Multicluster

DTIC Science & Technology

1993-03-01

CLUSTER A CLUSTER B .UDP D "Orequeqes ProxyDistribute 0 Figure 4-4: HOSTALL Implementation HOST_ALL is implemented as follows. The kernel looks up the...it includes the HOSTALL request as an argument. The generic CronusHost object is managed by the Cronus Kernel. A kernel that receives a ProxyDistnbute...request uses its cached service information to send the HOSTALL request to each host in its cluster via UDP. If the kernel has no cached information

Multi-cluster processor operating only select number of clusters during each phase based on program statistic monitored at predetermined intervals

DOEpatents

Balasubramonian, Rajeev [Sandy, UT; Dwarkadas, Sandhya [Rochester, NY; Albonesi, David [Ithaca, NY

2009-02-10

In a processor having multiple clusters which operate in parallel, the number of clusters in use can be varied dynamically. At the start of each program phase, the configuration option for an interval is run to determine the optimal configuration, which is used until the next phase change is detected. The optimum instruction interval is determined by starting with a minimum interval and doubling it until a low stability factor is reached.

Resilient workflows for computational mechanics platforms

NASA Astrophysics Data System (ADS)

Nguyên, Toàn; Trifan, Laurentiu; Désidéri, Jean-Antoine

2010-06-01

Workflow management systems have recently been the focus of much interest and many research and deployment for scientific applications worldwide [26, 27]. Their ability to abstract the applications by wrapping application codes have also stressed the usefulness of such systems for multidiscipline applications [23, 24]. When complex applications need to provide seamless interfaces hiding the technicalities of the computing infrastructures, their high-level modeling, monitoring and execution functionalities help giving production teams seamless and effective facilities [25, 31, 33]. Software integration infrastructures based on programming paradigms such as Python, Mathlab and Scilab have also provided evidence of the usefulness of such approaches for the tight coupling of multidisciplne application codes [22, 24]. Also high-performance computing based on multi-core multi-cluster infrastructures open new opportunities for more accurate, more extensive and effective robust multi-discipline simulations for the decades to come [28]. This supports the goal of full flight dynamics simulation for 3D aircraft models within the next decade, opening the way to virtual flight-tests and certification of aircraft in the future [23, 24, 29].

A Hidden Markov Model for Urban-Scale Traffic Estimation Using Floating Car Data.

PubMed

Wang, Xiaomeng; Peng, Ling; Chi, Tianhe; Li, Mengzhu; Yao, Xiaojing; Shao, Jing

2015-01-01

Urban-scale traffic monitoring plays a vital role in reducing traffic congestion. Owing to its low cost and wide coverage, floating car data (FCD) serves as a novel approach to collecting traffic data. However, sparse probe data represents the vast majority of the data available on arterial roads in most urban environments. In order to overcome the problem of data sparseness, this paper proposes a hidden Markov model (HMM)-based traffic estimation model, in which the traffic condition on a road segment is considered as a hidden state that can be estimated according to the conditions of road segments having similar traffic characteristics. An algorithm based on clustering and pattern mining rather than on adjacency relationships is proposed to find clusters with road segments having similar traffic characteristics. A multi-clustering strategy is adopted to achieve a trade-off between clustering accuracy and coverage. Finally, the proposed model is designed and implemented on the basis of a real-time algorithm. Results of experiments based on real FCD confirm the applicability, accuracy, and efficiency of the model. In addition, the results indicate that the model is practicable for traffic estimation on urban arterials and works well even when more than 70% of the probe data are missing.

Collinear cluster tri-partition - the brightest observations and their treating

NASA Astrophysics Data System (ADS)

Pyatkov, Yu V.; Kamanin, D. V.; Lavrova, J. E.; Mkaza, N.; Malaza, V.; Strekalovsky, A. O.

2017-06-01

Careful studies of the fission fragments mass correlation distributions let us to reveal specific linear structures in the region of a big missing mass. It became possible due to applying of effective cleaning of this region from the background linked with scattered fragments. One of the most pronounced structure looks like a rectangle bounded by the magic nuclei. The fission events aggregated in the rectangle show a very low total kinetic energy. We propose possible scenario of forming and decay of the multi-cluster prescission configuration decisive for the experimental findings. This approach is valid as well for treating of another rare decay modes discovered in the past.

Acculturation stress, drinking, and intimate partner violence among Hispanic couples in the U.S.

PubMed

Caetano, Raul; Ramisetty-Mikler, Suhasini; Caetano Vaeth, Patrice A; Harris, T Robert

2007-11-01

This article examines the cross-sectional association between acculturation, acculturation stress, drinking, and intimate partner violence (IPV) among Hispanic couples in the U.S. The data being analyzed come from a multicluster random household sample of couples interviewed as part of the second wave of a 5-year national longitudinal study. The overall survey response rate for the second wave is 72%. Participants are Hispanic couples 18 years of age or older (N = 387). Results show that, among men, lower acculturation is positively associated with higher acculturation stress, which is directly related to a greater likelihood of involvement in IPV. These associations are also present among women. However, data for women show an additional path linking higher levels of acculturation directly to IPV. Drinking is not associated with IPV, independent of gender. Acculturation, directly or through acculturation stress, increases the likelihood of IPV.

Evaluation of SLAR and thematic mapper MSS data for forest cover mapping using computer-aided analysis techniques

NASA Technical Reports Server (NTRS)

Hoffer, R. M. (Principal Investigator); Knowlton, D. J.; Dean, M. E.

1981-01-01

A set of training statistics for the 30 meter resolution simulated thematic mapper MSS data was generated based on land use/land cover classes. In addition to this supervised data set, a nonsupervised multicluster block of training statistics is being defined in order to compare the classification results and evaluate the effect of the different training selection methods on classification performance. Two test data sets, defined using a stratified sampling procedure incorporating a grid system with dimensions of 50 lines by 50 columns, and another set based on an analyst supervised set of test fields were used to evaluate the classifications of the TMS data. The supervised training data set generated training statistics, and a per point Gaussian maximum likelihood classification of the 1979 TMS data was obtained. The August 1980 MSS data was radiometrically adjusted. The SAR data was redigitized and the SAR imagery was qualitatively analyzed.

A Multi-Discipline, Multi-Genre Digital Library for Research and Education

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Maly, Kurt; Shen, Stewart N. T.

2004-01-01

We describe NCSTRL+, a unified, canonical digital library for educational and scientific and technical information (STI). NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible digital library (DL) that provides access to over 100 university departments and laboratories. NCSTRL+ implements two new technologies: cluster functionality and publishing "buckets". We have extended the Dienst protocol, the protocol underlying NCSTRL, to provide the ability to "cluster" independent collections into a logically centralized digital library based upon subject category classification, type of organization, and genres of material. The concept of "buckets" provides a mechanism for publishing and managing logically linked entities with multiple data formats. The NCSTRL+ prototype DL contains the holdings of NCSTRL and the NASA Technical Report Server (NTRS). The prototype demonstrates the feasibility of publishing into a multi-cluster DL, searching across clusters, and storing and presenting buckets of information.

NCSTRL+: Adding Multi-Discipline and Multi-Genre Support to the Dienst Protocol Using Clusters and Buckets

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Maly, Kurt; Shen, Stewart N. T.; Zubair, Mohammad

1998-01-01

We describe NCSTRL+, a unified, canonical digital library for scientific and technical information (STI). NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible digital library (DL) that provides access to over 100 university departments and laboratories. NCSTRL+ implements two new technologies: cluster functionality and publishing buckets. We have extended Dienst, the protocol underlying NCSTRL, to provide the ability to cluster independent collections into a logically centralized digital library based upon subject category classification, type of organization, and genres of material. The bucket construct provides a mechanism for publishing and managing logically linked entities with multiple data forms as a single object. The NCSTRL+ prototype DL contains the holdings of NCSTRL and the NASA Technical Report Server (NTRS). The prototype demonstrates the feasibility of publishing into a multi-cluster DL, searching across clusters, and storing and presenting buckets of information.

SIAM Conference on Parallel Processing for Scientific Computing, 4th, Chicago, IL, Dec. 11-13, 1989, Proceedings

NASA Technical Reports Server (NTRS)

Dongarra, Jack (Editor); Messina, Paul (Editor); Sorensen, Danny C. (Editor); Voigt, Robert G. (Editor)

1990-01-01

Attention is given to such topics as an evaluation of block algorithm variants in LAPACK and presents a large-grain parallel sparse system solver, a multiprocessor method for the solution of the generalized Eigenvalue problem on an interval, and a parallel QR algorithm for iterative subspace methods on the CM2. A discussion of numerical methods includes the topics of asynchronous numerical solutions of PDEs on parallel computers, parallel homotopy curve tracking on a hypercube, and solving Navier-Stokes equations on the Cedar Multi-Cluster system. A section on differential equations includes a discussion of a six-color procedure for the parallel solution of elliptic systems using the finite quadtree structure, data parallel algorithms for the finite element method, and domain decomposition methods in aerodynamics. Topics dealing with massively parallel computing include hypercube vs. 2-dimensional meshes and massively parallel computation of conservation laws. Performance and tools are also discussed.

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 ...

Derivation of the Boltzmann Equation for Financial Brownian Motion: Direct Observation of the Collective Motion of High-Frequency Traders.

PubMed

Kanazawa, Kiyoshi; Sueshige, Takumi; Takayasu, Hideki; Takayasu, Misako

2018-03-30

A microscopic model is established for financial Brownian motion from the direct observation of the dynamics of high-frequency traders (HFTs) in a foreign exchange market. Furthermore, a theoretical framework parallel to molecular kinetic theory is developed for the systematic description of the financial market from microscopic dynamics of HFTs. We report first on a microscopic empirical law of traders' trend-following behavior by tracking the trajectories of all individuals, which quantifies the collective motion of HFTs but has not been captured in conventional order-book models. We next introduce the corresponding microscopic model of HFTs and present its theoretical solution paralleling molecular kinetic theory: Boltzmann-like and Langevin-like equations are derived from the microscopic dynamics via the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy. Our model is the first microscopic model that has been directly validated through data analysis of the microscopic dynamics, exhibiting quantitative agreements with mesoscopic and macroscopic empirical results.

Derivation of the Boltzmann Equation for Financial Brownian Motion: Direct Observation of the Collective Motion of High-Frequency Traders

NASA Astrophysics Data System (ADS)

Kanazawa, Kiyoshi; Sueshige, Takumi; Takayasu, Hideki; Takayasu, Misako

2018-03-01

A microscopic model is established for financial Brownian motion from the direct observation of the dynamics of high-frequency traders (HFTs) in a foreign exchange market. Furthermore, a theoretical framework parallel to molecular kinetic theory is developed for the systematic description of the financial market from microscopic dynamics of HFTs. We report first on a microscopic empirical law of traders' trend-following behavior by tracking the trajectories of all individuals, which quantifies the collective motion of HFTs but has not been captured in conventional order-book models. We next introduce the corresponding microscopic model of HFTs and present its theoretical solution paralleling molecular kinetic theory: Boltzmann-like and Langevin-like equations are derived from the microscopic dynamics via the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy. Our model is the first microscopic model that has been directly validated through data analysis of the microscopic dynamics, exhibiting quantitative agreements with mesoscopic and macroscopic empirical results.

Generic distortion model for metrology under optical microscopes

NASA Astrophysics Data System (ADS)

Liu, Xingjian; Li, Zhongwei; Zhong, Kai; Chao, YuhJin; Miraldo, Pedro; Shi, Yusheng

2018-04-01

For metrology under optical microscopes, lens distortion is the dominant source of error. Previous distortion models and correction methods mostly rely on the assumption that parametric distortion models require a priori knowledge of the microscopes' lens systems. However, because of the numerous optical elements in a microscope, distortions can be hardly represented by a simple parametric model. In this paper, a generic distortion model considering both symmetric and asymmetric distortions is developed. Such a model is obtained by using radial basis functions (RBFs) to interpolate the radius and distortion values of symmetric distortions (image coordinates and distortion rays for asymmetric distortions). An accurate and easy to implement distortion correction method is presented. With the proposed approach, quantitative measurement with better accuracy can be achieved, such as in Digital Image Correlation for deformation measurement when used with an optical microscope. The proposed technique is verified by both synthetic and real data experiments.

Buckets, Clusters and Dienst

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Maly, Kurt; Shen, Stewart N. T.

1997-01-01

In this paper we describe NCSTRL+, a unified, canonical digital library for scientific and technical information (STI). NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible digital library (DL) that provides access to over 80 university departments and laboratories. NCSTRL+ implements two new technologies: cluster functionality and publishing "buckets." We have extended the Dienst protocol, the protocol underlying NCSTRL, to provide the ability to "cluster" independent collections into a logically centralized digital library based upon subject category classification, type of organization, and genres of material. The concept of "buckets" provides a mechanism for publishing and managing logically linked entities with multiple data formats. The NCSTRL+ prototype DL contains the holdings of NCSTRL and the NASA Technical Report Server (NTRS). The prototype demonstrates the feasibility of publishing into a multi-cluster DL, searching across clusters, and storing and presenting buckets of information. We show that the overhead for these additional capabilities is minimal to both the author and the user when compared to the equivalent process within NCSTRL.

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.

Performance Models for the Spike Banded Linear System Solver

DOE PAGES

Manguoglu, Murat; Saied, Faisal; Sameh, Ahmed; ...

2011-01-01

With availability of large-scale parallel platforms comprised of tens-of-thousands of processors and beyond, there is significant impetus for the development of scalable parallel sparse linear system solvers and preconditioners. An integral part of this design process is the development of performance models capable of predicting performance and providing accurate cost models for the solvers and preconditioners. There has been some work in the past on characterizing performance of the iterative solvers themselves. In this paper, we investigate the problem of characterizing performance and scalability of banded preconditioners. Recent work has demonstrated the superior convergence properties and robustness of banded preconditioners,more » compared to state-of-the-art ILU family of preconditioners as well as algebraic multigrid preconditioners. Furthermore, when used in conjunction with efficient banded solvers, banded preconditioners are capable of significantly faster time-to-solution. Our banded solver, the Truncated Spike algorithm is specifically designed for parallel performance and tolerance to deep memory hierarchies. Its regular structure is also highly amenable to accurate performance characterization. Using these characteristics, we derive the following results in this paper: (i) we develop parallel formulations of the Truncated Spike solver, (ii) we develop a highly accurate pseudo-analytical parallel performance model for our solver, (iii) we show excellent predication capabilities of our model – based on which we argue the high scalability of our solver. Our pseudo-analytical performance model is based on analytical performance characterization of each phase of our solver. These analytical models are then parameterized using actual runtime information on target platforms. An important consequence of our performance models is that they reveal underlying performance bottlenecks in both serial and parallel formulations. All of our results are validated on diverse heterogeneous multiclusters – platforms for which performance prediction is particularly challenging. Finally, we provide predict the scalability of the Spike algorithm using up to 65,536 cores with our model. In this paper we extend the results presented in the Ninth International Symposium on Parallel and Distributed Computing.« less

Handy Microscopic Close-Range Videogrammetry

NASA Astrophysics Data System (ADS)

Esmaeili, F.; Ebadi, H.

2017-09-01

The modeling of small-scale objects is used in different applications such as medicine, industry, and cultural heritage. The capability of modeling small-scale objects using imaging with the help of hand USB digital microscopes and use of videogrammetry techniques has been implemented and evaluated in this paper. Use of this equipment and convergent imaging of the environment for modeling, provides an appropriate set of images for generation of three-dimensional models. The results of the measurements made with the help of a microscope micrometer calibration ruler have demonstrated that self-calibration of a hand camera-microscope set can help obtain a three-dimensional detail extraction precision of about 0.1 millimeters on small-scale environments.

