopic techniques. Ultimately, the samples showing the most promising electrical characteristics of permittivity, dissipation factor and equivalent series resistance were chosen to manufacture devices for subsequent testing.

Origin of probabilities and their application to the multiverse

NASA Astrophysics Data System (ADS)

Albrecht, Andreas; Phillips, Daniel

2014-12-01

We argue using simple models that all successful practical uses of probabilities originate in quantum fluctuations in the microscopic physical world around us, often propagated to macroscopic scales. Thus we claim there is no physically verified fully classical theory of probability. We comment on the general implications of this view, and specifically question the application of purely classical probabilities to cosmology in cases where key questions are known to have no quantum answer. We argue that the ideas developed here may offer a way out of the notorious measure problems of eternal inflation.

Neutral evolution in a biological population as diffusion in phenotype space: reproduction with local mutation but without selection.

PubMed

Lawson, Daniel John; Jensen, Henrik Jeldtoft

2007-03-02

The process of "evolutionary diffusion," i.e., reproduction with local mutation but without selection in a biological population, resembles standard diffusion in many ways. However, evolutionary diffusion allows the formation of localized peaks that undergo drift, even in the infinite population limit. We relate a microscopic evolution model to a stochastic model which we solve fully. This allows us to understand the large population limit, relates evolution to diffusion, and shows that independent local mutations act as a diffusion of interacting particles taking larger steps.

Numerical simulation of cavitation and atomization using a fully compressible three-phase model

NASA Astrophysics Data System (ADS)

Mithun, Murali-Girija; Koukouvinis, Phoevos; Gavaises, Manolis

2018-06-01

The aim of this paper is to present a fully compressible three-phase (liquid, vapor, and air) model and its application to the simulation of in-nozzle cavitation effects on liquid atomization. The model employs a combination of the homogeneous equilibrium barotropic cavitation model with an implicit sharp interface capturing volume of fluid (VOF) approximation. The numerical predictions are validated against the experimental results obtained for injection of water into the air from a step nozzle, which is designed to produce asymmetric cavitation along its two sides. Simulations are performed for three injection pressures, corresponding to three different cavitation regimes, referred to as cavitation inception, developing cavitation, and hydraulic flip. Model validation is achieved by qualitative comparison of the cavitation, spray pattern, and spray cone angles. The flow turbulence in this study is resolved using the large-eddy simulation approach. The simulation results indicate that the major parameters that influence the primary atomization are cavitation, liquid turbulence, and, to a smaller extent, the Rayleigh-Taylor and Kelvin-Helmholtz aerodynamic instabilities developing on the liquid-air interface. Moreover, the simulations performed indicate that periodic entrainment of air into the nozzle occurs at intermediate cavitation numbers, corresponding to developing cavitation (as opposed to incipient and fully developed cavitation regimes); this transient effect causes a periodic shedding of the cavitation and air clouds and contributes to improved primary atomization. Finally, the cone angle of the spray is found to increase with increased injection pressure but drops drastically when hydraulic flip occurs, in agreement with the relevant experiments.

Modeling and simulating two cut-to-length harvesting systems in central Appalachian hardwoods

Treesearch

Jingxin Wang; Chris B. LeDoux; Yaoxiang Li

2003-01-01

The production rates and costs of two cut-to-length harvesting systems was simulated using a modular ground-based simulation model and stand yield data from fully stocked, second growth even aged central Appalachian hardwood forests. The two harvesters simulated were a modified John Deere 988 tracked excavator with a model RP 1600 single grip sawhead and an excavator...

Characterization of microscopic deformation through two-point spatial correlation functions

NASA Astrophysics Data System (ADS)

Huang, Guan-Rong; Wu, Bin; Wang, Yangyang; Chen, Wei-Ren

2018-01-01

The molecular rearrangements of most fluids under flow and deformation do not directly follow the macroscopic strain field. In this work, we describe a phenomenological method for characterizing such nonaffine deformation via the anisotropic pair distribution function (PDF). We demonstrate how the microscopic strain can be calculated in both simple shear and uniaxial extension, by perturbation expansion of anisotropic PDF in terms of real spherical harmonics. Our results, given in the real as well as the reciprocal space, can be applied in spectrum analysis of small-angle scattering experiments and nonequilibrium molecular dynamics simulations of soft matter under flow.

Characterization of microscopic deformation through two-point spatial correlation functions.

PubMed

Huang, Guan-Rong; Wu, Bin; Wang, Yangyang; Chen, Wei-Ren

2018-01-01

The molecular rearrangements of most fluids under flow and deformation do not directly follow the macroscopic strain field. In this work, we describe a phenomenological method for characterizing such nonaffine deformation via the anisotropic pair distribution function (PDF). We demonstrate how the microscopic strain can be calculated in both simple shear and uniaxial extension, by perturbation expansion of anisotropic PDF in terms of real spherical harmonics. Our results, given in the real as well as the reciprocal space, can be applied in spectrum analysis of small-angle scattering experiments and nonequilibrium molecular dynamics simulations of soft matter under flow.

Departure of microscopic friction from macroscopic drag in molecular fluid dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanasaki, Itsuo; Fujiwara, Daiki; Kawano, Satoyuki, E-mail: kawano@me.es.osaka-u.ac.jp

2016-03-07

Friction coefficient of the Langevin equation and drag of spherical macroscopic objects in steady flow at low Reynolds numbers are usually regarded as equivalent. We show that the microscopic friction can be different from the macroscopic drag when the mass is taken into account for particles with comparable scale to the surrounding fluid molecules. We illustrate it numerically by molecular dynamics simulation of chloride ion in water. Friction variation by the atomistic mass effect beyond the Langevin regime can be of use in the drag reduction technology as well as the electro or thermophoresis.

Band to Band Tunneling (BBT) Induced Leakage Current Enhancement in Irradiated Fully Depleted SOI Devices

NASA Technical Reports Server (NTRS)

Adell, Phillipe C.; Barnaby, H. J.; Schrimpf, R. D.; Vermeire, B.

2007-01-01

We propose a model, validated with simulations, describing how band-to-band tunneling (BBT) affects the leakage current degradation in some irradiated fully-depleted SOI devices. The dependence of drain current on gate voltage, including the apparent transition to a high current regime is explained.

Microscopic analysis of "iron spot" on blue-and-white porcelain from Jingdezhen imperial kiln in early Ming dynasty (14th-15th century).

PubMed

Wang, Wenxuan; Zhu, Jian; Jiang, Jianxin; Xu, Changqing; Wu, Shurong; Guan, Li; Zhang, Zhaoxia; Wu, Menglei; Du, Jingnan

2016-11-01

"Sumali," as an imported cobalt ore from overseas, was a sort of precious and valuable pigment used for imperial kilns only, which produces characteristic "iron spot" to blue-and-white porcelain in early Ming Dynasty (A.D. 14th-15th century). Although there were some old studies on it, the morphology and formation of iron spot has not been fully investigated and understood. Therefore, five selected samples with typical spot from Jingdezhen imperial kiln in Ming Yongle periods (A.D. 1403-1424) were analyzed by various microscopic analysis including 3D digital microscope, SEM-EDS and EPMA. According to SEM images, samples can be divided into three groups: un-reflected "iron spot" without crystals, un-reflected "iron spot" with crystals and reflected "iron spot" with crystals. Furthermore, 3D micro-images revealed that "iron spots" separate out dendritic or snow-shaped crystals of iron only on and parallel to the surface of glaze for which "iron spot" show strong metallic luster. Combining with microscopic observation and microanalysis on crystallization and non-crystallization areas, it indicates that firing oxygen concentration is the ultimate causation of forming reflective iron spot which has a shallower distribution below the surface and limits crystals growing down. More details about characters of "iron spot" used "Sumali" were found and provided new clues to coloration, formation mechanism and porcelain producing technology of imperial kiln from 14th to 15th centuries of China. © 2016 Wiley Periodicals, Inc.