Refining Students' Explanations of an Unfamiliar Physical Phenomenon-Microscopic Friction

NASA Astrophysics Data System (ADS)

Corpuz, Edgar De Guzman; Rebello, N. Sanjay

2017-08-01

The first phase of this multiphase study involves modeling of college students' thinking of friction at the microscopic level. Diagnostic interviews were conducted with 11 students with different levels of physics backgrounds. A phenomenographic approach of data analysis was used to generate categories of responses which subsequently were used to generate a model of explanation. Most of the students interviewed consistently used mechanical interactions in explaining microscopic friction. According to these students, friction is due to the interlocking or rubbing of atoms. Our data suggest that students' explanations of microscopic friction are predominantly influenced by their macroscopic experiences. In the second phase of the research, teaching experiment was conducted with 18 college students to investigate how students' explanations of microscopic friction can be refined by a series of model-building activities. Data were analyzed using Redish's two-level transfer framework. Our results show that through sequences of hands-on and minds-on activities, including cognitive dissonance and resolution, it is possible to facilitate the refinement of students' explanations of microscopic friction. The activities seemed to be productive in helping students activate associations that refine their ideas about microscopic friction.

Investigating Students' Mental Models and Knowledge Construction of Microscopic Friction. I. Implications for Curriculum Design and Development

ERIC Educational Resources Information Center

Corpuz, Edgar D.; Rebello, N. Sanjay

2011-01-01

In this paper, we discuss the first phase of a multiphase study aimed at investigating the dynamics of students' knowledge construction in the context of unfamiliar physical phenomenon--microscopic friction. The first phase of this study involved the investigation of the variations in students' mental models of microscopic friction. Clinical…

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...

Microscopic vision modeling method by direct mapping analysis for micro-gripping system with stereo light microscope.

PubMed

Wang, Yuezong; Zhao, Zhizhong; Wang, Junshuai

2016-04-01

We present a novel and high-precision microscopic vision modeling method, which can be used for 3D data reconstruction in micro-gripping system with stereo light microscope. This method consists of four parts: image distortion correction, disparity distortion correction, initial vision model and residual compensation model. First, the method of image distortion correction is proposed. Image data required by image distortion correction comes from stereo images of calibration sample. The geometric features of image distortions can be predicted though the shape deformation of lines constructed by grid points in stereo images. Linear and polynomial fitting methods are applied to correct image distortions. Second, shape deformation features of disparity distribution are discussed. The method of disparity distortion correction is proposed. Polynomial fitting method is applied to correct disparity distortion. Third, a microscopic vision model is derived, which consists of two models, i.e., initial vision model and residual compensation model. We derive initial vision model by the analysis of direct mapping relationship between object and image points. Residual compensation model is derived based on the residual analysis of initial vision model. The results show that with maximum reconstruction distance of 4.1mm in X direction, 2.9mm in Y direction and 2.25mm in Z direction, our model achieves a precision of 0.01mm in X and Y directions and 0.015mm in Z direction. Comparison of our model with traditional pinhole camera model shows that two kinds of models have a similar reconstruction precision of X coordinates. However, traditional pinhole camera model has a lower precision of Y and Z coordinates than our model. The method proposed in this paper is very helpful for the micro-gripping system based on SLM microscopic vision. Copyright © 2016 Elsevier Ltd. All rights reserved.

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...

Hands-On and Minds-On Modeling Activities to Improve Students' Conceptions of Microscopic Friction

NASA Astrophysics Data System (ADS)

Corpuz, Edgar G.; Rebello, N. Sanjay

2007-11-01

In this paper we discuss the development and validation of hands-on and minds-on modeling activities geared towards improving students' understanding of microscopic friction. We will also present our investigation on the relative effectiveness of the use of the developed instructional material with two lecture formats—traditional and videotaped lectures. Results imply that through a series of carefully designed hands-on and minds-on modeling activities, it is possible to facilitate the refinement of students' ideas of microscopic friction.

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 ...

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...

A Novel Hyperspectral Microscopic Imaging System for Evaluating Fresh Degree of Pork.

PubMed

Xu, Yi; Chen, Quansheng; Liu, Yan; Sun, Xin; Huang, Qiping; Ouyang, Qin; Zhao, Jiewen

2018-04-01

This study proposed a rapid microscopic examination method for pork freshness evaluation by using the self-assembled hyperspectral microscopic imaging (HMI) system with the help of feature extraction algorithm and pattern recognition methods. Pork samples were stored for different days ranging from 0 to 5 days and the freshness of samples was divided into three levels which were determined by total volatile basic nitrogen (TVB-N) content. Meanwhile, hyperspectral microscopic images of samples were acquired by HMI system and processed by the following steps for the further analysis. Firstly, characteristic hyperspectral microscopic images were extracted by using principal component analysis (PCA) and then texture features were selected based on the gray level co-occurrence matrix (GLCM). Next, features data were reduced dimensionality by fisher discriminant analysis (FDA) for further building classification model. Finally, compared with linear discriminant analysis (LDA) model and support vector machine (SVM) model, good back propagation artificial neural network (BP-ANN) model obtained the best freshness classification with a 100 % accuracy rating based on the extracted data. The results confirm that the fabricated HMI system combined with multivariate algorithms has ability to evaluate the fresh degree of pork accurately in the microscopic level, which plays an important role in animal food quality control.

A Novel Hyperspectral Microscopic Imaging System for Evaluating Fresh Degree of Pork

PubMed Central

Xu, Yi; Chen, Quansheng; Liu, Yan; Sun, Xin; Huang, Qiping; Ouyang, Qin; Zhao, Jiewen

2018-01-01

Abstract This study proposed a rapid microscopic examination method for pork freshness evaluation by using the self-assembled hyperspectral microscopic imaging (HMI) system with the help of feature extraction algorithm and pattern recognition methods. Pork samples were stored for different days ranging from 0 to 5 days and the freshness of samples was divided into three levels which were determined by total volatile basic nitrogen (TVB-N) content. Meanwhile, hyperspectral microscopic images of samples were acquired by HMI system and processed by the following steps for the further analysis. Firstly, characteristic hyperspectral microscopic images were extracted by using principal component analysis (PCA) and then texture features were selected based on the gray level co-occurrence matrix (GLCM). Next, features data were reduced dimensionality by fisher discriminant analysis (FDA) for further building classification model. Finally, compared with linear discriminant analysis (LDA) model and support vector machine (SVM) model, good back propagation artificial neural network (BP-ANN) model obtained the best freshness classification with a 100 % accuracy rating based on the extracted data. The results confirm that the fabricated HMI system combined with multivariate algorithms has ability to evaluate the fresh degree of pork accurately in the microscopic level, which plays an important role in animal food quality control. PMID:29805285

Towards a social psychology-based microscopic model of driver behavior and decision-making : modifying Lewin's field theory

DOT National Transportation Integrated Search

2014-01-01

Central to effective roadway design is the ability to understand how drivers behave as they traverse a segment of : roadway. While simple and complex microscopic models have been used over the years to analyse driver behaviour, : most models: 1.) inc...

Nurse/physician communication through a sensemaking lens: shifting the paradigm to improve patient safety.

PubMed

Manojlovich, Milisa

2010-11-01

Physician-nurse communication has been identified as one of the main obstacles to progress in patient safety. Breakdowns in communication between physicians and nurses often result in errors, many of which are preventable. Recent research into nurse/physician communication has borrowed heavily from team literature, tending to study communication as one behavior in a larger cluster of behaviors. The multicluster approach to team research has not provided enough analysis of and attention to communication alone. Research into communication specifically is needed to understand its crucial role in teamwork and safety. A critique of the research literature on nurse/physician communication published since 1992 revealed 3 dominant themes: settings and context, consensus building, and conflict resolution. A fourth implicit theme, the temporal nature of communication, emerged as well. These themes were used to frame a discussion on sensemaking: an iterative process arising from dialogue when 2 or more people share their unique perspectives. As a theoretical model, sensemaking may offer an alternative lens through which to view the phenomenon of nurse/physician communication and advance our understanding of how nurse/physician communication can promote patient safety. Sensemaking may represent a paradigm shift with the potential to affect 2 spheres of influence: clinical practice and health care outcomes. Sensemaking may also hold promise as an intervention because through sensemaking consensus may be built and errors possibly prevented. Engaging in sensemaking may overcome communication barriers without realigning power bases, incorporate contextual influences without drawing attention away from communicators, and inform actions arising from communication.

A Bottom-Up Approach to Understanding Protein Layer Formation at Solid-Liquid Interfaces

PubMed Central

Kastantin, Mark; Langdon, Blake B.; Schwartz, Daniel K.

2014-01-01

A common goal across different fields (e.g. separations, biosensors, biomaterials, pharmaceuticals) is to understand how protein behavior at solid-liquid interfaces is affected by environmental conditions. Temperature, pH, ionic strength, and the chemical and physical properties of the solid surface, among many factors, can control microscopic protein dynamics (e.g. adsorption, desorption, diffusion, aggregation) that contribute to macroscopic properties like time-dependent total protein surface coverage and protein structure. These relationships are typically studied through a top-down approach in which macroscopic observations are explained using analytical models that are based upon reasonable, but not universally true, simplifying assumptions about microscopic protein dynamics. Conclusions connecting microscopic dynamics to environmental factors can be heavily biased by potentially incorrect assumptions. In contrast, more complicated models avoid several of the common assumptions but require many parameters that have overlapping effects on predictions of macroscopic, average protein properties. Consequently, these models are poorly suited for the top-down approach. Because the sophistication incorporated into these models may ultimately prove essential to understanding interfacial protein behavior, this article proposes a bottom-up approach in which direct observations of microscopic protein dynamics specify parameters in complicated models, which then generate macroscopic predictions to compare with experiment. In this framework, single-molecule tracking has proven capable of making direct measurements of microscopic protein dynamics, but must be complemented by modeling to combine and extrapolate many independent microscopic observations to the macro-scale. The bottom-up approach is expected to better connect environmental factors to macroscopic protein behavior, thereby guiding rational choices that promote desirable protein behaviors. PMID:24484895

Microscopic prediction of speech recognition for listeners with normal hearing in noise using an auditory model.

PubMed

Jürgens, Tim; Brand, Thomas

2009-11-01

This study compares the phoneme recognition performance in speech-shaped noise of a microscopic model for speech recognition with the performance of normal-hearing listeners. "Microscopic" is defined in terms of this model twofold. First, the speech recognition rate is predicted on a phoneme-by-phoneme basis. Second, microscopic modeling means that the signal waveforms to be recognized are processed by mimicking elementary parts of human's auditory processing. The model is based on an approach by Holube and Kollmeier [J. Acoust. Soc. Am. 100, 1703-1716 (1996)] and consists of a psychoacoustically and physiologically motivated preprocessing and a simple dynamic-time-warp speech recognizer. The model is evaluated while presenting nonsense speech in a closed-set paradigm. Averaged phoneme recognition rates, specific phoneme recognition rates, and phoneme confusions are analyzed. The influence of different perceptual distance measures and of the model's a-priori knowledge is investigated. The results show that human performance can be predicted by this model using an optimal detector, i.e., identical speech waveforms for both training of the recognizer and testing. The best model performance is yielded by distance measures which focus mainly on small perceptual distances and neglect outliers.

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.

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 ...

Two level approach to safety planning incorporating the Highway Safety Manual (HSM) network screening : [summary].

DOT National Transportation Integrated Search

2014-04-01

In this project, University of Central Florida researchers combined two types of safety analysis, microscopic and macroscopic, to overcome their limitations. Microscopic models focus on traffic flows and related parameters. Macroscopic models are bas...

Effect of double layers on magnetosphere-ionosphere coupling

NASA Technical Reports Server (NTRS)

Lysak, Robert L.; Hudson, Mary K.

1987-01-01

The Earth's auroral zone contains dynamic processes occurring on scales from the length of an auroral zone field line which characterizes Alfven wave propagation to the scale of microscopic processes which occur over a few Debye lengths. These processes interact in a time-dependent fashion since the current carried by the Alfven waves can excite microscopic turbulence which can in turn provide dissipation of the Alfven wave energy. This review will first describe the dynamic aspects of auroral current structures with emphasis on consequences for models of microscopic turbulence. A number of models of microscopic turbulence will be introduced into a large-scale model of Alfven wave propagation to determine the effect of various models on the overall structure of auroral currents. In particular, the effects of a double layer electric field which scales with the plasma temperature and Debye length is compared with the effect of anomalous resistivity due to electrostatic ion cyclotron turbulence in which the electric field scales with the magnetic field strength. It is found that the double layer model is less diffusive than in the resistive model leading to the possibility of narrow, intense current structures.

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.

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.

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.

[Remote Slit Lamp Microscope Consultation System Based on Web].

PubMed

Chen, Junfa; Zhuo, Yong; Liu, Zuguo; Chen, Yanping

2015-11-01

To realize the remote operation of the slit lamp microscope for department of ophthalmology consultation, and visual display the real-time status of remote slit lamp microscope, a remote slit lamp microscope consultation system based on B/S structure is designed and implemented. Through framing the slit lamp microscope on the website system, the realtime acquisition and transmission of remote control and image data is realized. The three dimensional model of the slit lamp microscope is established and rendered on the web by using WebGL technology. The practical application results can well show the real-time interactive of the remote consultation system.

The Design and Construction of a Simple Transmission Electron Microscope for Educational Purposes.

ERIC Educational Resources Information Center

Hearsey, Paul K.

This document presents a model for a simple transmission electron microscope for educational purposes. This microscope could demonstrate thermonic emission, particle acceleration, electron deflection, and flourescence. It is designed to be used in high school science courses, particularly physics, taking into account the size, weight, complexity…

A Study of the Nature of Students' Models of Microscopic Processes in the Context of Modern Physics Experiments.

ERIC Educational Resources Information Center

Thacker, Beth Ann

2003-01-01

Interviews university students in modern physics about their understanding of three fundamental experiments. Explores their development of models of microscopic processes. Uses interactive demonstrations to probe student understanding of modern physics experiments in two high school physics classes. Analyzes the nature of students' models and the…

Adaptive optical microscope for brain imaging in vivo

NASA Astrophysics Data System (ADS)

Wang, Kai

2017-04-01

The optical heterogeneity of biological tissue imposes a major limitation to acquire detailed structural and functional information deep in the biological specimens using conventional microscopes. To restore optimal imaging performance, we developed an adaptive optical microscope based on direct wavefront sensing technique. This microscope can reliably measure and correct biological samples induced aberration. We demonstrated its performance and application in structural and functional brain imaging in various animal models, including fruit fly, zebrafish and mouse.

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.

Electronic structure and microscopic model of V(2)GeO(4)F(2)-a quantum spin system with S = 1.

PubMed

Rahaman, Badiur; Saha-Dasgupta, T

2007-07-25

We present first-principles density functional calculations and downfolding studies of the electronic and magnetic properties of the oxide-fluoride quantum spin system V(2)GeO(4)F(2). We discuss explicitly the nature of the exchange paths and provide quantitative estimates of magnetic exchange couplings. A microscopic modelling based on analysis of the electronic structure of this systems puts it in the interesting class of weakly coupled alternating chain S = 1 systems. Based on the microscopic model, we make inferrences about its spin excitation spectra, which needs to be tested by rigorous experimental study.

Enhancing microscopic cascading contributions to higher-order nonlinear-optical responses through forced geometric constraints

NASA Astrophysics Data System (ADS)

Dawson, Nathan J.; Andrews, James H.; Crescimanno, Michael

2012-10-01

We review a model that was developed to take into account all possible microscopic cascading schemes in a single species system out to the fifth order using a self-consistent field approach. This model was designed to study the effects of boundaries in mesoscopic systems with constrained boundaries. These geometric constraints on the macroscopic structure show how the higher-ordered susceptibilities are manipulated by increasing the surface to volume ratio, while the microscopic structure influences the local field from all other molecules in the system. In addition to the review, we discuss methods of modeling real systems of molecules, where efforts are currently underway.

Low-energy nuclear spectroscopy in a microscopic multiphonon approach

NASA Astrophysics Data System (ADS)

Lo Iudice, N.; Ponomarev, V. Yu; Stoyanov, Ch; Sushkov, A. V.; Voronov, V. V.