A high speed multifocal multiphoton fluorescence lifetime imaging microscope for live-cell FRET imaging

PubMed Central

Poland, Simon P.; Krstajić, Nikola; Monypenny, James; Coelho, Simao; Tyndall, David; Walker, Richard J.; Devauges, Viviane; Richardson, Justin; Dutton, Neale; Barber, Paul; Li, David Day-Uei; Suhling, Klaus; Ng, Tony; Henderson, Robert K.; Ameer-Beg, Simon M.

2015-01-01

We demonstrate diffraction limited multiphoton imaging in a massively parallel, fully addressable time-resolved multi-beam multiphoton microscope capable of producing fluorescence lifetime images with sub-50ps temporal resolution. This imaging platform offers a significant improvement in acquisition speed over single-beam laser scanning FLIM by a factor of 64 without compromising in either the temporal or spatial resolutions of the system. We demonstrate FLIM acquisition at 500 ms with live cells expressing green fluorescent protein. The applicability of the technique to imaging protein-protein interactions in live cells is exemplified by observation of time-dependent FRET between the epidermal growth factor receptor (EGFR) and the adapter protein Grb2 following stimulation with the receptor ligand. Furthermore, ligand-dependent association of HER2-HER3 receptor tyrosine kinases was observed on a similar timescale and involved the internalisation and accumulation or receptor heterodimers within endosomes. These data demonstrate the broad applicability of this novel FLIM technique to the spatio-temporal dynamics of protein-protein interaction. PMID:25780724

Multi-approach characterization of the Rhodope marbles, Greece used in monuments

NASA Astrophysics Data System (ADS)

Dotsika, Elissavet; Raco, Brunella; Psomiadis, David; Poutoukis, Dimitrios; Zisi, Nikoleta

2010-05-01

Northern Greece has many archaeological sites featuring buildings and objects entirely or partly constructed from marble whose provenance is doubtful. In Northern Greece, the most probable source of such marble is the Rhodope Mountains. For the purpose of supporting further provenance studies, these marbles are fully scientifically characterized. The sampling took place in several ancient quarries which were on trade routes of Hellenistic, Roman or Byzantine settlements. Trade of marble in N. Greece is proved to have been equally important as in S. Greece, comparing the qualitative marble of Thassos with the best marbles of the south (e.g. Paros, Naxos etc.). The techniques used are petrographic and geochemical (microscope, X-Ray diffraction patterns, Scanning Electron Microscope) methods and stable isotope ratio analysis (δ13C and δ18O). The use of a multi-technique approach with combined parameters allows the best possible discrimination. This scientific investigation both supplements the isotopic database and proves that in N. Greece people used also imported marbles.

Turning Microscopy in the Medical Curriculum Digital: Experiences from The Faculty of Health and Medical Sciences at University of Copenhagen

PubMed Central

Vainer, Ben; Mortensen, Niels Werner; Poulsen, Steen Seier; Sørensen, Allan Have; Olsen, Jørgen; Saxild, Hans Henrik; Johansen, Flemming Fryd

2017-01-01

Familiarity with the structure and composition of normal tissue and an understanding of the changes that occur during disease is pivotal to the study of the human body. For decades, microscope slides have been central to teaching pathology in medical courses and related subjects at the University of Copenhagen. Students had to learn how to use a microscope and envisage three-dimensional processes that occur in the body from two-dimensional glass slides. Here, we describe how a PathXL virtual microscopy system for teaching pathology and histology at the Faculty has recently been implemented, from an administrative, an economic, and a teaching perspective. This fully automatic digital microscopy system has been received positively by both teachers and students, and a decision was made to convert all courses involving microscopy to the virtual microscopy format. As a result, conventional analog microscopy will be phased out from the fall of 2016. PMID:28382225

Improper magnetic ferroelectricity of nearly pure electronic nature in helicoidal spiral CaMn7O12

NASA Astrophysics Data System (ADS)

Lim, Jin Soo; Saldana-Greco, Diomedes; Rappe, Andrew M.

2018-01-01

Helicoidal magnetic order breaks inversion symmetry in quadruple perovskite CaMn7O12 , generating one of the largest spin-induced ferroelectric polarizations measured to date. Here, the microscopic origin of the polarization, including exchange interactions, coupling to the spin helicity, and charge density redistribution, is explored via first-principles calculations. The B -site Mn4 + (Mn3) spin adopts a noncentrosymmetric configuration, stabilized not only by spin-orbit coupling (SOC), but also by the fully anisotropic Hubbard J parameter in the absence of SOC, to break inversion symmetry and generate polarization. Berry phase computed polarization (Pelec=2169 μ C /m2 ) exhibits nearly pure electronic behavior, with negligible Mn displacements (≈0.7 m Å ). Orbital-resolved density of states shows that p -d orbital mixing is microscopically driven by nonrelativistic exchange striction within the commensurate ionic structure. Persistent electronic polarization induced by helical spin order in the nearly inversion-symmetric ionic crystal lattice suggests opportunities for ultrafast magnetoelectric response.

Transport-related triplet states and hyperfine couplings in organic tandem solar cells probed by pulsed electrically detected magnetic resonance spectroscopy

NASA Astrophysics Data System (ADS)

Kraffert, Felix; Bahro, Daniel; Meier, Christoph; Denne, Maximilian; Colsmann, Alexander; Behrends, Jan

2017-09-01

Tandem solar cells constitute the most successful organic photovoltaic devices with power conversion efficiencies comparable to thin-film silicon solar cells. Especially their high open-circuit voltage - only achievable by a well-adjusted layer stacking - leads to their high efficiencies. Nevertheless, the microscopic processes causing the lossless recombination of charge carriers within the recombination zone are not well understood yet. We show that advanced pulsed electrically detected magnetic resonance techniques such as electrically detected (ED)-Rabi nutation measurements and electrically detected hyperfine sublevel correlation (ED-HYSCORE) spectroscopy help to understand the role of triplet excitons in these microscopic processes. We investigate fully working miniaturised organic tandem solar cells and detect current-influencing doublet states in different layers as well as triplet excitons located on the fullerene-based acceptor. We apply ED-HYSCORE in order to study the nuclear spin environment of the relevant electron/hole spins and detect a significant amount of the low abundant 13C nuclei coupled to the observer spins.

Digital holographic microscopy for detection of Trypanosoma cruzi parasites in fresh blood mounts

NASA Astrophysics Data System (ADS)

Romero, G. G.; Monaldi, A. C.; Alanís, E. E.