2012-04-01

The low-lying spectra of heavy nuclei are investigated within the quasiparticle-phonon model. This microscopic approach goes beyond the quasiparticle random-phase approximation by treating a Hamiltonian of separable form in a microscopic multiphonon basis. It is therefore able to describe the anharmonic features of collective modes as well as the multiphonon states, whose experimental evidence is continuously growing. The method can be put in close correspondence with the proton-neutron interacting boson model. By associating the microscopic isoscalar and isovector quadrupole phonons with proton-neutron symmetric and mixed-symmetry quadrupole bosons, respectively, the microscopic states can be classified, just as in the algebraic model, according to their phonon content and their symmetry. In addition, these states disclose the nuclear properties which are to be ascribed to genuine shell effects, not included in the algebraic approach. Due to its flexibility, the method can be implemented numerically for systematic studies of spectroscopic properties throughout entire regions of vibrational nuclei. The spectra and multipole transition strengths so computed are in overall good agreement with the experimental data. By exploiting the correspondence of the method with the interacting boson model, it is possible to embed the microscopic states into this algebraic frame and, therefore, face the study of nuclei far from shell closures, not directly accessible to merely microscopic approaches. Here, it is shown how this task is accomplished through systematic investigations of magnetic dipole and, especially, electric dipole modes along paths moving from the vibrational to the transitional regions. The method is very well suited to the study of well-deformed nuclei. It provides reliable descriptions of low-lying magnetic as well as electric multipole modes of nuclei throughout the rare-earth and actinide regions. Attention is focused here on the low-lying 0+ states produced in large abundance in recent experiments. The analysis shows that the quasiparticle-phonon model accounts for the occurrence of so many 0+ levels and discloses their nature.

Microscopic particle-rotor model for the low-lying spectrum of Λ hypernuclei

NASA Astrophysics Data System (ADS)

Mei, H.; Hagino, K.; Yao, J. M.; Motoba, T.

2014-12-01

We propose a novel method for low-lying states of hypernuclei based on the particle-rotor model, in which hypernuclear states are constructed by coupling the hyperon to low-lying states of the core nucleus. In contrast to the conventional particle-rotor model, we employ a microscopic approach for the core states; that is, the generator coordinate method (GCM) with the particle number and angular momentum projections. We apply this microscopic particle-rotor model to Λ9Be as an example employing a point-coupling version of the relativistic mean-field Lagrangian. A reasonable agreement with the experimental data for the low-spin spectrum is achieved using the Λ N coupling strengths determined to reproduce the binding energy of the Λ particle.

Construction of a microscopic agent-based model for firms' dynamics

NASA Astrophysics Data System (ADS)

Iyetomi, Hiroshi; Aoyama, Hideaki; Fujiwara, Yoshi; Ikeda, Yuichi; Kaizoji, Taisei; Soma, Wataru

2005-07-01

A workable microscopic model for firms' dynamics has been constructed. The model consists of firm agents and a bank agent dynamics of which are described by balance sheets. The size distribution of firms and the temporal evolution of the bank show critical dependence on whether or not firms use perfect information on their financial conditions to draw up next production plans.

CPV hybrid system in ISFOC building, first results

NASA Astrophysics Data System (ADS)

Trujillo, Pablo; Alamillo, César; Gil, Eduardo; de la Rubia, Óscar; Martínez, María; Rubio, Francisca; Cadavid, Andros; Navarro, José; Hillenbrand, Sascha; Ballesteros-Sánchez, Isabel; Castillo-Cagigal, Manuel; Masa-Bote, Daniel; Matallanas, Eduardo; Caamaño-Martín, Estefanía; Gutiérrez, Álvaro

2012-10-01

PV Off-Grid systems have demonstrated to be a good solution for the electrification of remote areas [1]. A hybrid system is one kind of these systems. The principal characteristic is that it uses PV as the main generator and has a backup power supply, like a diesel generator, for instance, that is used when the CPV generation is not enough to meet demand. To study the use of CPV in these systems, ISFOC has installed a demonstration hybrid system at its headquarters. This hybrid system uses CPV technology as main generator and the utility grid as the backup generator. A group of batteries have been mounted as well to store the remaining energy from the CPV generator when nedeed. The energy flows are managed by a SMA system based on Sunny Island inverters and a Multicluster-Box (figure 1). The Load is the air-conditioning system of the building, as it has a consumption profile higher than the CPV generator and can be controlled by software [2]. The first results of this system, as well as the first chances of improvement, as the need of a bigger CPV generator and a better management of the energy stored in the batteries, are presented in this paper.

Basin stability measure of different steady states in coupled oscillators

NASA Astrophysics Data System (ADS)

Rakshit, Sarbendu; Bera, Bidesh K.; Majhi, Soumen; Hens, Chittaranjan; Ghosh, Dibakar

2017-04-01

In this report, we investigate the stabilization of saddle fixed points in coupled oscillators where individual oscillators exhibit the saddle fixed points. The coupled oscillators may have two structurally different types of suppressed states, namely amplitude death and oscillation death. The stabilization of saddle equilibrium point refers to the amplitude death state where oscillations are ceased and all the oscillators converge to the single stable steady state via inverse pitchfork bifurcation. Due to multistability features of oscillation death states, linear stability theory fails to analyze the stability of such states analytically, so we quantify all the states by basin stability measurement which is an universal nonlocal nonlinear concept and it interplays with the volume of basins of attractions. We also observe multi-clustered oscillation death states in a random network and measure them using basin stability framework. To explore such phenomena we choose a network of coupled Duffing-Holmes and Lorenz oscillators which are interacting through mean-field coupling. We investigate how basin stability for different steady states depends on mean-field density and coupling strength. We also analytically derive stability conditions for different steady states and confirm by rigorous bifurcation analysis.

Semi-supervised and unsupervised extreme learning machines.

PubMed

Huang, Gao; Song, Shiji; Gupta, Jatinder N D; Wu, Cheng

2014-12-01

Extreme learning machines (ELMs) have proven to be efficient and effective learning mechanisms for pattern classification and regression. However, ELMs are primarily applied to supervised learning problems. Only a few existing research papers have used ELMs to explore unlabeled data. In this paper, we extend ELMs for both semi-supervised and unsupervised tasks based on the manifold regularization, thus greatly expanding the applicability of ELMs. The key advantages of the proposed algorithms are as follows: 1) both the semi-supervised ELM (SS-ELM) and the unsupervised ELM (US-ELM) exhibit learning capability and computational efficiency of ELMs; 2) both algorithms naturally handle multiclass classification or multicluster clustering; and 3) both algorithms are inductive and can handle unseen data at test time directly. Moreover, it is shown in this paper that all the supervised, semi-supervised, and unsupervised ELMs can actually be put into a unified framework. This provides new perspectives for understanding the mechanism of random feature mapping, which is the key concept in ELM theory. Empirical study on a wide range of data sets demonstrates that the proposed algorithms are competitive with the state-of-the-art semi-supervised or unsupervised learning algorithms in terms of accuracy and efficiency.

The Influence Of Environment On The Star Formation Properties Of Galaxies

NASA Astrophysics Data System (ADS)

Rodriguez Del Pino, Bruno

2015-10-01

This thesis explores the properties of galaxies that reside in regions of high density and the influence of the environment in their evolution. n particular, it aims to shed more light on the understanding of how galaxies stop forming stars, becoming passive objects, and the role played by environment in this process. The work presented here includes the study of the properties of galaxies in clusters at two different stages of their evolution: we first look at cluster galaxies that have recently stopped forming stars, and then we investigate the influence of environment on galaxies while they are still forming stars. The first study is based on Integral Field Spectroscopic (IFS) observations of a sample of disk `k+a' galaxies in a cluster at z 0.3. The `k+a' spectral feature imply a recent suppression of star formation in the galaxies, and therefore the study of their properties is crucial to understanding how the suppression happened. We study the kinematics and spatial distributions of the different stellar populations inhabiting these galaxies. We found that the last stars that were formed (i.e., younger stars) are rotationally-supported and behave similar to the older stars. Moreover, the spatial distribution of the young stars also resembles that of the older stellar populations, although the young stars tend to be more concentrated towards the central regions of the galaxies. These findings indicate that the process responsible for the suppression of the star formation in the cluster disk galaxies had to be gentle, withouth perturbing significantly the old stellar disks. However, a significant number of galaxies with centrally-concentrated young populations were found to have close companions, therefore implying that galaxy-galaxy interactions might also contribute to the cessation of the star formation. These results provide very valuable information on the putative transformation of star-forming galaxies into passive S0s. We then move to the study of the star formation properties and nuclear activity in galaxies in a multi-cluster system at z 0.165. We employ Tuneable Filter observations to map the Halpha and N[II] emission lines. We show the feasibility and advantages of using these type of observations to map emission lines in a large number of objects at a single redshift, and developed a procedure for the reduction and analysis of the data. We find a large number of optical AGN that were not previously detected as X-ray point sources. The probability that a galaxy hosts an AGN is not found to correlate with environment. From the analysis of the integrated star formation properties of the galaxies in the multi-cluster system we observe a significant number of galaxies with suppressed star formation with respect to the field. Although stellar mass is the main driver of the suppression of star formation, once its effect is removed, we find that galaxies in the core regions have reduced specific star formation rates (SSFRs) with respect to the infall regions. Moreover, the environment influences galaxies differently depending on their stellar mass. Galaxies with low masses experience a change in morphology (from irregulars and spirals to early-types) and colour (blue to red) as they fall into regions of higher density. However, many massive spiral galaxies retain their disk morphologies and the visibility of their spiral arms all the way to the core regions. Before becoming passive, these galaxies experience a phase exhibiting red colours and relatively high SSFRs. A significant fraction of the spiral galaxies with relatively high masses go through this phase, which could represent the transition towards becoming S0s. We finish by presenting some interesting results on the spatial distribution of the emission-line regions in the cluster galaxies. We develop a method to create emission-line images, which successfully preserves the flux within the emission lines. Our analysis on the concentrations and sizes of the star-forming regions shows that the star-forming regions of cluster galaxies are generally more concentrated than the underlying stellar populations. However, we find no differences in the spatial distribution of the star formation between galaxies in the infall and in the core regions, but the star formation is more concentrated than in the field galaxies studied in previous works. These results imply that the process responsible for the concentration or truncation of the star formation in the galaxies took place before entering the multi-cluster system of our study.

Effect of microscopic modeling of skin in electrical and thermal analysis of transcranial direct current stimulation

NASA Astrophysics Data System (ADS)

Gomez-Tames, Jose; Sugiyama, Yukiya; Laakso, Ilkka; Tanaka, Satoshi; Koyama, Soichiro; Sadato, Norihiro; Hirata, Akimasa

2016-12-01

Transcranial direct current stimulation (tDCS) is a neuromodulation scheme where a small current is delivered to the brain via two electrodes attached to the scalp. The electrode design is an important topic, not only as regards efficacy, but also from a safety perspective, as tDCS may be related to skin lesions that are sometimes observed after stimulation. Previous computational models of tDCS have omitted the effects of microscopic structures in the skin, and the different soak conditions of the electrodes, and model validation has been limited. In this study, multiphysics and multiscale analysis are proposed to demonstrate the importance of microscopic modeling of the skin, in order to clarify the effects of the internal electric field, and to examine temperature elevation around the electrodes. This novel microscopic model of the skin layer took into consideration the effect of saline/water penetration in hair follicles and sweat ducts on the field distribution around the electrodes. The temperature elevation in the skin was then computed by solving the bioheat equation. Also, a multiscale model was introduced to account for macroscopic and microscopic tissues of the head and skin, which was validated by measurement of the head resistance during tDCS. As a result, the electric field in the microscopic model of the skin was less localized when the follicles/ducts were filled with saline instead of hair or tap water. Temperature elevation was also lessened with saline, in comparison with other substances. Saline, which may penetrate the hair follicles and sweat ducts, suppressed the field concentration around the electrodes. For conventional magnitudes of current injection, and a head resistance of less than 10 kΩ, the temperature elevation in the skin when using saline-soaked electrodes was low, less than 0.1 °C, and unlikely to cause adverse thermal effects.

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.

Nematic elastomers: from a microscopic model to macroscopic elasticity theory.

PubMed

Xing, Xiangjun; Pfahl, Stephan; Mukhopadhyay, Swagatam; Goldbart, Paul M; Zippelius, Annette

2008-05-01

A Landau theory is constructed for the gelation transition in cross-linked polymer systems possessing spontaneous nematic ordering, based on symmetry principles and the concept of an order parameter for the amorphous solid state. This theory is substantiated with help of a simple microscopic model of cross-linked dimers. Minimization of the Landau free energy in the presence of nematic order yields the neoclassical theory of the elasticity of nematic elastomers and, in the isotropic limit, the classical theory of isotropic elasticity. These phenomenological theories of elasticity are thereby derived from a microscopic model, and it is furthermore demonstrated that they are universal mean-field descriptions of the elasticity for all chemical gels and vulcanized media.

Nano Goes to School: A Teaching Model of the Atomic Force Microscope

ERIC Educational Resources Information Center

Planinsic, Gorazd; Kovac, Janez

2008-01-01

The paper describes a teaching model of the atomic force microscope (AFM), which proved to be successful in the role of an introduction to nanoscience in high school. The model can demonstrate the two modes of operation of the AFM (contact mode and oscillating mode) as well as some basic principles that limit the resolution of the method. It can…

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

Naulleau, Patrick; Mochi, Iacopo; Goldberg, Kenneth A.

Defect free masks remain one of the most significant challenges facing the commercialization of extreme ultraviolet (EUV) lithography. Progress on this front requires high-performance wavelength-specific metrology of EUV masks, including high-resolution and aerial-image microscopy performed near the 13.5 nm wavelength. Arguably the most cost-effective and rapid path to proliferating this capability is through the development of Fresnel zoneplate-based microscopes. Given the relative obscurity of such systems, however, modeling tools are not necessarily optimized to deal with them and their imaging properties are poorly understood. Here we present a modeling methodology to analyze zoneplate microscopes based on commercially available optical modelingmore » software and use the technique to investigate the imaging performance of an off-axis EUV microscope design. The modeling predicts that superior performance can be achieved by tilting the zoneplate, making it perpendicular to the chief ray at the center of the field, while designing the zoneplate to explicitly work in that tilted plane. Although the examples presented here are in the realm of EUV mask inspection, the methods described and analysis results are broadly applicable to zoneplate microscopes in general, including full-field soft-x-ray microscopes rou tinely used in the synchrotron community.« less

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

Naulleau, Patrick P.; Mochi, Iacopo; Goldberg, Kenneth A.

Defect free masks remain one of the most significant challenges facing the commercialization of extreme ultraviolet (EUV) lithography. Progress on this front requires high-performance wavelength-specific metrology of EUV masks, including high-resolution and aerial-image microscopy performed near the 13.5 nm wavelength. Arguably the most cost-effective and rapid path to proliferating this capability is through the development of Fresnel zoneplate-based microscopes. Given the relative obscurity of such systems, however, modeling tools are not necessarily optimized to deal with them and their imaging properties are poorly understood. Here we present a modeling methodology to analyze zoneplate microscopes based on commercially available optical modelingmore » software and use the technique to investigate the imaging performance of an off-axis EUV microscope design. The modeling predicts that superior performance can be achieved by tilting the zoneplate, making it perpendicular to the chief ray at the center of the field, while designing the zoneplate to explicitly work in that tilted plane. Although the examples presented here are in the realm of EUV mask inspection, the methods described and analysis results are broadly applicable to zoneplate microscopes in general, including full-field soft-x-ray microscopes routinely used in the synchrotron community.« less

Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets

PubMed Central

Aubry, Marc; Monnier, Annabelle; Chicault, Celine; de Tayrac, Marie; Galibert, Marie-Dominique; Burgun, Anita; Mosser, Jean

2006-01-01

Background Large-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO) implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes. This terminology allows a coherent and consistent description of the knowledge about gene functions. The GO terms related to genes come primarily from semi-automatic annotations made by trained biologists (annotation based on evidence) or text-mining of the published scientific literature (literature profiling). Results We report an original functional annotation method based on a combination of evidence and literature that overcomes the weaknesses and the limitations of each approach. It relies on the Gene Ontology Annotation database (GOA Human) and the PubGene biomedical literature index. We support these annotations with statistically associated GO terms and retrieve associative relations across the three GO hierarchies to emphasise the major pathways involved by a gene cluster. Both annotation methods and associative relations were quantitatively evaluated with a reference set of 7397 genes and a multi-cluster study of 14 clusters. We also validated the biological appropriateness of our hybrid method with the annotation of a single gene (cdc2) and that of a down-regulated cluster of 37 genes identified by a transcriptome study of an in vitro enterocyte differentiation model (CaCo-2 cells). Conclusion The combination of both approaches is more informative than either separate approach: literature mining can enrich an annotation based only on evidence. Text-mining of the literature can also find valuable associated MEDLINE references that confirm the relevance of the annotation. Eventually, GO terms networks can be built with associative relations in order to highlight cooperative and competitive pathways and their connected molecular functions. PMID:16674810

Correction of image drift and distortion in a scanning electron microscopy.