2012-03-01

An off-axis holographic microscope, in a transmission mode, calibrated to automatically detect the presence of Trypanosoma cruzi in blood is developed as an alternative diagnosis tool for Chagas disease. Movements of the microorganisms are detected by measuring the phase shift they produce on the transmitted wave front. A thin layer of blood infected by Trypanosoma cruzi parasites is examined in the holographic microscope, the images of the visual field being registered with a CCD camera. Two consecutive holograms of the same visual field are subtracted point by point and a phase contrast image of the resulting hologram is reconstructed by means of the angular spectrum propagation algorithm. This method enables the measurement of phase distributions corresponding to temporal differences between digital holograms in order to detect whether parasites are present or not. Experimental results obtained using this technique show that it is an efficient alternative that can be incorporated successfully as a part of a fully automatic system for detection and counting of this type of microorganisms.

Stencil lithography of superconducting contacts on MBE-grown topological insulator thin films

NASA Astrophysics Data System (ADS)

Schüffelgen, Peter; Rosenbach, Daniel; Neumann, Elmar; Stehno, Martin P.; Lanius, Martin; Zhao, Jialin; Wang, Meng; Sheehan, Brendan; Schmidt, Michael; Gao, Bo; Brinkman, Alexander; Mussler, Gregor; Schäpers, Thomas; Grützmacher, Detlev

2017-11-01

Topological insulator (Bi0.06Sb0.94)2Te3 thin films grown by molecular beam epitaxy have been capped in-situ with a 2 nm Al film to conserve the pristine topological surface states. Subsequently, a shadow mask - structured by means of focus ion beam - was in-situ placed underneath the sample to deposit a thick layer of Al on well-defined microscopically small areas. The 2 nm thin Al layer fully oxidizes after exposure to air and in this way protects the TI surface from degradation. The thick Al layer remains metallic underneath a 3-4 nm thick native oxide layer and therefore serves as (super-) conducting contacts. Superconductor-Topological Insulator-Superconductor junctions with lateral dimensions in the nm range have then been fabricated via an alternative stencil lithography technique. Despite the in-situ deposition, transport measurements and transmission electron microscope analysis indicate a low transparency, due to an intermixed region at the interface between topological insulator thin film and metallic Al.

Real-world hydrologic assessment of a fully-distributed hydrological model in a parallel computing environment

NASA Astrophysics Data System (ADS)

Vivoni, Enrique R.; Mascaro, Giuseppe; Mniszewski, Susan; Fasel, Patricia; Springer, Everett P.; Ivanov, Valeriy Y.; Bras, Rafael L.

2011-10-01

SummaryA major challenge in the use of fully-distributed hydrologic models has been the lack of computational capabilities for high-resolution, long-term simulations in large river basins. In this study, we present the parallel model implementation and real-world hydrologic assessment of the Triangulated Irregular Network (TIN)-based Real-time Integrated Basin Simulator (tRIBS). Our parallelization approach is based on the decomposition of a complex watershed using the channel network as a directed graph. The resulting sub-basin partitioning divides effort among processors and handles hydrologic exchanges across boundaries. Through numerical experiments in a set of nested basins, we quantify parallel performance relative to serial runs for a range of processors, simulation complexities and lengths, and sub-basin partitioning methods, while accounting for inter-run variability on a parallel computing system. In contrast to serial simulations, the parallel model speed-up depends on the variability of hydrologic processes. Load balancing significantly improves parallel speed-up with proportionally faster runs as simulation complexity (domain resolution and channel network extent) increases. The best strategy for large river basins is to combine a balanced partitioning with an extended channel network, with potential savings through a lower TIN resolution. Based on these advances, a wider range of applications for fully-distributed hydrologic models are now possible. This is illustrated through a set of ensemble forecasts that account for precipitation uncertainty derived from a statistical downscaling model.

The Influence of Investor Number on a Microscopic Market Model

NASA Astrophysics Data System (ADS)

Hellthaler, T.

The stock market model of Levy, Persky, Solomon is simulated for much larger numbers of investors. While small markets can lead to realistically looking prices, the resulting prices of large markets oscillate smoothly in a semi-regular fashion.

Study of a Martian Aeolian Sand Analog with MECA Microscopy

NASA Technical Reports Server (NTRS)

Marshall, J.; Kuhlman, K.; Stevens, R.; Meyyappan, M.

2001-01-01

MECA microscopy (built for Mars '01) is simulated to show the potential of in situ microscopic analyses of surface materials on Mars. In particular, the value of nanotechnology is demonstrated. Additional information is contained in the original extended abstract.

Improved simulation of driver behavior : modeling protected and permitted left-turn operations at signalized intersections.

DOT National Transportation Integrated Search

2011-04-01

"This report documents the findings from a research project that is focused on modeling protected and permitted left-turn operations at signalized intersection approaches. The projects primary objective is to document the microscopic characteristi...

Microscope in orbit calibration procedure for a test of the equivalence principle at 10(-15).

PubMed

Pradels, G; Touboul, P

2003-01-01

The scientific objectives of the MICROSCOPE space mission impose a very fine calibration of the on-board accelerometers. However the required performance cannot be achieved on ground because of the presence of high disturbing sources. On-board the CHAMP satellite, accelerometers similar in the concept to the MICROSCOPE instrument, have already flown and analysis of the provided data then allowed to characterise the vibration environment at low altitude as well as the fluctuation of the drag. The requirements of the in-orbit calibration procedure for the MICROSCOPE instrument are demonstrated by modelling the expected applied acceleration signals with the developed analytic model of the mission. The proposed approach exploits the drag-free system of the satellite and the sensitivity of the accelerometers. A specific simulator of the attitude control system of the satellite has been developed and tests of the proposed solution are performed using nominal conditions or disturbing conditions as observed during the CHAMP mission. c2003 International Astronautical Federation. Published by Elsevier Science Ldt. All rights reserved.

Drag and drop simulation: from pictures to full three-dimensional simulations

NASA Astrophysics Data System (ADS)

Bergmann, Michel; Iollo, Angelo

2014-11-01

We present a suite of methods to achieve ``drag and drop'' simulation, i.e., to fully automatize the process to perform thee-dimensional flow simulations around a bodies defined by actual images of moving objects. The overall approach requires a skeleton graph generation to get level set function from pictures, optimal transportation to get body velocity on the surface and then flow simulation thanks to a cartesian method based on penalization. We illustrate this paradigm simulating the swimming of a mackerel fish.

Evaluating the effectiveness of active vehicle safety systems.

PubMed

Jeong, Eunbi; Oh, Cheol

2017-03-01

Advanced vehicle safety systems have been widely introduced in transportation systems and are expected to enhance traffic safety. However, these technologies mainly focus on assisting individual vehicles that are equipped with them, and less effort has been made to identify the effect of vehicular technologies on the traffic stream. This study proposed a methodology to assess the effectiveness of active vehicle safety systems (AVSSs), which represent a promising technology to prevent traffic crashes and mitigate injury severity. The proposed AVSS consists of longitudinal and lateral vehicle control systems, which corresponds to the Level 2 vehicle automation presented by the National Highway Safety Administration (NHTSA). The effectiveness evaluation for the proposed technology was conducted in terms of crash potential reduction and congestion mitigation. A microscopic traffic simulator, VISSIM, was used to simulate freeway traffic stream and collect vehicle-maneuvering data. In addition, an external application program interface, VISSIM's COM-interface, was used to implement the AVSS. A surrogate safety assessment model (SSAM) was used to derive indirect safety measures to evaluate the effectiveness of the AVSS. A 16.7-km freeway stretch between the Nakdong and Seonsan interchanges on Korean freeway 45 was selected for the simulation experiments to evaluate the effectiveness of AVSS. A total of five simulation runs for each evaluation scenario were conducted. For the non-incident conditions, the rear-end and lane-change conflicts were reduced by 78.8% and 17.3%, respectively, under the level of service (LOS) D traffic conditions. In addition, the average delay was reduced by 55.5%. However, the system's effectiveness was weakened in the LOS A-C categories. Under incident traffic conditions, the number of rear-end conflicts was reduced by approximately 9.7%. Vehicle delays were reduced by approximately 43.9% with 100% of market penetration rate (MPR). These results imply that from the perspective of traffic operations and control to address the safety and congestion issues of a traffic stream, smarter management strategies that consider both traffic conditions and MPR are required to fully exploit the effectiveness of the AVSS in the field. Copyright © 2017 Elsevier Ltd. All rights reserved.

Hydrated Electron Transfer to Nucleobases in Aqueous Solutions Revealed by Ab Initio Molecular Dynamics Simulations.

PubMed

Zhao, Jing; Wang, Mei; Fu, Aiyun; Yang, Hongfang; Bu, Yuxiang

2015-08-03

We present an ab initio molecular dynamics (AIMD) simulation study into the transfer dynamics of an excess electron from its cavity-shaped hydrated electron state to a hydrated nucleobase (NB)-bound state. In contrast to the traditional view that electron localization at NBs (G/A/C/T), which is the first step for electron-induced DNA damage, is related only to dry or prehydrated electrons, and a fully hydrated electron no longer transfers to NBs, our AIMD simulations indicate that a fully hydrated electron can still transfer to NBs. We monitored the transfer dynamics of fully hydrated electrons towards hydrated NBs in aqueous solutions by using AIMD simulations and found that due to solution-structure fluctuation and attraction of NBs, a fully hydrated electron can transfer to a NB gradually over time. Concurrently, the hydrated electron cavity gradually reorganizes, distorts, and even breaks. The transfer could be completed in about 120-200 fs in four aqueous NB solutions, depending on the electron-binding ability of hydrated NBs and the structural fluctuation of the solution. The transferring electron resides in the π*-type lowest unoccupied molecular orbital of the NB, which leads to a hydrated NB anion. Clearly, the observed transfer of hydrated electrons can be attributed to the strong electron-binding ability of hydrated NBs over the hydrated electron cavity, which is the driving force, and the transfer dynamics is structure-fluctuation controlled. This work provides new insights into the evolution dynamics of hydrated electrons and provides some helpful information for understanding the DNA-damage mechanism in solution. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ultra-low loss fully-etched grating couplers for perfectly vertical coupling compatible with DUV lithography tools

NASA Astrophysics Data System (ADS)

Dabos, G.; Pleros, N.; Tsiokos, D.

2016-03-01

Hybrid integration of VCSELs onto silicon-on-insulator (SOI) substrates has emerged as an attractive approach for bridging the gap between cost-effective and energy-efficient directly modulated laser sources and silicon-based PICs by leveraging flip-chip (FC) bonding techniques and silicon grating couplers (GCs). In this context, silicon GCs, should comply with the process requirements imposed by the complimentary-metal-oxide-semiconductor manufacturing tools addressing in parallel the challenges originating from the perfectly vertical incidence. Firstly, fully etched GCs compatible with deep-ultraviolet lithography tools offering high coupling efficiencies are imperatively needed to maintain low fabrication cost. Secondly, GC's tolerance to VCSEL bonding misalignment errors is a prerequisite for practical deployment. Finally, a major challenge originating from the perfectly vertical coupling scheme is the minimization of the direct back-reflection to the VCSEL's outgoing facet which may destabilize its operation. Motivated from the above challenges, we used numerical simulation tools to design an ultra-low loss, bidirectional VCSEL-to-SOI optical coupling scheme for either TE or TM polarization, based on low-cost fully etched GCs with a Si-layer of 340 nm without employing bottom reflectors or optimizing the buried-oxide layer. Comprehensive 2D Finite-Difference-Time- Domain simulations have been performed. The reported GC layout remains fully compatible with the back-end-of-line (BEOL) stack associated with the 3D integration technology exploiting all the inter-metal-dielectric (IMD) layers of the CMOS fab. Simulation results predicted for the first time in fully etched structures a coupling efficiency of as low as -0.87 dB at 1548 nm and -1.47 dB at 1560 nm with a minimum direct back-reflection of -27.4 dB and -14.2 dB for TE and TM polarization, respectively.

Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, J.; Martí, J., E-mail: jordi.marti@upc.edu; Calero, C.

2014-03-14

Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in themore » membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10{sup −5} cm{sup 2}/s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10{sup −8} cm{sup 2}/s). In the intermediate regime of sub-diffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2–8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of its interaction with lipids. We have thoroughly analyzed the physical meaning of all spectral features from lipid atomic sites and correlated them with experimental data. Our findings include a “wagging of the tails” frequency around 30 cm{sup −1}, which essentially corresponds to motions of the tail-group along the instantaneous plane formed by the two lipid tails, i.e., in-plane oscillations are clearly of bigger importance than those along the normal-to-the plane direction.« less

Conservative tightly-coupled simulations of stochastic multiscale systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taverniers, Søren; Pigarov, Alexander Y.; Tartakovsky, Daniel M., E-mail: dmt@ucsd.edu

2016-05-15

Multiphysics problems often involve components whose macroscopic dynamics is driven by microscopic random fluctuations. The fidelity of simulations of such systems depends on their ability to propagate these random fluctuations throughout a computational domain, including subdomains represented by deterministic solvers. When the constituent processes take place in nonoverlapping subdomains, system behavior can be modeled via a domain-decomposition approach that couples separate components at the interfaces between these subdomains. Its coupling algorithm has to maintain a stable and efficient numerical time integration even at high noise strength. We propose a conservative domain-decomposition algorithm in which tight coupling is achieved by employingmore » either Picard's or Newton's iterative method. Coupled diffusion equations, one of which has a Gaussian white-noise source term, provide a computational testbed for analysis of these two coupling strategies. Fully-converged (“implicit”) coupling with Newton's method typically outperforms its Picard counterpart, especially at high noise levels. This is because the number of Newton iterations scales linearly with the amplitude of the Gaussian noise, while the number of Picard iterations can scale superlinearly. At large time intervals between two subsequent inter-solver communications, the solution error for single-iteration (“explicit”) Picard's coupling can be several orders of magnitude higher than that for implicit coupling. Increasing the explicit coupling's communication frequency reduces this difference, but the resulting increase in computational cost can make it less efficient than implicit coupling at similar levels of solution error, depending on the communication frequency of the latter and the noise strength. This trend carries over into higher dimensions, although at high noise strength explicit coupling may be the only computationally viable option.« less

A Lattice-Boltzmann model to simulate diffractive nonlinear ultrasound beam propagation in a dissipative fluid medium

NASA Astrophysics Data System (ADS)