PubMed

Jin, P; Li, X

2015-12-01

Continuous research on small-scale mechanical structures and systems has attracted strong demand for ultrafine deformation and strain measurements. Conventional optical microscope cannot meet such requirements owing to its lower spatial resolution. Therefore, high-resolution scanning electron microscope has become the preferred system for high spatial resolution imaging and measurements. However, scanning electron microscope usually is contaminated by distortion and drift aberrations which cause serious errors to precise imaging and measurements of tiny structures. This paper develops a new method to correct drift and distortion aberrations of scanning electron microscope images, and evaluates the effect of correction by comparing corrected images with scanning electron microscope image of a standard sample. The drift correction is based on the interpolation scheme, where a series of images are captured at one location of the sample and perform image correlation between the first image and the consequent images to interpolate the drift-time relationship of scanning electron microscope images. The distortion correction employs the axial symmetry model of charged particle imaging theory to two images sharing with the same location of one object under different imaging fields of view. The difference apart from rigid displacement between the mentioned two images will give distortion parameters. Three-order precision is considered in the model and experiment shows that one pixel maximum correction is obtained for the employed high-resolution electron microscopic system. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Diffuse-Interface Modelling of Flow in Porous Media

NASA Astrophysics Data System (ADS)

Addy, Doug; Pradas, Marc; Schmuck, Marcus; Kalliadasis, Serafim

2016-11-01

Multiphase flows are ubiquitous in a wide spectrum of scientific and engineering applications, and their computational modelling often poses many challenges associated with the presence of free boundaries and interfaces. Interfacial flows in porous media encounter additional challenges and complexities due to their inherently multiscale behaviour. Here we investigate the dynamics of interfaces in porous media using an effective convective Cahn-Hilliard (CH) equation recently developed in from a Stokes-CH equation for microscopic heterogeneous domains by means of a homogenization methodology, where the microscopic details are taken into account as effective tensor coefficients which are given by a Poisson equation. The equations are decoupled under appropriate assumptions and solved in series using a classic finite-element formulation with the open-source software FEniCS. We investigate the effects of different microscopic geometries, including periodic and non-periodic, at the bulk fluid flow, and find that our model is able to describe the effective macroscopic behaviour without the need to resolve the microscopic details.

Josephson flux-flow oscillator: The microscopic tunneling approach

NASA Astrophysics Data System (ADS)

Gulevich, D. R.; Koshelets, V. P.; Kusmartsev, F. V.

2017-07-01

We elaborate a theoretical description of large Josephson junctions which is based on Werthamer's microscopic tunneling theory. The model naturally incorporates coupling of electromagnetic radiation to the tunnel currents and, therefore, is particularly suitable for description of the self-coupling effect in Josephson junction. In our numerical calculations we treat the arising integro-differential equation, which describes temporal evolution of the superconducting phase difference coupled to the electromagnetic field, by the Odintsov-Semenov-Zorin algorithm. This allows us to avoid evaluation of the time integrals at each time step while taking into account all the memory effects. To validate the obtained microscopic model of large Josephson junction we focus our attention on the Josephson flux-flow oscillator. The proposed microscopic model of flux-flow oscillator does not involve the phenomenological damping parameter, rather the damping is taken into account naturally in the tunnel current amplitudes calculated at a given temperature. The theoretically calculated current-voltage characteristics is compared to our experimental results obtained for a set of fabricated flux-flow oscillators of different lengths.

The Scanning Theremin Microscope: A Model Scanning Probe Instrument for Hands-On Activities

ERIC Educational Resources Information Center

Quardokus, Rebecca C.; Wasio, Natalie A.; Kandel, S. Alex

2014-01-01

A model scanning probe microscope, designed using similar principles of operation to research instruments, is described. Proximity sensing is done using a capacitance probe, and a mechanical linkage is used to scan this probe across surfaces. The signal is transduced as an audio tone using a heterodyne detection circuit analogous to that used in…

Implementing microscopic charcoal in a global climate-aerosol model

NASA Astrophysics Data System (ADS)

Gilgen, Anina; Lohmann, Ulrike; Brügger, Sandra; Adolf, Carole; Ickes, Luisa

2017-04-01

Information about past fire activity is crucial to validate fire models and to better understand their deficiencies. Several paleofire records exist, among them ice cores and sediments, which preserve fire tracers like levoglucosan, vanillic acid, or charcoal particles. In this work, we implement microscopic charcoal particles (maximum dimension 10-100 μm) into the global climate-aerosol model ECHAM6.3HAM2.3. Since we are not aware of any reliable estimates of microscopic charcoal emissions, we scaled black carbon emissions from GFAS to capture the charcoal fluxes from a calibration dataset. After that, model results were compared with a validation dataset. The coarse model resolution (T63L31; 1.9°x1.9°) impedes the model to capture local variability of charcoal fluxes. However, variability on the global scale is pronounced due to highly-variable fire emissions. In future, we plan to model charcoal fluxes in the past 1-2 centuries using fire emissions provided from fire models. Furthermore, we intend to compare modelled charcoal fluxes from prescribed fire emissions with those calculated by an interactive fire model.

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.

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.

On microscopic theory of radiative nuclear reaction characteristics

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

Kamerdzhiev, S. P.; Achakovskiy, O. I., E-mail: oachakovskiy@ippe.ru; Avdeenkov, A. V.

2016-07-15

A survey of some results in the modern microscopic theory of properties of nuclear reactions with gamma rays is given. First of all, we discuss the impact of Phonon Coupling (PC) on the Photon Strength Function (PSF) because it represents the most natural physical source of additional strength found for Sn isotopes in recent experiments that could not be explained within the standard HFB + QRPA approach. The self-consistent version of the Extended Theory of Finite Fermi Systems in the Quasiparticle Time Blocking Approximation is applied. It uses the HFB mean field and includes both the QRPA and PC effectsmore » on the basis of the SLy4 Skyrme force. With our microscopic E1 PSFs, the following properties have been calculated for many stable and unstable even–even semi-magic Sn and Ni isotopes as well as for double-magic {sup 132}Sn and {sup 208}Pb using the reaction codes EMPIRE and TALYS with several Nuclear Level Density (NLD) models: (1) the neutron capture cross sections; (2) the corresponding neutron capture gamma spectra; (3) the average radiative widths of neutron resonances. In all the properties considered, the PC contribution turned out to be significant, as compared with the standard QRPA one, and necessary to explain the available experimental data. The results with the phenomenological so-called generalized superfluid NLD model turned out to be worse, on the whole, than those obtained with the microscopic HFB + combinatorial NLD model. The very topical question about the M1 resonance contribution to PSFs is also discussed.Finally, we also discuss the modern microscopic NLD models based on the self-consistent HFB method and show their relevance to explain the experimental data as compared with the phenomenological models. The use of these self-consistent microscopic approaches is of particular relevance for nuclear astrophysics, but also for the study of double-magic nuclei.« less

Electrolyte solutions at curved electrodes. II. Microscopic approach

NASA Astrophysics Data System (ADS)

Reindl, Andreas; Bier, Markus; Dietrich, S.

2017-04-01

Density functional theory is used to describe electrolyte solutions in contact with electrodes of planar or spherical shape. For the electrolyte solutions, we consider the so-called civilized model, in which all species present are treated on equal footing. This allows us to discuss the features of the electric double layer in terms of the differential capacitance. The model provides insight into the microscopic structure of the electric double layer, which goes beyond the mesoscopic approach studied in Paper I. This enables us to judge the relevance of microscopic details, such as the radii of the particles forming the electrolyte solutions or the dipolar character of the solvent particles, and to compare the predictions of various models. Similar to Paper I, a general behavior is observed for small radii of the electrode in that in this limit the results become independent of the surface charge density and of the particle radii. However, for large electrode radii, non-trivial behaviors are observed. Especially the particle radii and the surface charge density strongly influence the capacitance. From the comparison with the Poisson-Boltzmann approach, it becomes apparent that the shape of the electrode determines whether the microscopic details of the full civilized model have to be taken into account or whether already simpler models yield acceptable predictions.

Electrolyte solutions at curved electrodes. II. Microscopic approach.

PubMed

Reindl, Andreas; Bier, Markus; Dietrich, S

2017-04-21

Density functional theory is used to describe electrolyte solutions in contact with electrodes of planar or spherical shape. For the electrolyte solutions, we consider the so-called civilized model, in which all species present are treated on equal footing. This allows us to discuss the features of the electric double layer in terms of the differential capacitance. The model provides insight into the microscopic structure of the electric double layer, which goes beyond the mesoscopic approach studied in Paper I. This enables us to judge the relevance of microscopic details, such as the radii of the particles forming the electrolyte solutions or the dipolar character of the solvent particles, and to compare the predictions of various models. Similar to Paper I, a general behavior is observed for small radii of the electrode in that in this limit the results become independent of the surface charge density and of the particle radii. However, for large electrode radii, non-trivial behaviors are observed. Especially the particle radii and the surface charge density strongly influence the capacitance. From the comparison with the Poisson-Boltzmann approach, it becomes apparent that the shape of the electrode determines whether the microscopic details of the full civilized model have to be taken into account or whether already simpler models yield acceptable predictions.

Automated adaptive inference of phenomenological dynamical models

NASA Astrophysics Data System (ADS)

Daniels, Bryan

Understanding the dynamics of biochemical systems can seem impossibly complicated at the microscopic level: detailed properties of every molecular species, including those that have not yet been discovered, could be important for producing macroscopic behavior. The profusion of data in this area has raised the hope that microscopic dynamics might be recovered in an automated search over possible models, yet the combinatorial growth of this space has limited these techniques to systems that contain only a few interacting species. We take a different approach inspired by coarse-grained, phenomenological models in physics. Akin to a Taylor series producing Hooke's Law, forgoing microscopic accuracy allows us to constrain the search over dynamical models to a single dimension. This makes it feasible to infer dynamics with very limited data, including cases in which important dynamical variables are unobserved. We name our method Sir Isaac after its ability to infer the dynamical structure of the law of gravitation given simulated planetary motion data. Applying the method to output from a microscopically complicated but macroscopically simple biological signaling model, it is able to adapt the level of detail to the amount of available data. Finally, using nematode behavioral time series data, the method discovers an effective switch between behavioral attractors after the application of a painful stimulus.

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.

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.

Investigating students' mental models and knowledge construction of microscopic friction. II. Implications for curriculum design and development

NASA Astrophysics Data System (ADS)

Corpuz, Edgar D.; Rebello, N. Sanjay

2011-12-01

Our previous research showed that students’ mental models of friction at the atomic level are significantly influenced by their macroscopic ideas. For most students, friction is due to the meshing of bumps and valleys and rubbing of atoms. The aforementioned results motivated us to further investigate how students can be helped to improve their present models of microscopic friction. Teaching interviews were conducted to study the dynamics of their model construction as they interacted with the interviewer, the scaffolding activities, and/or with each other. In this paper, we present the different scaffolding activities and the variation in the ideas that students generated as they did the hands-on and minds-on scaffolding activities. Results imply that through a series of carefully designed scaffolding activities, it is possible to facilitate the refinement of students’ ideas of microscopic friction.

Testing microscopically derived descriptions of nuclear collectivity: Coulomb excitation of 22Mg

NASA Astrophysics Data System (ADS)

Henderson, J.; Hackman, G.; Ruotsalainen, P.; Stroberg, S. R.; Launey, K. D.; Holt, J. D.; Ali, F. A.; Bernier, N.; Bentley, M. A.; Bowry, M.; Caballero-Folch, R.; Evitts, L. J.; Frederick, R.; Garnsworthy, A. B.; Garrett, P. E.; Jigmeddorj, B.; Kilic, A. I.; Lassen, J.; Measures, J.; Muecher, D.; Olaizola, B.; O'Sullivan, E.; Paetkau, O.; Park, J.; Smallcombe, J.; Svensson, C. E.; Wadsworth, R.; Wu, C. Y.

2018-07-01

Many-body nuclear theory utilizing microscopic or chiral potentials has developed to the point that collectivity might be studied within a microscopic or ab initio framework without the use of effective charges; for example with the proper evolution of the E2 operator, or alternatively, through the use of an appropriate and manageable subset of particle-hole excitations. We present a precise determination of E2 strength in 22Mg and its mirror 22Ne by Coulomb excitation, allowing for rigorous comparisons with theory. No-core symplectic shell-model calculations were performed and agree with the new B (E 2) values while in-medium similarity-renormalization-group calculations consistently underpredict the absolute strength, with the missing strength found to have both isoscalar and isovector components. The discrepancy between two microscopic models demonstrates the sensitivity of E2 strength to the choice of many-body approximation employed.

Microscopic Description of Spontaneous Emission in Stark Chirped Rapid Adiabatic Passages

NASA Astrophysics Data System (ADS)

Shi, Xuan; Yuan, Hao; Zhao, Hong-Quan

2018-01-01

A microscopic approach describing the effect of spontaneous emission in the stark-chirped rapid adiabatic passages (SCRAPs) for quantum computation is presented. Apart from the phenomenological model, this microscopic one can investigate the dependence of the population dynamics both on the temperature of the environment and the decay rate γ. With flux-biased Josephson qubits as a specifical example, we study the efficiency of the SCRAP for realizing the basic Pauli-X and iSWAP gates. Our results show clearly that the behavior of the population transfer described by the microscopic model is similar with the phenomenological one at zero temperature. In the limit of very high temperature, the population probabilities of the qubit states exhibit strong stability properties. High efficiency for the quantum gate manipulations in SCRAPs is available against the weak decay rate γ ≪ 1 at low temperature.

An orientation-independent DIC microscope allows high resolution imaging of epithelial cell migration and wound healing in a cnidarian model.

PubMed

Malamy, J E; Shribak, M

2018-06-01

Epithelial cell dynamics can be difficult to study in intact animals or tissues. Here we use the medusa form of the hydrozoan Clytia hemisphaerica, which is covered with a monolayer of epithelial cells, to test the efficacy of an orientation-independent differential interference contrast microscope for in vivo imaging of wound healing. Orientation-independent differential interference contrast provides an unprecedented resolution phase image of epithelial cells closing a wound in a live, nontransgenic animal model. In particular, the orientation-independent differential interference contrast microscope equipped with a 40x/0.75NA objective lens and using the illumination light with wavelength 546 nm demonstrated a resolution of 460 nm. The repair of individual cells, the adhesion of cells to close a gap, and the concomitant contraction of these cells during closure is clearly visualized. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

From fluid dynamics to microscopic transport approach

NASA Astrophysics Data System (ADS)

Saini, Abhilasha; Bhardwaj, Sudhir; Keswani, Bright

2018-05-01

Here we are exploring the widespread features or the characteristics of the microscopic transport modeling and also the speculations made for the approach to fit it to the dynamics of high energy heavy ion collisions, when we see its expansion in space-time dimensions. The explanation of initial stages of the hot and high dense region, the hydrodynamics is instigated and further moderate stages of reaction are complemented to microscopic transport.

Agent-Based Model with Asymmetric Trading and Herding for Complex Financial Systems

PubMed Central

Chen, Jun-Jie; Zheng, Bo; Tan, Lei

2013-01-01

Background For complex financial systems, the negative and positive return-volatility correlations, i.e., the so-called leverage and anti-leverage effects, are particularly important for the understanding of the price dynamics. However, the microscopic origination of the leverage and anti-leverage effects is still not understood, and how to produce these effects in agent-based modeling remains open. On the other hand, in constructing microscopic models, it is a promising conception to determine model parameters from empirical data rather than from statistical fitting of the results. Methods To study the microscopic origination of the return-volatility correlation in financial systems, we take into account the individual and collective behaviors of investors in real markets, and construct an agent-based model. The agents are linked with each other and trade in groups, and particularly, two novel microscopic mechanisms, i.e., investors’ asymmetric trading and herding in bull and bear markets, are introduced. Further, we propose effective methods to determine the key parameters in our model from historical market data. Results With the model parameters determined for six representative stock-market indices in the world, respectively, we obtain the corresponding leverage or anti-leverage effect from the simulation, and the effect is in agreement with the empirical one on amplitude and duration. At the same time, our model produces other features of the real markets, such as the fat-tail distribution of returns and the long-term correlation of volatilities. Conclusions We reveal that for the leverage and anti-leverage effects, both the investors’ asymmetric trading and herding are essential generation mechanisms. Among the six markets, however, the investors’ trading is approximately symmetric for the five markets which exhibit the leverage effect, thus contributing very little. These two microscopic mechanisms and the methods for the determination of the key parameters can be applied to other complex systems with similar asymmetries. PMID:24278146

Agent-based model with asymmetric trading and herding for complex financial systems.