Abdi, Mohamad; Hajihasani, Mojtaba; Gharibzadeh, Shahriar; Tavakkoli, Jahan

2012-12-01

Ultrasound waves have been widely used in diagnostic and therapeutic medical applications. Accurate and effective simulation of ultrasound beam propagation and its interaction with tissue has been proved to be important. The nonlinear nature of the ultrasound beam propagation, especially in the therapeutic regime, plays an important role in the mechanisms of interaction with tissue. There are three main approaches in current computational fluid dynamics (CFD) methods to model and simulate nonlinear ultrasound beams: macroscopic, mesoscopic and microscopic approaches. In this work, a mesoscopic CFD method based on the Lattice-Boltzmann model (LBM) was investigated. In the developed method, the Boltzmann equation is evolved to simulate the flow of a Newtonian fluid with the collision model instead of solving the Navier-Stokes, continuity and state equations which are used in conventional CFD methods. The LBM has some prominent advantages over conventional CFD methods, including: (1) its parallel computational nature; (2) taking microscopic boundaries into account; and (3) capability of simulating in porous and inhomogeneous media. In our proposed method, the propagating medium is discretized with a square grid in 2 dimensions with 9 velocity vectors for each node. Using the developed model, the nonlinear distortion and shock front development of a finiteamplitude diffractive ultrasonic beam in a dissipative fluid medium was computed and validated against the published data. The results confirm that the LBM is an accurate and effective approach to model and simulate nonlinearity in finite-amplitude ultrasound beams with Mach numbers of up to 0.01 which, among others, falls within the range of therapeutic ultrasound regime such as high intensity focused ultrasound (HIFU) beams. A comparison between the HIFU nonlinear beam simulations using the proposed model and pseudospectral methods in a 2D geometry is presented.

Comparing stochastic proton interactions simulated using TOPAS-nBio to experimental data from fluorescent nuclear track detectors

NASA Astrophysics Data System (ADS)

Underwood, T. S. A.; Sung, W.; McFadden, C. H.; McMahon, S. J.; Hall, D. C.; McNamara, A. L.; Paganetti, H.; Sawakuchi, G. O.; Schuemann, J.

2017-04-01

Whilst Monte Carlo (MC) simulations of proton energy deposition have been well-validated at the macroscopic level, their microscopic validation remains lacking. Equally, no gold-standard yet exists for experimental metrology of individual proton tracks. In this work we compare the distributions of stochastic proton interactions simulated using the TOPAS-nBio MC platform against confocal microscope data for Al2O3:C,Mg fluorescent nuclear track detectors (FNTDs). We irradiated 8× 4× 0.5 mm3 FNTD chips inside a water phantom, positioned at seven positions along a pristine proton Bragg peak with a range in water of 12 cm. MC simulations were implemented in two stages: (1) using TOPAS to model the beam properties within a water phantom and (2) using TOPAS-nBio with Geant4-DNA physics to score particle interactions through a water surrogate of Al2O3:C,Mg. The measured median track integrated brightness (IB) was observed to be strongly correlated to both (i) voxelized track-averaged linear energy transfer (LET) and (ii) frequency mean microdosimetric lineal energy, \\overline{{{y}F}} , both simulated in pure water. Histograms of FNTD track IB were compared against TOPAS-nBio histograms of the number of terminal electrons per proton, scored in water with mass-density scaled to mimic Al2O3:C,Mg. Trends between exposure depths observed in TOPAS-nBio simulations were experimentally replicated in the study of FNTD track IB. Our results represent an important first step towards the experimental validation of MC simulations on the sub-cellular scale and suggest that FNTDs can enable experimental study of the microdosimetric properties of individual proton tracks.

Comparing stochastic proton interactions simulated using TOPAS-nBio to experimental data from fluorescent nuclear track detectors.

PubMed

Underwood, T S A; Sung, W; McFadden, C H; McMahon, S J; Hall, D C; McNamara, A L; Paganetti, H; Sawakuchi, G O; Schuemann, J

2017-04-21

Whilst Monte Carlo (MC) simulations of proton energy deposition have been well-validated at the macroscopic level, their microscopic validation remains lacking. Equally, no gold-standard yet exists for experimental metrology of individual proton tracks. In this work we compare the distributions of stochastic proton interactions simulated using the TOPAS-nBio MC platform against confocal microscope data for Al 2 O 3 :C,Mg fluorescent nuclear track detectors (FNTDs). We irradiated [Formula: see text] mm 3 FNTD chips inside a water phantom, positioned at seven positions along a pristine proton Bragg peak with a range in water of 12 cm. MC simulations were implemented in two stages: (1) using TOPAS to model the beam properties within a water phantom and (2) using TOPAS-nBio with Geant4-DNA physics to score particle interactions through a water surrogate of Al 2 O 3 :C,Mg. The measured median track integrated brightness (IB) was observed to be strongly correlated to both (i) voxelized track-averaged linear energy transfer (LET) and (ii) frequency mean microdosimetric lineal energy, [Formula: see text], both simulated in pure water. Histograms of FNTD track IB were compared against TOPAS-nBio histograms of the number of terminal electrons per proton, scored in water with mass-density scaled to mimic Al 2 O 3 :C,Mg. Trends between exposure depths observed in TOPAS-nBio simulations were experimentally replicated in the study of FNTD track IB. Our results represent an important first step towards the experimental validation of MC simulations on the sub-cellular scale and suggest that FNTDs can enable experimental study of the microdosimetric properties of individual proton tracks.

Energy-weighted dynamical scattering simulations of electron diffraction modalities in the scanning electron microscope.

PubMed

Pascal, Elena; Singh, Saransh; Callahan, Patrick G; Hourahine, Ben; Trager-Cowan, Carol; Graef, Marc De

2018-04-01

Transmission Kikuchi diffraction (TKD) has been gaining momentum as a high resolution alternative to electron back-scattered diffraction (EBSD), adding to the existing electron diffraction modalities in the scanning electron microscope (SEM). The image simulation of any of these measurement techniques requires an energy dependent diffraction model for which, in turn, knowledge of electron energies and diffraction distances distributions is required. We identify the sample-detector geometry and the effect of inelastic events on the diffracting electron beam as the important factors to be considered when predicting these distributions. However, tractable models taking into account inelastic scattering explicitly are lacking. In this study, we expand the Monte Carlo (MC) energy-weighting dynamical simulations models used for EBSD [1] and ECP [2] to the TKD case. We show that the foil thickness in TKD can be used as a means of energy filtering and compare band sharpness in the different modalities. The current model is shown to correctly predict TKD patterns and, through the dictionary indexing approach, to produce higher quality indexed TKD maps than conventional Hough transform approach, especially close to grain boundaries. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Mechanical modelling of tooth wear

PubMed Central

Kallonen, Aki

2016-01-01

Different diets wear teeth in different ways and generate distinguishable wear and microwear patterns that have long been the basis of palaeodiet reconstructions. Little experimental research has been performed to study them together. Here, we show that an artificial mechanical masticator, a chewing machine, occluding real horse teeth in continuous simulated chewing (of 100 000 chewing cycles) is capable of replicating microscopic wear features and gross wear on teeth that resemble wear in specimens collected from nature. Simulating pure attrition (chewing without food) and four plant material diets of different abrasives content (at n = 5 tooth pairs per group), we detected differences in microscopic wear features by stereomicroscopy of the chewing surface in the number and quality of pits and scratches that were not always as expected. Using computed tomography scanning in one tooth per diet, absolute wear was quantified as the mean height change after the simulated chewing. Absolute wear increased with diet abrasiveness, originating from phytoliths and grit. In combination, our findings highlight that differences in actual dental tissue loss can occur at similar microwear patterns, cautioning against a direct transformation of microwear results into predictions about diet or tooth wear rate. PMID:27411727

Developments in optical modeling methods for metrology

NASA Astrophysics Data System (ADS)

Davidson, Mark P.