PubMed

Chen, Jun-Jie; Zheng, Bo; Tan, Lei

2013-01-01

For complex financial systems, the negative and positive return-volatility correlations, i.e., the so-called leverage and anti-leverage effects, are particularly important for the understanding of the price dynamics. However, the microscopic origination of the leverage and anti-leverage effects is still not understood, and how to produce these effects in agent-based modeling remains open. On the other hand, in constructing microscopic models, it is a promising conception to determine model parameters from empirical data rather than from statistical fitting of the results. To study the microscopic origination of the return-volatility correlation in financial systems, we take into account the individual and collective behaviors of investors in real markets, and construct an agent-based model. The agents are linked with each other and trade in groups, and particularly, two novel microscopic mechanisms, i.e., investors' asymmetric trading and herding in bull and bear markets, are introduced. Further, we propose effective methods to determine the key parameters in our model from historical market data. With the model parameters determined for six representative stock-market indices in the world, respectively, we obtain the corresponding leverage or anti-leverage effect from the simulation, and the effect is in agreement with the empirical one on amplitude and duration. At the same time, our model produces other features of the real markets, such as the fat-tail distribution of returns and the long-term correlation of volatilities. We reveal that for the leverage and anti-leverage effects, both the investors' asymmetric trading and herding are essential generation mechanisms. Among the six markets, however, the investors' trading is approximately symmetric for the five markets which exhibit the leverage effect, thus contributing very little. These two microscopic mechanisms and the methods for the determination of the key parameters can be applied to other complex systems with similar asymmetries.

Molecular engineering of colloidal liquid crystals using DNA origami

NASA Astrophysics Data System (ADS)

Siavashpouri, Mahsa; Wachauf, Christian; Zakhary, Mark; Praetorius, Florian; Dietz, Hendrik; Dogic, Zvonimir

Understanding the microscopic origin of cholesteric phase remains a foundational, yet unresolved problem in the field of liquid crystals. Lack of experimental model system that allows for the systematic control of the microscopic chiral structure makes it difficult to investigate this problem for several years. Here, using DNA origami technology, we systematically vary the chirality of the colloidal particles with molecular precision and establish a quantitative relationship between the microscopic structure of particles and the macroscopic cholesteric pitch. Our study presents a new methodology for predicting bulk behavior of diverse phases based on the microscopic architectures of the constituent molecules.

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

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.

Multimodal optical workstation for simultaneous linear, nonlinear microscopy and nanomanipulation: upgrading a commercial confocal inverted microscope.

PubMed

Mathew, Manoj; Santos, Susana I C O; Zalvidea, Dobryna; Loza-Alvarez, Pablo

2009-07-01

In this work we propose and build a multimodal optical workstation that extends a commercially available confocal microscope (Nikon Confocal C1-Si) to include nonlinear/multiphoton microscopy and optical manipulation/stimulation tools such as nanosurgery. The setup allows both subsystems (confocal and nonlinear) to work independently and simultaneously. The workstation enables, for instance, nanosurgery along with simultaneous confocal and brightfield imaging. The nonlinear microscopy capabilities are added around the commercial confocal microscope by exploiting all the flexibility offered by this microscope and without need for any mechanical or electronic modification of the confocal microscope systems. As an example, the standard differential interference contrast condenser and diascopic detector in the confocal microscope are readily used as a forward detection mount for second harmonic generation imaging. The various capabilities of this workstation, as applied directly to biology, are demonstrated using the model organism Caenorhabditis elegans.

Evaluation of a completely robotized neurosurgical operating microscope.

PubMed

Kantelhardt, Sven R; Finke, Markus; Schweikard, Achim; Giese, Alf

2013-01-01

Operating microscopes are essential for most neurosurgical procedures. Modern robot-assisted controls offer new possibilities, combining the advantages of conventional and automated systems. We evaluated the prototype of a completely robotized operating microscope with an integrated optical coherence tomography module. A standard operating microscope was fitted with motors and control instruments, with the manual control mode and balance preserved. In the robot mode, the microscope was steered by a remote control that could be fixed to a surgical instrument. External encoders and accelerometers tracked microscope movements. The microscope was additionally fitted with an optical coherence tomography-scanning module. The robotized microscope was tested on model systems. It could be freely positioned, without forcing the surgeon to take the hands from the instruments or avert the eyes from the oculars. Positioning error was about 1 mm, and vibration faded in 1 second. Tracking of microscope movements, combined with an autofocus function, allowed determination of the focus position within the 3-dimensional space. This constituted a second loop of navigation independent from conventional infrared reflector-based techniques. In the robot mode, automated optical coherence tomography scanning of large surface areas was feasible. The prototype of a robotized optical coherence tomography-integrated operating microscope combines the advantages of a conventional manually controlled operating microscope with a remote-controlled positioning aid and a self-navigating microscope system that performs automated positioning tasks such as surface scans. This demonstrates that, in the future, operating microscopes may be used to acquire intraoperative spatial data, volume changes, and structural data of brain or brain tumor tissue.

Electronic structure and microscopic model of CoNb2O6

NASA Astrophysics Data System (ADS)

Molla, Kaimujjaman; Rahaman, Badiur

2018-05-01

We present the first principle density functional calculations to figure out the underlying spin model of CoNb2O6. The first principles calculations define the main paths of superexchange interaction between Co spins in this compound. We discuss the nature of the exchange paths and provide quantitative estimates of magnetic exchange couplings. A microscopic modeling based on analysis of the electronic structure of this system puts it in the interesting class of weakly couple geometrically frustrated isosceles triangular Ising antiferromagnet.

Clogging and depinning of ballistic active matter systems in disordered media

NASA Astrophysics Data System (ADS)

Reichhardt, C.; Reichhardt, C. J. O.

2018-05-01

We numerically examine ballistic active disks driven through a random obstacle array. Formation of a pinned or clogged state occurs at much lower obstacle densities for the active disks than for passive disks. As a function of obstacle density, we identify several distinct phases including a depinned fluctuating cluster state, a pinned single-cluster or jammed state, a pinned multicluster state, a pinned gel state, and a pinned disordered state. At lower active disk densities, a drifting uniform liquid forms in the absence of obstacles, but when even a small number of obstacles are introduced, the disks organize into a pinned phase-separated cluster state in which clusters nucleate around the obstacles, similar to a wetting phenomenon. We examine how the depinning threshold changes as a function of disk or obstacle density and find a crossover from a collectively pinned cluster state to a disordered plastic depinning transition as a function of increasing obstacle density. We compare this to the behavior of nonballistic active particles and show that as we vary the activity from completely passive to completely ballistic, a clogged phase-separated state appears in both the active and passive limits, while for intermediate activity, a readily flowing liquid state appears and there is an optimal activity level that maximizes the flux through the sample.

Mapping Informative Clusters in a Hierarchial Framework of fMRI Multivariate Analysis

PubMed Central

Xu, Rui; Zhen, Zonglei; Liu, Jia

2010-01-01

Pattern recognition methods have become increasingly popular in fMRI data analysis, which are powerful in discriminating between multi-voxel patterns of brain activities associated with different mental states. However, when they are used in functional brain mapping, the location of discriminative voxels varies significantly, raising difficulties in interpreting the locus of the effect. Here we proposed a hierarchical framework of multivariate approach that maps informative clusters rather than voxels to achieve reliable functional brain mapping without compromising the discriminative power. In particular, we first searched for local homogeneous clusters that consisted of voxels with similar response profiles. Then, a multi-voxel classifier was built for each cluster to extract discriminative information from the multi-voxel patterns. Finally, through multivariate ranking, outputs from the classifiers were served as a multi-cluster pattern to identify informative clusters by examining interactions among clusters. Results from both simulated and real fMRI data demonstrated that this hierarchical approach showed better performance in the robustness of functional brain mapping than traditional voxel-based multivariate methods. In addition, the mapped clusters were highly overlapped for two perceptually equivalent object categories, further confirming the validity of our approach. In short, the hierarchical framework of multivariate approach is suitable for both pattern classification and brain mapping in fMRI studies. PMID:21152081

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 ...

Characterization of articular cartilage by combining microscopic analysis with a fibril-reinforced finite-element model.

PubMed

Julkunen, Petro; Kiviranta, Panu; Wilson, Wouter; Jurvelin, Jukka S; Korhonen, Rami K

2007-01-01

Load-bearing characteristics of articular cartilage are impaired during tissue degeneration. Quantitative microscopy enables in vitro investigation of cartilage structure but determination of tissue functional properties necessitates experimental mechanical testing. The fibril-reinforced poroviscoelastic (FRPVE) model has been used successfully for estimation of cartilage mechanical properties. The model includes realistic collagen network architecture, as shown by microscopic imaging techniques. The aim of the present study was to investigate the relationships between the cartilage proteoglycan (PG) and collagen content as assessed by quantitative microscopic findings, and model-based mechanical parameters of the tissue. Site-specific variation of the collagen network moduli, PG matrix modulus and permeability was analyzed. Cylindrical cartilage samples (n=22) were harvested from various sites of the bovine knee and shoulder joints. Collagen orientation, as quantitated by polarized light microscopy, was incorporated into the finite-element model. Stepwise stress-relaxation experiments in unconfined compression were conducted for the samples, and sample-specific models were fitted to the experimental data in order to determine values of the model parameters. For comparison, Fourier transform infrared imaging and digital densitometry were used for the determination of collagen and PG content in the same samples, respectively. The initial and strain-dependent fibril network moduli as well as the initial permeability correlated significantly with the tissue collagen content. The equilibrium Young's modulus of the nonfibrillar matrix and the strain dependency of permeability were significantly associated with the tissue PG content. The present study demonstrates that modern quantitative microscopic methods in combination with the FRPVE model are feasible methods to characterize the structure-function relationships of articular cartilage.

Continuum-kinetic-microscopic model of lung clearance due to core-annular fluid entrainment

PubMed Central

Mitran, Sorin

2013-01-01

The human lung is protected against aspirated infectious and toxic agents by a thin liquid layer lining the interior of the airways. This airway surface liquid is a bilayer composed of a viscoelastic mucus layer supported by a fluid film known as the periciliary liquid. The viscoelastic behavior of the mucus layer is principally due to long-chain polymers known as mucins. The airway surface liquid is cleared from the lung by ciliary transport, surface tension gradients, and airflow shear forces. This work presents a multiscale model of the effect of airflow shear forces, as exerted by tidal breathing and cough, upon clearance. The composition of the mucus layer is complex and variable in time. To avoid the restrictions imposed by adopting a viscoelastic flow model of limited validity, a multiscale computational model is introduced in which the continuum-level properties of the airway surface liquid are determined by microscopic simulation of long-chain polymers. A bridge between microscopic and continuum levels is constructed through a kinetic-level probability density function describing polymer chain configurations. The overall multiscale framework is especially suited to biological problems due to the flexibility afforded in specifying microscopic constituents, and examining the effects of various constituents upon overall mucus transport at the continuum scale. PMID:23729842

Continuum-kinetic-microscopic model of lung clearance due to core-annular fluid entrainment

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

Mitran, Sorin, E-mail: mitran@unc.edu

2013-07-01

The human lung is protected against aspirated infectious and toxic agents by a thin liquid layer lining the interior of the airways. This airway surface liquid is a bilayer composed of a viscoelastic mucus layer supported by a fluid film known as the periciliary liquid. The viscoelastic behavior of the mucus layer is principally due to long-chain polymers known as mucins. The airway surface liquid is cleared from the lung by ciliary transport, surface tension gradients, and airflow shear forces. This work presents a multiscale model of the effect of airflow shear forces, as exerted by tidal breathing and cough,more » upon clearance. The composition of the mucus layer is complex and variable in time. To avoid the restrictions imposed by adopting a viscoelastic flow model of limited validity, a multiscale computational model is introduced in which the continuum-level properties of the airway surface liquid are determined by microscopic simulation of long-chain polymers. A bridge between microscopic and continuum levels is constructed through a kinetic-level probability density function describing polymer chain configurations. The overall multiscale framework is especially suited to biological problems due to the flexibility afforded in specifying microscopic constituents, and examining the effects of various constituents upon overall mucus transport at the continuum scale.« less

Continuum-kinetic-microscopic model of lung clearance due to core-annular fluid entrainment

NASA Astrophysics Data System (ADS)

Mitran, Sorin

2013-07-01

The human lung is protected against aspirated infectious and toxic agents by a thin liquid layer lining the interior of the airways. This airway surface liquid is a bilayer composed of a viscoelastic mucus layer supported by a fluid film known as the periciliary liquid. The viscoelastic behavior of the mucus layer is principally due to long-chain polymers known as mucins. The airway surface liquid is cleared from the lung by ciliary transport, surface tension gradients, and airflow shear forces. This work presents a multiscale model of the effect of airflow shear forces, as exerted by tidal breathing and cough, upon clearance. The composition of the mucus layer is complex and variable in time. To avoid the restrictions imposed by adopting a viscoelastic flow model of limited validity, a multiscale computational model is introduced in which the continuum-level properties of the airway surface liquid are determined by microscopic simulation of long-chain polymers. A bridge between microscopic and continuum levels is constructed through a kinetic-level probability density function describing polymer chain configurations. The overall multiscale framework is especially suited to biological problems due to the flexibility afforded in specifying microscopic constituents, and examining the effects of various constituents upon overall mucus transport at the continuum scale.

A Monte Carlo model of hot electron trapping and detrapping in SiO2

NASA Astrophysics Data System (ADS)

Kamocsai, R. L.; Porod, W.

1991-02-01

High-field stressing and oxide degradation of SiO2 are studied using a microscopic model of electron heating and charge trapping and detrapping. Hot electrons lead to a charge buildup in the oxide according to the dynamic trapping-detrapping model by Nissan-Cohen and co-workers [Y. Nissan-Cohen, J. Shappir, D. Frohman-Bentchkowsky, J. Appl. Phys. 58, 2252 (1985)]. Detrapping events are modeled as trap-to-band impact ionization processes initiated by high energy conduction electrons. The detailed electronic distribution function obtained from Monte Carlo transport simulations is utilized for the determination of the detrapping rates. We apply our microscopic model to the calculation of the flat-band voltage shift in silicon dioxide as a function of the electric field, and we show that our model is able to reproduce the experimental results. We also compare these results to the predictions of the empirical trapping-detrapping model which assumes a heuristic detrapping cross section. Our microscopic theory accounts for the nonlocal nature of impact ionization which leads to a dark space close to the injecting cathode, which is unaccounted for in the empirical model.

Laser-induced surface deformation microscope for the study of the dynamic viscoelasticity of plasma membrane in a living cell.

PubMed

Morisaku, Toshinori; Yui, Hiroharu

2018-05-15

A laser-induced surface deformation (LISD) microscope is developed and applied to measurement of the dynamic relaxation responses of the plasma membrane in a living cell. A laser beam is tightly focused on an optional area of cell surface and the focused light induces microscopic deformation on the surface via radiation pressure. The LISD microscope not only allows non-contact and destruction-free measurement but provides power spectra of the surface responses depending on the frequency of the intensity of the laser beam. An optical system for the LISD is equipped via a microscope, allowing us to measure the relaxation responses in sub-cellular-sized regions of the plasma membrane. In addition, the forced oscillation caused by the radiation pressure for surface deformation extends the upper limit of the frequency range in the obtained power spectra to 106 Hz, which enables us to measure relaxation responses in local regions within the plasma membrane. From differences in power-law exponents at higher frequencies, it is realized that a cancerous cell obeys a weaker single power-law than a normal fibroblast cell. Furthermore, the power spectrum of a keratinocyte cell obeys a power-law with two exponents, indicating that alternative mechanical models to a conventional soft glassy rheology model (where single power-laws explain cells' responses below about 103 Hz) are needed for the understanding over a wider frequency range. The LISD microscope would contribute to investigation of microscopic cell rheology, which is important for clarifying the mechanisms of cell migration and tissue construction.

General multi-group macroscopic modeling for thermo-chemical non-equilibrium gas mixtures.

PubMed

Liu, Yen; Panesi, Marco; Sahai, Amal; Vinokur, Marcel

2015-04-07

This paper opens a new door to macroscopic modeling for thermal and chemical non-equilibrium. In a game-changing approach, we discard conventional theories and practices stemming from the separation of internal energy modes and the Landau-Teller relaxation equation. Instead, we solve the fundamental microscopic equations in their moment forms but seek only optimum representations for the microscopic state distribution function that provides converged and time accurate solutions for certain macroscopic quantities at all times. The modeling makes no ad hoc assumptions or simplifications at the microscopic level and includes all possible collisional and radiative processes; it therefore retains all non-equilibrium fluid physics. We formulate the thermal and chemical non-equilibrium macroscopic equations and rate coefficients in a coupled and unified fashion for gases undergoing completely general transitions. All collisional partners can have internal structures and can change their internal energy states after transitions. The model is based on the reconstruction of the state distribution function. The internal energy space is subdivided into multiple groups in order to better describe non-equilibrium state distributions. The logarithm of the distribution function in each group is expressed as a power series in internal energy based on the maximum entropy principle. The method of weighted residuals is applied to the microscopic equations to obtain macroscopic moment equations and rate coefficients succinctly to any order. The model's accuracy depends only on the assumed expression of the state distribution function and the number of groups used and can be self-checked for accuracy and convergence. We show that the macroscopic internal energy transfer, similar to mass and momentum transfers, occurs through nonlinear collisional processes and is not a simple relaxation process described by, e.g., the Landau-Teller equation. Unlike the classical vibrational energy relaxation model, which can only be applied to molecules, the new model is applicable to atoms, molecules, ions, and their mixtures. Numerical examples and model validations are carried out with two gas mixtures using the maximum entropy linear model: one mixture consists of nitrogen molecules undergoing internal excitation and dissociation and the other consists of nitrogen atoms undergoing internal excitation and ionization. Results show that the original hundreds to thousands of microscopic equations can be reduced to two macroscopic equations with almost perfect agreement for the total number density and total internal energy using only one or two groups. We also obtain good prediction of the microscopic state populations using 5-10 groups in the macroscopic equations.

Heat Source Characterization In A TREAT Fuel Particle Using Coupled Neutronics Binary Collision Monte-Carlo Calculations

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

Schunert, Sebastian; Schwen, Daniel; Ghassemi, Pedram

This work presents a multi-physics, multi-scale approach to modeling the Transient Test Reactor (TREAT) currently prepared for restart at the Idaho National Laboratory. TREAT fuel is made up of microscopic fuel grains (r ˜ 20µm) dispersed in a graphite matrix. The novelty of this work is in coupling a binary collision Monte-Carlo (BCMC) model to the Finite Element based code Moose for solving a microsopic heat-conduction problem whose driving source is provided by the BCMC model tracking fission fragment energy deposition. This microscopic model is driven by a transient, engineering scale neutronics model coupled to an adiabatic heating model. Themore » macroscopic model provides local power densities and neutron energy spectra to the microscpic model. Currently, no feedback from the microscopic to the macroscopic model is considered. TREAT transient 15 is used to exemplify the capabilities of the multi-physics, multi-scale model, and it is found that the average fuel grain temperature differs from the average graphite temperature by 80 K despite the low-power transient. The large temperature difference has strong implications on the Doppler feedback a potential LEU TREAT core would see, and it underpins the need for multi-physics, multi-scale modeling of a TREAT LEU core.« less

Particle-hole symmetry in generalized seniority, microscopic interacting boson (fermion) model, nucleon-pair approximation, and other models

NASA Astrophysics Data System (ADS)

Jia, L. Y.

2016-06-01

The particle-hole symmetry (equivalence) of the full shell-model Hilbert space is straightforward and routinely used in practical calculations. In this work I show that this symmetry is preserved in the subspace truncated up to a certain generalized seniority and give the explicit transformation between the states in the two types (particle and hole) of representations. Based on the results, I study particle-hole symmetry in popular theories that could be regarded as further truncations on top of the generalized seniority, including the microscopic interacting boson (fermion) model, the nucleon-pair approximation, and other models.

Emergent Societal Effects of Crimino-Social Forces in an Animat Agent Model

NASA Astrophysics Data System (ADS)

Scogings, Chris J.; Hawick, Ken A.

Societal behaviour can be studied at a causal level by perturbing a stable multi-agent model with new microscopic behaviours and observing the statistical response over an ensemble of simulated model systems. We report on the effects of introducing criminal and law-enforcing behaviours into a large scale animat agent model and describe the complex spatial agent patterns and population changes that result. Our well-established predator-prey substrate model provides a background framework against which these new microscopic behaviours can be trialled and investigated. We describe some quantitative results and some surprising conclusions concerning the overall societal health when individually anti-social behaviour is introduced.

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.

Hybrid Multiscale Finite Volume Method for Advection-Diffusion Equations Subject to Heterogeneous Reactive Boundary Conditions

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

Barajas-Solano, David A.; Tartakovsky, A. M.

2016-10-13

We present a hybrid scheme for the coupling of macro and microscale continuum models for reactive contaminant transport in fractured and porous media. The transport model considered is the advection-dispersion equation, subject to linear heterogeneous reactive boundary conditions. The Multiscale Finite Volume method (MsFV) is employed to define an approximation to the microscale concentration field defined in terms of macroscopic or \\emph{global} degrees of freedom, together with local interpolator and corrector functions capturing microscopic spatial variability. The macroscopic mass balance relations for the MsFV global degrees of freedom are coupled with the macroscopic model, resulting in a global problem for the simultaneous time-stepping of all macroscopic degrees of freedom throughout the domain. In order to perform the hybrid coupling, the micro and macroscale models are applied over overlapping subdomains of the simulation domain, with the overlap denoted as the handshake subdomainmore » $$\\Omega^{hs}$$, over which continuity of concentration and transport fluxes between models is enforced. Continuity of concentration is enforced by posing a restriction relation between models over $$\\Omega^{hs}$$. Continuity of fluxes is enforced by prolongating the macroscopic model fluxes across the boundary of $$\\Omega^{hs}$$ to microscopic resolution. The microscopic interpolator and corrector functions are solutions to local microscopic advection-diffusion problems decoupled from the global degrees of freedom and from each other by virtue of the MsFV decoupling ansatz. The error introduced by the decoupling ansatz is reduced iteratively by the preconditioned GMRES algorithm, with the hybrid MsFV operator serving as the preconditioner.« less

Teaching Biology to Visually Handicapped Students. Resource Manual.

ERIC Educational Resources Information Center

Ricker, Kenneth S.

This resource manual presents numerous techniques for adapting science activities to the visually handicapped student, applicable to introductory biology courses in which microscopes are used extensively in the laboratory. Chapters include information on the following: alternative microscopic viewing techniques, physical models, tactile diagrams,…

Multiresolution multiscale active mask segmentation of fluorescence microscope images

NASA Astrophysics Data System (ADS)

Srinivasa, Gowri; Fickus, Matthew; Kovačević, Jelena

2009-08-01

We propose an active mask segmentation framework that combines the advantages of statistical modeling, smoothing, speed and flexibility offered by the traditional methods of region-growing, multiscale, multiresolution and active contours respectively. At the crux of this framework is a paradigm shift from evolving contours in the continuous domain to evolving multiple masks in the discrete domain. Thus, the active mask framework is particularly suited to segment digital images. We demonstrate the use of the framework in practice through the segmentation of punctate patterns in fluorescence microscope images. Experiments reveal that statistical modeling helps the multiple masks converge from a random initial configuration to a meaningful one. This obviates the need for an involved initialization procedure germane to most of the traditional methods used to segment fluorescence microscope images. While we provide the mathematical details of the functions used to segment fluorescence microscope images, this is only an instantiation of the active mask framework. We suggest some other instantiations of the framework to segment different types of images.

Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

PubMed

Štys, Dalibor; Urban, Jan; Vaněk, Jan; Císař, Petr

2011-06-01

We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space. This space is reflected as colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them.

Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

PubMed

Stys, Dalibor; Urban, Jan; Vanek, Jan; Císar, Petr

2010-07-01

We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space reflected in space an colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them. Copyright 2010 Elsevier Ltd. All rights reserved.

Surface properties for α-cluster nuclear matter

NASA Astrophysics Data System (ADS)

Castro, J. J.; Soto, J. R.; Yépez, E.

2013-03-01

We introduce a new microscopic model for α-cluster matter, which simulates the properties of ordinary nuclear matter and α-clustering in a curved surface of a large but finite nucleus. The model is based on a nested icosahedral fullerene-like multiple-shell structure, where each vertex is occupied by a microscopic α-particle. The novel aspect of this model is that it allows a consistent description of nuclear surface properties from microscopic parameters to be made without using the leptodermous expansion. In particular, we show that the calculated surface energy is in excellent agreement with the corresponding coefficient of the Bethe-Weizäcker semi-empirical mass formula. We discuss the properties of the surface α-cluster state, which resembles an ultra cold bosonic quantum gas trapped in an optical lattice. By comparing the surface and interior states we are able to estimate the α preformation probability. Possible extensions of this model to study nuclear dynamics through surface vibrations and departures from approximate sphericity are mentioned.

Nonlinear field equations for aligning self-propelled rods.

PubMed

Peshkov, Anton; Aranson, Igor S; Bertin, Eric; Chaté, Hugues; Ginelli, Francesco

2012-12-28

We derive a set of minimal and well-behaved nonlinear field equations describing the collective properties of self-propelled rods from a simple microscopic starting point, the Vicsek model with nematic alignment. Analysis of their linear and nonlinear dynamics shows good agreement with the original microscopic model. In particular, we derive an explicit expression for density-segregated, banded solutions, allowing us to develop a more complete analytic picture of the problem at the nonlinear level.

Unexpected distribution of ν 1 f 7 / 2 strength in Ca 49

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

Crawford, H. L.; Macchiavelli, A. O.; Fallon, P.

Here, the calcium isotopes have emerged as a critical testing ground for new microscopically derived shell-model interactions, and a great deal of experimental and theoretical focus has been directed toward this region. We investigate the relative spectroscopic strengths associated with 1f 7/2 neutron hole states in 47,49Ca following one-neutron knockout reactions from 48,50Ca. The observed reduction of strength populating the 7/2 – 1 state in 49Ca, as compared to 47Ca, is inconsistent with shell-model calculations using both phenomenological interactions such as GXPF1, and interactions derived from microscopically based two- and three-nucleon forces. The result suggests a fragmentation of the lmore » = 3 strength to higher-lying states as suggested by the microscopic calculations, but the observed magnitude of the reduction is not reproduced in any shell-model description.« less

Growth Angle: A Microscopic View

NASA Technical Reports Server (NTRS)

Mazuruk, Konstantin; Croll, Arne; Volz, Martin P.

2017-01-01

A microscopic continuum mechanical model of the growth angle is proposed. It is based on the van der Waals type framework that is used for surface force phenomena. The obtained augmented Laplace type integro-differential equations are, in general, difficult to analyze. Here we focused primarily on the particular case of equal melt and crystal surface energies. We derived an approximate equation for the meniscus shape, and obtained an analytical relationship between the contact and the growth angle. Interestingly, the same result can be obtained using the macroscopic model of Herring. The case of a macroscopically sharp corner is also considered. For this case, the macroscopic angle is not defined and it can be any angle between the contact angles of both flat surfaces. The microscopic model yields the smooth shape for the meniscus that also is not unique, but depends on the initial position of the meniscus.

Unexpected distribution of ν 1 f 7 / 2 strength in Ca 49

DOE PAGES

Crawford, H. L.; Macchiavelli, A. O.; Fallon, P.; ...

2017-06-21

Here, the calcium isotopes have emerged as a critical testing ground for new microscopically derived shell-model interactions, and a great deal of experimental and theoretical focus has been directed toward this region. We investigate the relative spectroscopic strengths associated with 1f 7/2 neutron hole states in 47,49Ca following one-neutron knockout reactions from 48,50Ca. The observed reduction of strength populating the 7/2 – 1 state in 49Ca, as compared to 47Ca, is inconsistent with shell-model calculations using both phenomenological interactions such as GXPF1, and interactions derived from microscopically based two- and three-nucleon forces. The result suggests a fragmentation of the lmore » = 3 strength to higher-lying states as suggested by the microscopic calculations, but the observed magnitude of the reduction is not reproduced in any shell-model description.« less

Optimal indolence: a normative microscopic approach to work and leisure

PubMed Central

Niyogi, Ritwik K.; Breton, Yannick-Andre; Solomon, Rebecca B.; Conover, Kent; Shizgal, Peter; Dayan, Peter

2014-01-01

Dividing limited time between work and leisure when both have their attractions is a common everyday decision. We provide a normative control-theoretic treatment of this decision that bridges economic and psychological accounts. We show how our framework applies to free-operant behavioural experiments in which subjects are required to work (depressing a lever) for sufficient total time (called the price) to receive a reward. When the microscopic benefit-of-leisure increases nonlinearly with duration, the model generates behaviour that qualitatively matches various microfeatures of subjects’ choices, including the distribution of leisure bout durations as a function of the pay-off. We relate our model to traditional accounts by deriving macroscopic, molar, quantities from microscopic choices. PMID:24284898

Analytical model of the optical vortex microscope.

PubMed

Płocinniczak, Łukasz; Popiołek-Masajada, Agnieszka; Masajada, Jan; Szatkowski, Mateusz

2016-04-20

This paper presents an analytical model of the optical vortex scanning microscope. In this microscope the Gaussian beam with an embedded optical vortex is focused into the sample plane. Additionally, the optical vortex can be moved inside the beam, which allows fine scanning of the sample. We provide an analytical solution of the whole path of the beam in the system (within paraxial approximation)-from the vortex lens to the observation plane situated on the CCD camera. The calculations are performed step by step from one optical element to the next. We show that at each step, the expression for light complex amplitude has the same form with only four coefficients modified. We also derive a simple expression for the vortex trajectory of small vortex displacements.

Incorporating interfacial phenomena in solidification models

NASA Technical Reports Server (NTRS)

Beckermann, Christoph; Wang, Chao Yang

1994-01-01

A general methodology is available for the incorporation of microscopic interfacial phenomena in macroscopic solidification models that include diffusion and convection. The method is derived from a formal averaging procedure and a multiphase approach, and relies on the presence of interfacial integrals in the macroscopic transport equations. In a wider engineering context, these techniques are not new, but their application in the analysis and modeling of solidification processes has largely been overlooked. This article describes the techniques and demonstrates their utility in two examples in which microscopic interfacial phenomena are of great importance.

Diamond Quantum Nanoemitters: Cross Discipline Research on Hyperbolic Optical Systems for Control of Quantum Nanoemitters

DTIC Science & Technology

2017-05-05

results of this project there are: (1) the investigation of the effect of phonons on the optical properties of solid state emitters. A microscopic ...In  what  follows  we  list  the  main  results  and  undergoing  research.   2. Results 2.1   Microscopic  modeling...fluorescent  markers   for   biological   measurements.   Here,   we   present   a   first-­‐principles   microscopic   description

Modeling Evolution on Nearly Neutral Network Fitness Landscapes

NASA Astrophysics Data System (ADS)

Yakushkina, Tatiana; Saakian, David B.

2017-08-01

To describe virus evolution, it is necessary to define a fitness landscape. In this article, we consider the microscopic models with the advanced version of neutral network fitness landscapes. In this problem setting, we suppose a fitness difference between one-point mutation neighbors to be small. We construct a modification of the Wright-Fisher model, which is related to ordinary infinite population models with nearly neutral network fitness landscape at the large population limit. From the microscopic models in the realistic sequence space, we derive two versions of nearly neutral network models: with sinks and without sinks. We claim that the suggested model describes the evolutionary dynamics of RNA viruses better than the traditional Wright-Fisher model with few sequences.