1999-06-01

Despite the fact that in recent years the scanning electron microscope has come to dominate the linewidth measurement application for wafer manufacturing, there are still many applications for optical metrology and alignment. These include mask metrology, stepper alignment, and overlay metrology. Most advanced non-optical lithographic technologies are also considering using topics for alignment. In addition, there have been a number of in-situ technologies proposed which use optical measurements to control one aspect or another of the semiconductor process. So optics is definitely not dying out in the semiconductor industry. In this paper a description of recent advances in optical metrology and alignment modeling is presented. The theory of high numerical aperture image simulation for partially coherent illumination is discussed. The implications of telecentric optics on the image simulation is also presented. Reciprocity tests are proposed as an important measure of numerical accuracy. Diffraction efficiencies for chrome gratings on reticles are one good way to test Kirchoff's approximation as compared to rigorous calculations. We find significant differences between the predictions of Kirchoff's approximation and rigorous methods. The methods for simulating brightfield, confocal, and coherence probe microscope imags are outlined, as are methods for describing aberrations such as coma, spherical aberration, and illumination aperture decentering.

Simulations of material mixing in laser-driven reshock experiments

NASA Astrophysics Data System (ADS)

Haines, Brian M.; Grinstein, Fernando F.; Welser-Sherrill, Leslie; Fincke, James R.

2013-02-01

We perform simulations of a laser-driven reshock experiment [Welser-Sherrill et al., High Energy Density Phys. (unpublished)] in the strong-shock high energy-density regime to better understand material mixing driven by the Richtmyer-Meshkov instability. Validation of the simulations is based on direct comparison of simulation and radiographic data. Simulations are also compared with published direct numerical simulation and the theory of homogeneous isotropic turbulence. Despite the fact that the flow is neither homogeneous, isotropic nor fully turbulent, there are local regions in which the flow demonstrates characteristics of homogeneous isotropic turbulence. We identify and isolate these regions by the presence of high levels of turbulent kinetic energy (TKE) and vorticity. After reshock, our analysis shows characteristics consistent with those of incompressible isotropic turbulence. Self-similarity and effective Reynolds number assessments suggest that the results are reasonably converged at the finest resolution. Our results show that in shock-driven transitional flows, turbulent features such as self-similarity and isotropy only fully develop once de-correlation, characteristic vorticity distributions, and integrated TKE, have decayed significantly. Finally, we use three-dimensional simulation results to test the performance of two-dimensional Reynolds-averaged Navier-Stokes simulations. In this context, we also test a presumed probability density function turbulent mixing model extensively used in combustion applications.

On-Orbit Gradiometry with the scientific instrument of the French Space Mission MICROSCOPE

NASA Astrophysics Data System (ADS)

Foulon, B.; Baghi, Q.; Panet, I.; Rodrigues, M.; Metris, G.; Touboul, P.

2017-12-01

The MICROSCOPE mission is fully dedicated to the in-orbit test of the universality of free fall, the so-called Weak Equivalence Principle (WEP). Based on a CNES Myriade microsatellite launched on the 25th of April 2016, MICROSCOPE is a CNES-ESA-ONERA-CNRS-OCA mission, the scientific objective of which is to test of the Equivalence Principle with an extraordinary accuracy at the level of 10-15. The measurement will be obtained from the T-SAGE (Twin Space Accelerometer for Gravitational Experimentation) instrument constituted by two ultrasensitive differential accelerometers. One differential electrostatic accelerometer, labeled SU-EP, contains, at its center, two proof masses made of Titanium and Platinum and is used for the test. The twin accelerometer, labeled SU-REF, contains two Platinum proof masses and is used as a reference instrument. Separated by a 17 cm-length arm, they are embarked in a very stable and soft environment on board a satellite equipped with a drag-free control system and orbiting on a sun synchronous circular orbit at 710 km above the Earth. In addition to the WEP test, this configuration can be interesting for various applications, and one of the proposed ideas is to use MICROSCOPE data for the measurement of Earth's gravitational gradient. Considering the gradiometer formed by the inner Platinum proof-masses of the two differential accelerometers and the arm along the Y-axis of the instrument which is perpendicular to the orbital plane, possibly 3 components of the gradient can be measured: Txy, Tyy and Tzy. Preliminary studies suggest that the errors can be lower than 10mE. Taking advantage of its higher altitude with respect to GOCE, the low frequency signature of Earth's potential seen by MICROSCOPE could provide an additional observable in gradiometry to discriminate between different models describing the large scales of the mass distribution in the Earth's deep mantle. The poster will shortly present the MICROSCOPE mission configuration. It will detail the actual in-flight performances of the accelerometers and of the attitude and position control, in order to evaluate the gradiometer error budget according to the satellite pointing mode configuration.

Microscopic Moves.

ERIC Educational Resources Information Center

Zurcher, Sandra L.

1991-01-01

Presents lessons to stimulate children's interest in science and develop communication skills by having students simulate the locomotion of an ameba, a paramecium, and an Euglena, and the cyclosis in the pondweed Elodea. Students practice communication skills by demonstrating their organism to the remainder of the class. (MDH)

Some Techniques for Teaching about the Structure and Function of Chromosomes.

ERIC Educational Resources Information Center

Lowery, Roger; Taylor, Neil; Nathan, Subhashni

2000-01-01

Presents a teaching activity that uses photographs and diagrams to simulate two microscopic laboratory techniques used to observe the structure of chromosomes. Techniques include observation of squashed onion root tips and the salivary glands of some fruitfly larvae. (WRM)

Charge heterogeneity of surfaces: mapping and effects on surface forces.

PubMed

Drelich, Jaroslaw; Wang, Yu U

2011-07-11

The DLVO theory treats the total interaction force between two surfaces in a liquid medium as an arithmetic sum of two components: Lifshitz-van der Waals and electric double layer forces. Despite the success of the DLVO model developed for homogeneous surfaces, a vast majority of surfaces of particles and materials in technological systems are of a heterogeneous nature with a mosaic structure composed of microscopic and sub-microscopic domains of different surface characteristics. In such systems, the heterogeneity of the surface can be more important than the average surface character. Attractions can be stronger, by orders of magnitude, than would be expected from the classical mean-field DLVO model when area-averaged surface charge or potential is employed. Heterogeneity also introduces anisotropy of interactions into colloidal systems, vastly ignored in the past. To detect surface heterogeneities, analytical tools which provide accurate and spatially resolved information about material surface chemistry and potential - particularly at microscopic and sub-microscopic resolutions - are needed. Atomic force microscopy (AFM) offers the opportunity to locally probe not only changes in material surface characteristic but also charges of heterogeneous surfaces through measurements of force-distance curves in electrolyte solutions. Both diffuse-layer charge densities and potentials can be calculated by fitting the experimental data with a DLVO theoretical model. The surface charge characteristics of the heterogeneous substrate as recorded by AFM allow the charge variation to be mapped. Based on the obtained information, computer modeling and simulation can be performed to study the interactions among an ensemble of heterogeneous particles and their collective motions. In this paper, the diffuse-layer charge mapping by the AFM technique is briefly reviewed, and a new Diffuse Interface Field Approach to colloid modeling and simulation is briefly discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