SEM-microphotogrammetry, a new take on an old method for generating high-resolution 3D models from SEM images.

PubMed

Ball, A D; Job, P A; Walker, A E L

2017-08-01

The method we present here uses a scanning electron microscope programmed via macros to automatically capture dozens of images at suitable angles to generate accurate, detailed three-dimensional (3D) surface models with micron-scale resolution. We demonstrate that it is possible to use these Scanning Electron Microscope (SEM) images in conjunction with commercially available software originally developed for photogrammetry reconstructions from Digital Single Lens Reflex (DSLR) cameras and to reconstruct 3D models of the specimen. These 3D models can then be exported as polygon meshes and eventually 3D printed. This technique offers the potential to obtain data suitable to reconstruct very tiny features (e.g. diatoms, butterfly scales and mineral fabrics) at nanometre resolution. Ultimately, we foresee this as being a useful tool for better understanding spatial relationships at very high resolution. However, our motivation is also to use it to produce 3D models to be used in public outreach events and exhibitions, especially for the blind or partially sighted. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

A nonlinear dynamical system approach for the yielding behaviour of a viscoplastic material.

PubMed

Burghelea, Teodor; Moyers-Gonzalez, Miguel; Sainudiin, Raazesh

2017-03-08

A nonlinear dynamical system model that approximates a microscopic Gibbs field model for the yielding of a viscoplastic material subjected to varying external stresses recently reported in R. Sainudiin, M. Moyers-Gonzalez and T. Burghelea, Soft Matter, 2015, 11(27), 5531-5545 is presented. The predictions of the model are in fair agreement with microscopic simulations and are in very good agreement with the micro-structural semi-empirical model reported in A. M. V. Putz and T. I. Burghelea, Rheol. Acta, 2009, 48, 673-689. With only two internal parameters, the nonlinear dynamical system model captures several key features of the solid-fluid transition observed in experiments: the effect of the interactions between microscopic constituents on the yield point, the abruptness of solid-fluid transition and the emergence of a hysteresis of the micro-structural states upon increasing/decreasing external forces. The scaling behaviour of the magnitude of the hysteresis with the degree of the steadiness of the flow is consistent with previous experimental observations. Finally, the practical usefulness of the approach is demonstrated by fitting a rheological data set measured with an elasto-viscoplastic material.

Classification and unification of the microscopic deterministic traffic models.

PubMed

Yang, Bo; Monterola, Christopher

2015-10-01

We identify a universal mathematical structure in microscopic deterministic traffic models (with identical drivers), and thus we show that all such existing models in the literature, including both the two-phase and three-phase models, can be understood as special cases of a master model by expansion around a set of well-defined ground states. This allows any two traffic models to be properly compared and identified. The three-phase models are characterized by the vanishing of leading orders of expansion within a certain density range, and as an example the popular intelligent driver model is shown to be equivalent to a generalized optimal velocity (OV) model. We also explore the diverse solutions of the generalized OV model that can be important both for understanding human driving behaviors and algorithms for autonomous driverless vehicles.

Protective effects of Sapindus mukorossi Gaertn against fatty liver disease induced by high fat diet in rats.

PubMed

Peng, Qiuxian; Zhang, Qin; Xiao, Wei; Shao, Meng; Fan, Qin; Zhang, Hongwei; Zou, Yukai; Li, Xin; Xu, Wenxue; Mo, Zhixian; Cai, Hongbing

2014-07-18

Study the effects of alcohol extract of Sapindus mukorossi Gaertn (AESM) on the metabolism of blood fat, morphology of fenestrated liver sinusoidal endothelial cells (LSEC), and the ultrastructure of liver cells of the rats with non-alcoholic fatty liver disease (NAFLD). Divide SD rats into control group, model group, simvastatin (7.2 mg/kg) group, and S.mukorossi Gaertn group with high dosage (0.5 g/kg), moderate dosage (0.1 g/kg), and low dosage (0.05 g/kg). After feeding with fat-rich nutrients for 3 weeks and establishing the model of hepatic adipose, conduct intragastric administration and provide the rats with fat-rich nutrients at the same time. At the 43rd day, take blood sample and measure aminotransferase and different indexes of blood fat; take hepatic tissue for pathological section, and observe the hepatic morphological patterns under light microscope; obtain and fix the hepatic tissue after injecting perfusate into the body, and observe the changes of fenestrated LSEC under scanning electron microscope; observe the ultrastructure of liver cells under transmission electron microscope. High-dosage alcohol extracts of S.mukorossi Gaertn can alleviate the AST, ALT, TC, TG, LDL, γ-GT, and ALP level, as well as raise the HDL and APN level in the serum of NAFLD-rat model. In addition, through the observation from light microscope and electron microscopes, the morphology of the hepatic tissue and liver cells as well as the recovery of the fenestrated LSEC in the treatment group has become normal. Alcohol extracts of S.mukorossi Gaertn can regulate the level of blood fat and improve the pathological changes of the hepatic tissues in NAFLD-rat model, which demonstrates the effects of down-regulating fat level and protecting liver. Copyright © 2014. Published by Elsevier Inc.

The plant virus microscope image registration method based on mismatches removing.

PubMed

Wei, Lifang; Zhou, Shucheng; Dong, Heng; Mao, Qianzhuo; Lin, Jiaxiang; Chen, Riqing

2016-01-01

The electron microscopy is one of the major means to observe the virus. The view of virus microscope images is limited by making specimen and the size of the camera's view field. To solve this problem, the virus sample is produced into multi-slice for information fusion and image registration techniques are applied to obtain large field and whole sections. Image registration techniques have been developed in the past decades for increasing the camera's field of view. Nevertheless, these approaches typically work in batch mode and rely on motorized microscopes. Alternatively, the methods are conceived just to provide visually pleasant registration for high overlap ratio image sequence. This work presents a method for virus microscope image registration acquired with detailed visual information and subpixel accuracy, even when overlap ratio of image sequence is 10% or less. The method proposed focus on the correspondence set and interimage transformation. A mismatch removal strategy is proposed by the spatial consistency and the components of keypoint to enrich the correspondence set. And the translation model parameter as well as tonal inhomogeneities is corrected by the hierarchical estimation and model select. In the experiments performed, we tested different registration approaches and virus images, confirming that the translation model is not always stationary, despite the fact that the images of the sample come from the same sequence. The mismatch removal strategy makes building registration of virus microscope images at subpixel accuracy easier and optional parameters for building registration according to the hierarchical estimation and model select strategies make the proposed method high precision and reliable for low overlap ratio image sequence. Copyright © 2015 Elsevier Ltd. All rights reserved.

Scatter of fatigue data owing to material microscopic effects

NASA Astrophysics Data System (ADS)

Tang, XueSong

2014-01-01

A common phenomenon of fatigue test data reported in the open literature such as S-N curves exhibits the scatter of points for a group of same specimens under the same loading condition. The reason is well known that the microstructure is different from specimen to specimen even in the same group. Specifically, a fatigue failure process is a multi-scale problem so that a fatigue failure model should have the ability to take the microscopic effect into account. A physically-based trans-scale crack model is established and the analytical solution is obtained by coupling the micro- and macro-scale. Obtained is the trans-scale stress intensity factor as well as the trans-scale strain energy density (SED) factor. By taking this trans-scale SEDF as a key controlling parameter for the fatigue crack propagation from micro- to macro-scale, a trans-scale fatigue crack growth model is proposed in this work which can reflect the microscopic effect and scale transition in a fatigue process. The fatigue test data of aluminum alloy LY12 plate specimens is chosen to check the model. Two S-N experimental curves for cyclic stress ratio R=0.02 and R=0.6 are selected. The scattering test data points and two S-N curves for both R=0.02 and R=0.6 are exactly re-produced by application of the proposed model. It is demonstrated that the proposed model is able to reflect the multiscaling effect in a fatigue process. The result also shows that the microscopic effect has a pronounced influence on the fatigue life of specimens.

Surface plasmon resonance microscopy: achieving a quantitative optical response

PubMed Central

Peterson, Alexander W.; Halter, Michael; Plant, Anne L.; Elliott, John T.

2016-01-01

Surface plasmon resonance (SPR) imaging allows real-time label-free imaging based on index of refraction, and changes in index of refraction at an interface. Optical parameter analysis is achieved by application of the Fresnel model to SPR data typically taken by an instrument in a prism based configuration. We carry out SPR imaging on a microscope by launching light into a sample, and collecting reflected light through a high numerical aperture microscope objective. The SPR microscope enables spatial resolution that approaches the diffraction limit, and has a dynamic range that allows detection of subnanometer to submicrometer changes in thickness of biological material at a surface. However, unambiguous quantitative interpretation of SPR changes using the microscope system could not be achieved using the Fresnel model because of polarization dependent attenuation and optical aberration that occurs in the high numerical aperture objective. To overcome this problem, we demonstrate a model to correct for polarization diattenuation and optical aberrations in the SPR data, and develop a procedure to calibrate reflectivity to index of refraction values. The calibration and correction strategy for quantitative analysis was validated by comparing the known indices of refraction of bulk materials with corrected SPR data interpreted with the Fresnel model. Subsequently, we applied our SPR microscopy method to evaluate the index of refraction for a series of polymer microspheres in aqueous media and validated the quality of the measurement with quantitative phase microscopy. PMID:27782542

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

Multi-compartment microscopic diffusion imaging

PubMed Central

Kaden, Enrico; Kelm, Nathaniel D.; Carson, Robert P.; Does, Mark D.; Alexander, Daniel C.

2017-01-01

This paper introduces a multi-compartment model for microscopic diffusion anisotropy imaging. The aim is to estimate microscopic features specific to the intra- and extra-neurite compartments in nervous tissue unconfounded by the effects of fibre crossings and orientation dispersion, which are ubiquitous in the brain. The proposed MRI method is based on the Spherical Mean Technique (SMT), which factors out the neurite orientation distribution and thus provides direct estimates of the microscopic tissue structure. This technique can be immediately used in the clinic for the assessment of various neurological conditions, as it requires only a widely available off-the-shelf sequence with two b-shells and high-angular gradient resolution achievable within clinically feasible scan times. To demonstrate the developed method, we use high-quality diffusion data acquired with a bespoke scanner system from the Human Connectome Project. This study establishes the normative values of the new biomarkers for a large cohort of healthy young adults, which may then support clinical diagnostics in patients. Moreover, we show that the microscopic diffusion indices offer direct sensitivity to pathological tissue alterations, exemplified in a preclinical animal model of Tuberous Sclerosis Complex (TSC), a genetic multi-organ disorder which impacts brain microstructure and hence may lead to neurological manifestations such as autism, epilepsy and developmental delay. PMID:27282476

Scanning SQUID Microscope and its Application in Detecting Weak Currents

NASA Astrophysics Data System (ADS)

Zhong, Chaorong; Li, Fei; Zhang, Fenghui; Ding, Hongsheng; Luo, Sheng; Lin, Dehua; He, Yusheng

A scanning SQUID microscope based on HTS dc SQUID has been developed. One of the applications of this microscope is to detect weak currents inside the sample. Considering that what being detected by the SQUID is the vertical component of the magnetic field on a plan where the SQUID lies, whereas the current which produces the magnetic field is actually located in a plan below the SQUID, a TWO PLAN model has been established. In this model Biot-Savart force laws and Fourier transformation were used to inverse the detected magnetic field into the underneath weak current. It has been shown that the distance between the current and the SQUID and the noise ratio of the experimental data have significant effects on the quality of the inverse process.

Modeling off-resonant nonlinear-optical cascading in mesoscopic thin films and guest-host molecular systems

NASA Astrophysics Data System (ADS)

Dawson, Nathan J.; Andrews, James H.; Crescimanno, Michael

2013-12-01

A model for off-resonant microscopic cascading of (hyper)polarizabilities is developed using a self-consistent field approach to study mesoscopic systems of nonlinear polarizable atoms and molecules. We find enhancements in the higher-order susceptibilities resulting from geometrical and boundary orientation effects. We include an example of the dependence on excitation beam cross sectional structure and a simplified derivation of the microscopic cascading of the nonlinear-optical response in guest-host systems.

Statistical fluctuations in pedestrian evacuation times and the effect of social contagion

NASA Astrophysics Data System (ADS)

Nicolas, Alexandre; Bouzat, Sebastián; Kuperman, Marcelo N.

2016-08-01

Mathematical models of pedestrian evacuation and the associated simulation software have become essential tools for the assessment of the safety of public facilities and buildings. While a variety of models is now available, their calibration and test against empirical data are generally restricted to global averaged quantities; the statistics compiled from the time series of individual escapes ("microscopic" statistics) measured in recent experiments are thus overlooked. In the same spirit, much research has primarily focused on the average global evacuation time, whereas the whole distribution of evacuation times over some set of realizations should matter. In the present paper we propose and discuss the validity of a simple relation between this distribution and the microscopic statistics, which is theoretically valid in the absence of correlations. To this purpose, we develop a minimal cellular automaton, with features that afford a semiquantitative reproduction of the experimental microscopic statistics. We then introduce a process of social contagion of impatient behavior in the model and show that the simple relation under test may dramatically fail at high contagion strengths, the latter being responsible for the emergence of strong correlations in the system. We conclude with comments on the potential practical relevance for safety science of calculations based on microscopic statistics.

The Analog Atomic Force Microscope: Measuring, Modeling, and Graphing for Middle School

ERIC Educational Resources Information Center

Goss, Valerie; Brandt, Sharon; Lieberman, Marya

2013-01-01

using an analog atomic force microscope (A-AFM) made from a cardboard box and mailing tubes. Varying numbers of ping pong balls inside the tubes mimic atoms on a surface. Students use a dowel to make macroscale measurements similar to those of a nanoscale AFM tip as it…

Simple Activities to Improve Students' Understanding of Microscopic Friction

ERIC Educational Resources Information Center

Corpuz, Edgar de Guzman; Rebello, N. Sanjay

2012-01-01

We are currently on the verge of several breakthroughs in nanoscience and technology, and we need to prepare our citizenry to be scientifically literate about the microscopic world. Previous research shows that students' mental models of friction at the atomic level are significantly influenced by their macroscopic ideas. Most students see…

Reasoning about Magnetism at the Microscopic Level

ERIC Educational Resources Information Center

Cheng, Meng-Fei; Cheng, Yufang; Hung, Shuo-Hsien

2014-01-01

Based on our experience of teaching physics in middle and senior secondary school, we have found that students have difficulty in reasoning at the microscopic level. Their reasoning is limited to the observational level so they have problems in developing scientific models of magnetism. Here, we suggest several practical activities and the use of…

Ionic charge accumulation at microscopic interfaces in filled composites

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

Zhu Yutao; Wang Xinheng; Xie Hengkun

1996-12-31

In this paper the charge accumulation process at microscopic interfaces in insulating materials filled with inorganic fillers is analyzed by using a unit model. Dynamic equations of interfacial ionic charge accumulation are proposed by the authors. The charge accumulation and its regulations are proved by TSC test results obtained on silica filled EPDM samples.

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.

Modelling the Active Hearing Process in Mosquitoes

NASA Astrophysics Data System (ADS)

Avitabile, Daniele; Homer, Martin; Jackson, Joe; Robert, Daniel; Champneys, Alan

2011-11-01

A simple microscopic mechanistic model is described of the active amplification within the Johnston's organ of the mosquito species Toxorhynchites brevipalpis. The model is based on the description of the antenna as a forced-damped oscillator coupled to a set of active threads (ensembles of scolopidia) that provide an impulsive force when they twitch. This twitching is in turn controlled by channels that are opened and closed if the antennal oscillation reaches a critical amplitude. The model matches both qualitatively and quantitatively with recent experiments. New results are presented using mathematical homogenization techniques to derive a mesoscopic model as a simple oscillator with nonlinear force and damping characteristics. It is shown how the results from this new model closely resemble those from the microscopic model as the number of threads approach physiologically correct values.

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.

A Mass Diffusion Model for Dry Snow Utilizing a Fabric Tensor to Characterize Anisotropy

NASA Astrophysics Data System (ADS)

Shertzer, Richard H.; Adams, Edward E.