Enhancing the performance of the light field microscope using wavefront coding

PubMed Central

Cohen, Noy; Yang, Samuel; Andalman, Aaron; Broxton, Michael; Grosenick, Logan; Deisseroth, Karl; Horowitz, Mark; Levoy, Marc

2014-01-01

Light field microscopy has been proposed as a new high-speed volumetric computational imaging method that enables reconstruction of 3-D volumes from captured projections of the 4-D light field. Recently, a detailed physical optics model of the light field microscope has been derived, which led to the development of a deconvolution algorithm that reconstructs 3-D volumes with high spatial resolution. However, the spatial resolution of the reconstructions has been shown to be non-uniform across depth, with some z planes showing high resolution and others, particularly at the center of the imaged volume, showing very low resolution. In this paper, we enhance the performance of the light field microscope using wavefront coding techniques. By including phase masks in the optical path of the microscope we are able to address this non-uniform resolution limitation. We have also found that superior control over the performance of the light field microscope can be achieved by using two phase masks rather than one, placed at the objective’s back focal plane and at the microscope’s native image plane. We present an extended optical model for our wavefront coded light field microscope and develop a performance metric based on Fisher information, which we use to choose adequate phase masks parameters. We validate our approach using both simulated data and experimental resolution measurements of a USAF 1951 resolution target; and demonstrate the utility for biological applications with in vivo volumetric calcium imaging of larval zebrafish brain. PMID:25322056

Improving z-tracking accuracy in the two-photon single-particle tracking microscope.

PubMed

Liu, C; Liu, Y-L; Perillo, E P; Jiang, N; Dunn, A K; Yeh, H-C

2015-10-12

Here, we present a method that can improve the z-tracking accuracy of the recently invented TSUNAMI (Tracking of Single particles Using Nonlinear And Multiplexed Illumination) microscope. This method utilizes a maximum likelihood estimator (MLE) to determine the particle's 3D position that maximizes the likelihood of the observed time-correlated photon count distribution. Our Monte Carlo simulations show that the MLE-based tracking scheme can improve the z-tracking accuracy of TSUNAMI microscope by 1.7 fold. In addition, MLE is also found to reduce the temporal correlation of the z-tracking error. Taking advantage of the smaller and less temporally correlated z-tracking error, we have precisely recovered the hybridization-melting kinetics of a DNA model system from thousands of short single-particle trajectories in silico . Our method can be generally applied to other 3D single-particle tracking techniques.

Development of the field of structural physiology

PubMed Central

FUJIYOSHI, Yoshinori

2015-01-01

Electron crystallography is especially useful for studying the structure and function of membrane proteins — key molecules with important functions in neural and other cells. Electron crystallography is now an established technique for analyzing the structures of membrane proteins in lipid bilayers that closely simulate their natural biological environment. Utilizing cryo-electron microscopes with helium-cooled specimen stages that were developed through a personal motivation to understand the functions of neural systems from a structural point of view, the structures of membrane proteins can be analyzed at a higher than 3 Å resolution. This review covers four objectives. First, I introduce the new research field of structural physiology. Second, I recount some of the struggles involved in developing cryo-electron microscopes. Third, I review the structural and functional analyses of membrane proteins mainly by electron crystallography using cryo-electron microscopes. Finally, I discuss multifunctional channels named “adhennels” based on structures analyzed using electron and X-ray crystallography. PMID:26560835

Microscopic properties of ionic liquid/organic semiconductor interfaces revealed by molecular dynamics simulations.

PubMed

Yokota, Yasuyuki; Miyamoto, Hiroo; Imanishi, Akihito; Takeya, Jun; Inagaki, Kouji; Morikawa, Yoshitada; Fukui, Ken-Ichi

2018-05-09

Electric double-layer transistors based on ionic liquid/organic semiconductor interfaces have been extensively studied during the past decade because of their high carrier densities at low operation voltages. Microscopic structures and the dynamics of ionic liquids likely determine the device performance; however, knowledge of these is limited by a lack of appropriate experimental tools. In this study, we investigated ionic liquid/organic semiconductor interfaces using molecular dynamics to reveal the microscopic properties of ionic liquids. The organic semiconductors include pentacene, rubrene, fullerene, and 7,7,8,8-tetracyanoquinodimethane (TCNQ). While ionic liquids close to the substrate always form the specific layered structures, the surface properties of organic semiconductors drastically alter the ionic dynamics. Ionic liquids at the fullerene interface behave as a two-dimensional ionic crystal because of the energy gain derived from the favorable electrostatic interaction on the corrugated periodic substrate.

Joint de-blurring and nonuniformity correction method for infrared microscopy imaging

NASA Astrophysics Data System (ADS)

Jara, Anselmo; Torres, Sergio; Machuca, Guillermo; Ramírez, Wagner; Gutiérrez, Pablo A.; Viafora, Laura A.; Godoy, Sebastián E.; Vera, Esteban

2018-05-01

In this work, we present a new technique to simultaneously reduce two major degradation artifacts found in mid-wavelength infrared microscopy imagery, namely the inherent focal-plane array nonuniformity noise and the scene defocus presented due to the point spread function of the infrared microscope. We correct both nuisances using a novel, recursive method that combines the constant range nonuniformity correction algorithm with a frame-by-frame deconvolution approach. The ability of the method to jointly compensate for both nonuniformity noise and blur is demonstrated using two different real mid-wavelength infrared microscopic video sequences, which were captured from two microscopic living organisms using a Janos-Sofradir mid-wavelength infrared microscopy setup. The performance of the proposed method is assessed on real and simulated infrared data by computing the root mean-square error and the roughness-laplacian pattern index, which was specifically developed for the present work.

Isotope analysis in the transmission electron microscope.

PubMed

Susi, Toma; Hofer, Christoph; Argentero, Giacomo; Leuthner, Gregor T; Pennycook, Timothy J; Mangler, Clemens; Meyer, Jannik C; Kotakoski, Jani

2016-10-10

The Ångström-sized probe of the scanning transmission electron microscope can visualize and collect spectra from single atoms. This can unambiguously resolve the chemical structure of materials, but not their isotopic composition. Here we differentiate between two isotopes of the same element by quantifying how likely the energetic imaging electrons are to eject atoms. First, we measure the displacement probability in graphene grown from either 12 C or 13 C and describe the process using a quantum mechanical model of lattice vibrations coupled with density functional theory simulations. We then test our spatial resolution in a mixed sample by ejecting individual atoms from nanoscale areas spanning an interface region that is far from atomically sharp, mapping the isotope concentration with a precision better than 20%. Although we use a scanning instrument, our method may be applicable to any atomic resolution transmission electron microscope and to other low-dimensional materials.

Improving z-tracking accuracy in the two-photon single-particle tracking microscope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, C.; Liu, Y.-L.; Perillo, E. P.

Here, we present a method that can improve the z-tracking accuracy of the recently invented TSUNAMI (Tracking of Single particles Using Nonlinear And Multiplexed Illumination) microscope. This method utilizes a maximum likelihood estimator (MLE) to determine the particle's 3D position that maximizes the likelihood of the observed time-correlated photon count distribution. Our Monte Carlo simulations show that the MLE-based tracking scheme can improve the z-tracking accuracy of TSUNAMI microscope by 1.7 fold. In addition, MLE is also found to reduce the temporal correlation of the z-tracking error. Taking advantage of the smaller and less temporally correlated z-tracking error, we havemore » precisely recovered the hybridization-melting kinetics of a DNA model system from thousands of short single-particle trajectories in silico. Our method can be generally applied to other 3D single-particle tracking techniques.« less

Controlling dispersion of graphene nanoplatelets in aqueous solution by ultrasonic technique

NASA Astrophysics Data System (ADS)

Wang, Baomin; Jiang, Ruishuang; Song, Wanzeng; Liu, Hui

2017-08-01

The homogenous graphene nanoplatelets (GNP) suspension had been prepared through ultrasonic exfoliation in the presence of methylcellulose (MC) as dispersant. The influence of different sonication times on dispersing of aqueous GNP suspension was monitored by UV-Vis absorbance, sedimentation test, optical microscope and transmission electron microscope (TEM). The study of UV-Vis absorbance verifies that the minimum sonication time to break the 0.1 g/L concentration of bundled GNPs is 20 min; furthermore, the GNP suspension achieved the best dispersion, when sonication time increased up to 80 min. From optical microscope images of GNPs, the agglomeration of GNPs was broken by enough sonication energy, and the distribution of GNPs particles became more uniform. The dispersing mechanism had been discussed and simulated by HRTEM image. The bundled GNPs were exfoliated by cavitation effect of ultrasonic irradiation, meanwhile, the dispersant adsorbed on the surface of GNPs prevented re-entanglement by forming steric hindrance.

Coupling Hydraulic Fracturing Propagation and Gas Well Performance for Simulation of Production in Unconventional Shale Gas Reservoirs

NASA Astrophysics Data System (ADS)

Wang, C.; Winterfeld, P. H.; Wu, Y. S.; Wang, Y.; Chen, D.; Yin, C.; Pan, Z.

2014-12-01

Hydraulic fracturing combined with horizontal drilling has made it possible to economically produce natural gas from unconventional shale gas reservoirs. An efficient methodology for evaluating hydraulic fracturing operation parameters, such as fluid and proppant properties, injection rates, and wellhead pressure, is essential for the evaluation and efficient design of these processes. Traditional numerical evaluation and optimization approaches are usually based on simulated fracture properties such as the fracture area. In our opinion, a methodology based on simulated production data is better, because production is the goal of hydraulic fracturing and we can calibrate this approach with production data that is already known. This numerical methodology requires a fully-coupled hydraulic fracture propagation and multi-phase flow model. In this paper, we present a general fully-coupled numerical framework to simulate hydraulic fracturing and post-fracture gas well performance. This three-dimensional, multi-phase simulator focuses on: (1) fracture width increase and fracture propagation that occurs as slurry is injected into the fracture, (2) erosion caused by fracture fluids and leakoff, (3) proppant subsidence and flowback, and (4) multi-phase fluid flow through various-scaled anisotropic natural and man-made fractures. Mathematical and numerical details on how to fully couple the fracture propagation and fluid flow parts are discussed. Hydraulic fracturing and production operation parameters, and properties of the reservoir, fluids, and proppants, are taken into account. The well may be horizontal, vertical, or deviated, as well as open-hole or cemented. The simulator is verified based on benchmarks from the literature and we show its application by simulating fracture network (hydraulic and natural fractures) propagation and production data history matching of a field in China. We also conduct a series of real-data modeling studies with different combinations of hydraulic fracturing parameters and present the methodology to design these operations with feedback of simulated production data. The unified model aids in the optimization of hydraulic fracturing design, operations, and production.

User's Guide of TOUGH2-EGS. A Coupled Geomechanical and Reactive Geochemical Simulator for Fluid and Heat Flow in Enhanced Geothermal Systems Version 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fakcharoenphol, Perapon; Xiong, Yi; Hu, Litang

TOUGH2-EGS is a numerical simulation program coupling geomechanics and chemical reactions for fluid and heat flows in porous media and fractured reservoirs of enhanced geothermal systems. The simulator includes the fully-coupled geomechanical (THM) module, the fully-coupled geochemical (THC) module, and the sequentially coupled reactive geochemistry (THMC) module. The fully-coupled flow-geomechanics model is developed from the linear elastic theory for the thermo-poro-elastic system and is formulated with the mean normal stress as well as pore pressure and temperature. The chemical reaction is sequentially coupled after solution of flow equations, which provides the flow velocity and phase saturation for the solute transportmore » calculation at each time step. In addition, reservoir rock properties, such as porosity and permeability, are subjected to change due to rock deformation and chemical reactions. The relationships between rock properties and geomechanical and chemical effects from poro-elasticity theories and empirical correlations are incorporated into the simulator. This report provides the user with detailed information on both mathematical models and instructions for using TOUGH2-EGS for THM, THC or THMC simulations. The mathematical models include the fluid and heat flow equations, geomechanical equation, reactive geochemistry equations, and discretization methods. Although TOUGH2-EGS has the capability for simulating fluid and heat flows coupled with both geomechanical and chemical effects, it is up to the users to select the specific coupling process, such as THM, THC, or THMC in a simulation. There are several example problems illustrating the applications of this program. These example problems are described in details and their input data are presented. The results demonstrate that this program can be used for field-scale geothermal reservoir simulation with fluid and heat flow, geomechanical effect, and chemical reaction in porous and fractured media.« less

Three-Dimensional Simulations of Electron Beams Focused by Periodic Permanent Magnets

NASA Technical Reports Server (NTRS)

Kory, Carol L.

1999-01-01

A fully three-dimensional (3D) model of an electron beam focused by a periodic permanent magnet (PPM) stack has been developed. First, the simulation code MAFIA was used to model a PPM stack using the magnetostatic solver. The exact geometry of the magnetic focusing structure was modeled; thus, no approximations were made regarding the off-axis fields. The fields from the static solver were loaded into the 3D particle-in-cell (PIC) solver of MAFIA where fully 3D behavior of the beam was simulated in the magnetic focusing field. The PIC solver computes the time-integration of electromagnetic fields simultaneously with the time integration of the equations of motion of charged particles that move under the influence of those fields. Fields caused by those moving charges are also taken into account; thus, effects like space charge and magnetic forces between particles are fully simulated. The electron beam is simulated by a number of macro-particles. These macro-particles represent a given charge Q amounting to that of several million electrons in order to conserve computational time and memory. Particle motion is unrestricted, so particle trajectories can cross paths and move in three dimensions under the influence of 3D electric and magnetic fields. Correspondingly, there is no limit on the initial current density distribution of the electron beam, nor its density distribution at any time during the simulation. Simulation results including beam current density, percent ripple and percent transmission will be presented, and the effects current, magnetic focusing strength and thermal velocities have on beam behavior will be demonstrated using 3D movies showing the evolution of beam characteristics in time and space. Unlike typical beam optics models, this 3D model allows simulation of asymmetric designs such as non- circularly symmetric electrostatic or magnetic focusing as well as the inclusion of input/output couplers.