2018-03-01

A homogenization algorithm for randomly distributed microstructures is applied to develop a mass diffusion model for dry snow. Homogenization is a multiscale approach linking constituent behavior at the microscopic level—among ice and air—to the macroscopic material—snow. Principles of continuum mechanics at the microscopic scale describe water vapor diffusion across an ice grain's surface to the air-filled pore space. Volume averaging and a localization assumption scale up and down, respectively, between microscopic and macroscopic scales. The model yields a mass diffusivity expression at the macroscopic scale that is, in general, a second-order tensor parameterized by both bulk and microstructural variables. The model predicts a mass diffusivity of water vapor through snow that is less than that through air. Mass diffusivity is expected to decrease linearly with ice volume fraction. Potential anisotropy in snow's mass diffusivity is captured due to the tensor representation. The tensor is built from directional data assigned to specific, idealized microstructural features. Such anisotropy has been observed in the field and laboratories in snow morphologies of interest such as weak layers of depth hoar and near-surface facets.

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.

Assessing delivery and quantifying efficacy of small interfering ribonucleic acid therapeutics in the skin using a dual-axis confocal microscope

NASA Astrophysics Data System (ADS)

Ra, Hyejun; Gonzalez-Gonzalez, Emilio; Smith, Bryan R.; Gambhir, Sanjiv S.; Kino, Gordon S.; Solgaard, Olav; Kaspar, Roger L.; Contag, Christopher H.

2010-05-01

Transgenic reporter mice and advances in imaging instrumentation are enabling real-time visualization of cellular mechanisms in living subjects and accelerating the development of novel therapies. Innovative confocal microscope designs are improving their utility for microscopic imaging of fluorescent reporters in living animals. We develop dual-axis confocal (DAC) microscopes for such in vivo studies and create mouse models where fluorescent proteins are expressed in the skin for the purpose of advancing skin therapeutics and transdermal delivery tools. Three-dimensional image volumes, through the different skin compartments of the epidermis and dermis, can be acquired in several seconds with the DAC microscope in living mice, and are comparable to histologic analyses of reporter protein expression patterns in skin sections. Intravital imaging with the DAC microscope further enables visualization of green fluorescent protein (GFP) reporter gene expression in the skin over time, and quantification of transdermal delivery of small interfering RNA (siRNA) and therapeutic efficacy. Visualization of transdermal delivery of nucleic acids will play an important role in the development of innovative strategies for treating skin pathologies.

Modelling hot air balloons

NASA Astrophysics Data System (ADS)

Brimicombe, N. W.

1991-07-01

Hot air balloons can be modelled in a number of different ways. The most satisfactory, but least useful model is at a microscopic level. Macroscopic models are easier to use but can be very misleading.

Performance of signal-to-noise ratio estimation for scanning electron microscope using autocorrelation Levinson-Durbin recursion model.

PubMed

Sim, K S; Lim, M S; Yeap, Z X

2016-07-01

A new technique to quantify signal-to-noise ratio (SNR) value of the scanning electron microscope (SEM) images is proposed. This technique is known as autocorrelation Levinson-Durbin recursion (ACLDR) model. To test the performance of this technique, the SEM image is corrupted with noise. The autocorrelation function of the original image and the noisy image are formed. The signal spectrum based on the autocorrelation function of image is formed. ACLDR is then used as an SNR estimator to quantify the signal spectrum of noisy image. The SNR values of the original image and the quantified image are calculated. The ACLDR is then compared with the three existing techniques, which are nearest neighbourhood, first-order linear interpolation and nearest neighbourhood combined with first-order linear interpolation. It is shown that ACLDR model is able to achieve higher accuracy in SNR estimation. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Identification of four Aconitum species used as "Caowu" in herbal markets by 3D reconstruction and microstructural comparison.

PubMed

Liu, Chan-Chan; Cheng, Ming-En; Peng, Huasheng; Duan, Hai-Yan; Huang, Luqi

2015-05-01

Authentication is the first priority when evaluating the quality of Chinese herbal medicines, particularly highly toxic medicines. The most commonly used authentication methods are morphological identification and microscopic identification. Unfortunately, these methods could not effectively evaluate some herbs with complex interior structures, such as root of Aconitum species with a circular conical shape and an interior structure with successive changes. Defining the part that should be selected as the standard plays an essential role in accurate microscopic identification. In this study, we first present a visual 3D model of Aconitum carmichaeli Debx. constructed obtained from microscopic analysis of serial sections. Based on this model, we concluded that the point of largest root diameter should be used as the standard for comparison and identification. The interior structure at this point is reproducible and its shape and appearance can easily be used to distinguish among species. We also report details of the interior structures of parts not shown in the 3D model, such as stone cells and cortical thickness. To demonstrate the usefulness of the results from the 3D model, we have distinguished the microscopic structures, at their largest segments, of the other three Aconitum species used for local habitat species of Caowu. This work provides the basis for resolution of some debate regarding the microstructural differences among these species. Thus, we conclude that the 3D model composed of serial sections has enabled the selection of a standard cross-section that will enable the accurate identification of Aconitum species in Chinese medicine. © 2015 Wiley Periodicals, Inc.

Breaking the polar-nonpolar division in solvation free energy prediction.

PubMed

Wang, Bao; Wang, Chengzhang; Wu, Kedi; Wei, Guo-Wei

2018-02-05

Implicit solvent models divide solvation free energies into polar and nonpolar additive contributions, whereas polar and nonpolar interactions are inseparable and nonadditive. We present a feature functional theory (FFT) framework to break this ad hoc division. The essential ideas of FFT are as follows: (i) representability assumption: there exists a microscopic feature vector that can uniquely characterize and distinguish one molecule from another; (ii) feature-function relationship assumption: the macroscopic features, including solvation free energy, of a molecule is a functional of microscopic feature vectors; and (iii) similarity assumption: molecules with similar microscopic features have similar macroscopic properties, such as solvation free energies. Based on these assumptions, solvation free energy prediction is carried out in the following protocol. First, we construct a molecular microscopic feature vector that is efficient in characterizing the solvation process using quantum mechanics and Poisson-Boltzmann theory. Microscopic feature vectors are combined with macroscopic features, that is, physical observable, to form extended feature vectors. Additionally, we partition a solvation dataset into queries according to molecular compositions. Moreover, for each target molecule, we adopt a machine learning algorithm for its nearest neighbor search, based on the selected microscopic feature vectors. Finally, from the extended feature vectors of obtained nearest neighbors, we construct a functional of solvation free energy, which is employed to predict the solvation free energy of the target molecule. The proposed FFT model has been extensively validated via a large dataset of 668 molecules. The leave-one-out test gives an optimal root-mean-square error (RMSE) of 1.05 kcal/mol. FFT predictions of SAMPL0, SAMPL1, SAMPL2, SAMPL3, and SAMPL4 challenge sets deliver the RMSEs of 0.61, 1.86, 1.64, 0.86, and 1.14 kcal/mol, respectively. Using a test set of 94 molecules and its associated training set, the present approach was carefully compared with a classic solvation model based on weighted solvent accessible surface area. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Mesoscopic model of actin-based propulsion.

PubMed

Zhu, Jie; Mogilner, Alex

2012-01-01

Two theoretical models dominate current understanding of actin-based propulsion: microscopic polymerization ratchet model predicts that growing and writhing actin filaments generate forces and movements, while macroscopic elastic propulsion model suggests that deformation and stress of growing actin gel are responsible for the propulsion. We examine both experimentally and computationally the 2D movement of ellipsoidal beads propelled by actin tails and show that neither of the two models can explain the observed bistability of the orientation of the beads. To explain the data, we develop a 2D hybrid mesoscopic model by reconciling these two models such that individual actin filaments undergoing nucleation, elongation, attachment, detachment and capping are embedded into the boundary of a node-spring viscoelastic network representing the macroscopic actin gel. Stochastic simulations of this 'in silico' actin network show that the combined effects of the macroscopic elastic deformation and microscopic ratchets can explain the observed bistable orientation of the actin-propelled ellipsoidal beads. To test the theory further, we analyze observed distribution of the curvatures of the trajectories and show that the hybrid model's predictions fit the data. Finally, we demonstrate that the model can explain both concave-up and concave-down force-velocity relations for growing actin networks depending on the characteristic time scale and network recoil. To summarize, we propose that both microscopic polymerization ratchets and macroscopic stresses of the deformable actin network are responsible for the force and movement generation.

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.

Microscopic models for bridging electrostatics and currents

NASA Astrophysics Data System (ADS)

Borghi, L.; DeAmbrosis, A.; Mascheretti, P.

2007-03-01

A teaching sequence based on the use of microscopic models to link electrostatic phenomena with direct currents is presented. The sequence, devised for high school students, was designed after initial work carried out with student teachers attending a school of specialization for teaching physics at high school, at the University of Pavia. The results obtained with them are briefly presented, because they directed our steps for the development of the teaching sequence. For both the design of the experiments and their interpretation, we drew inspiration from the original works of Alessandro Volta; in addition, a structural model based on the particular role of electrons as elementary charges both in electrostatic phenomena and in currents was proposed. The teaching sequence starts from experiments on charging objects by rubbing and by induction, and engages students in constructing microscopic models to interpret their observations. By using these models and by closely examining the ideas of tension and capacitance, the students acknowledge that a charging (or discharging) process is due to the motion of electrons that, albeit for short time intervals, represent a current. Finally, they are made to see that the same happens in transients of direct current circuits.

The fatigue life study of polyphenylene sulfide composites filled with continuous glass fibers

NASA Astrophysics Data System (ADS)

Ye, Junjie; Hong, Yun; Wang, Yongkun; Zhai, Zhi; Shi, Baoquan; Chen, Xuefeng

2018-04-01

In this study, an effective microscopic model is proposed to investigate the fatigue life of composites containing continuous glass fibers, which is surrounded by polyphenylene sulfide (PPS) matrix materials. The representative volume element is discretized by parametric elements. Moreover, the microscopic model is established by employing the relation between average surface displacements and average surface tractions. Based on the experimental data, the required fatigue failure parameters of the PPS are determined. Two different fiber arrangements are considered for comparisons. Numerical analyses indicated that the square edge packing provides a more accuracy. In addition, microscopic structural parameters (fiber volume fraction, fiber off-axis angle) effect on the fatigue life of Glass/PPS composites is further discussed. It is revealed that fiber strength degradation effects on the fatigue life of continuous fiber-reinforced composites can be ignored.

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.

Developing a novel international undergraduate surgical masterclass during a financial crisis: our 4-year experience.

PubMed

Sideris, Michail; Hanrahan, John; Tsoulfas, Georgios; Theodoulou, Iakovos; Dhaif, Fatema; Papalois, Vassilios; Papagrigoriadis, Savvas; Velmahos, George; Turner, Patricia; Papalois, Apostolos

2018-05-01

Essential Skills in the Management of Surgical Cases (ESMSC) is a novel 3-day international undergraduate surgical masterclass. Its current curriculum (Cores integrated for Research-Ci4R) is built on a tetracore, multiclustered architecture combining high-fidelity and low-fidelity simulation-based learning (SBL), with applied and basic science case-based workshops, and non-technical skills modules. We aimed to report our experience in setting up ESMSC during the global financial crisis. We report the evolution of our curriculum's methodology and summarised the research outcomes related to the objective performance improvement of delegates, the educational environment of the course and the use of mixed-fidelity SBL. Feedback from the last three series of the course was prospectively collected and analysed using univariate statistics on IBM SPSS V.23. 311 medical students across the European Union (EU) were selected from a competitive pool of 1280 applicants during seven series of the course between 2014 and 2017. During this period, curriculum 14 s evolved to the final Ci4R version, which integrates a tetracore structure combining 32 stations of in vivo, ex vivo and dry lab SBL with small group teaching workshops. Ci4R was positively perceived across different educational background students (p>0.05 for any comparison). ESMSC is considered an innovative and effective multidisciplinary teaching model by delegates, where it improves delegates objective performance in basic surgical skills. Our experience demonstrates provision of high-quality and free surgical education during a financial crisis, which evolved through a dynamic feedback mechanism. The prospective recording and subsequent analysis of curriculum evolution provides a blueprint to direct development of effective surgical education courses that can be adapted to local needs. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Auricular burns associated with operating microscope use during otologic surgery.

PubMed

Latuska, Richard F; Carlson, Matthew L; Neff, Brian A; Driscoll, Colin L; Wanna, George B; Haynes, David S

2014-02-01

To raise awareness of the potential hazard of auricular burns associated with operating microscope use during otologic surgery. Retrospective case series and summary of the Food and Drug Administration's (FDA) Manufacturer and User Facility Device Experience (MAUDE) database of voluntary adverse event reports pertaining to microscope related auricular thermal injuries. All patients who sustained auricular burns while using the operating microscope during otologic surgery at 2 tertiary academic referral centers. Surgical procedure, microscope model, intensity of illumination, length of procedure, focal length, location and severity of burn, and patient outcome. A total of 4 microscope-related auricular thermal injuries were identified from the authors' institutions. Additionally, 82 unique cases of soft tissue burns associated with the use of an operative microscope have been voluntarily reported to the FDA since 2004. A disproportionately large percent (∼ 30%) of these occurred within the field of otology, the majority of which were during tympanoplasty or tympanomastoidectomy procedures at focal length distances of 300 mm or less with xenon light source microscopes. Simultaneous advancements in light delivery technologies and lens optics have continued to improve the efficiency of the operating microscope; however, these improvements also increase the potential for thermal injuries. Although rare, a review of the FDA MAUDE database suggests that microscope-related soft tissue burns occur more frequently in otology than any other surgical specialty. A variety of factors may help explain this finding, including the unique anatomy of the external ear with thin skin and limited underlying adipose tissue. Preventative measures should be taken to decrease the risk of thermal injuries including use of the lowest comfortable light intensity, adjusting the aperture width to match the operative field, frequent wound irrigation, and covering exposed portions of the pinna with a moist surgical sponge.

IMIS: An intelligence microscope imaging system

NASA Technical Reports Server (NTRS)

Caputo, Michael; Hunter, Norwood; Taylor, Gerald

1994-01-01

Until recently microscope users in space relied on traditional microscopy techniques that required manual operation of the microscope and recording of observations in the form of written notes, drawings, or photographs. This method was time consuming and required the return of film and drawings from space for analysis. No real-time data analysis was possible. Advances in digital and video technologies along with recent developments in article intelligence will allow future space microscopists to have a choice of three additional modes of microscopy: remote coaching, remote control, and automation. Remote coaching requires manual operations of the microscope with instructions given by two-way audio/video transmission during critical phases of the experiment. When using the remote mode of microscopy, the Principal Investigator controls the microscope from the ground. The automated mode employs artificial intelligence to control microscope functions and is the only mode that can be operated in the other three modes as well. The purpose of this presentation is to discuss the advantages and disadvantages of the four modes of of microscopy and how the IMIS, a proposed intelligent microscope imaging system, can be used as a model for developing and testing concepts, operating procedures, and equipment design of specifications required to provide a comprehensive microscopy/imaging capability onboard Space Station Freedom.

A Computer-Controlled Classroom Model of an Atomic Force Microscope

ERIC Educational Resources Information Center

Engstrom, Tyler A.; Johnson, Matthew M.; Eklund, Peter C.; Russin, Timothy J.

2015-01-01

The concept of "seeing by feeling" as a way to circumvent limitations on sight is universal on the macroscopic scale--reading Braille, feeling one's way around a dark room, etc. The development of the atomic force microscope (AFM) in 1986 extended this concept to imaging in the nanoscale. While there are classroom demonstrations that use…

Microscopic saw mark analysis: an empirical approach.

PubMed

Love, Jennifer C; Derrick, Sharon M; Wiersema, Jason M; Peters, Charles

2015-01-01

Microscopic saw mark analysis is a well published and generally accepted qualitative analytical method. However, little research has focused on identifying and mitigating potential sources of error associated with the method. The presented study proposes the use of classification trees and random forest classifiers as an optimal, statistically sound approach to mitigate the potential for error of variability and outcome error in microscopic saw mark analysis. The statistical model was applied to 58 experimental saw marks created with four types of saws. The saw marks were made in fresh human femurs obtained through anatomical gift and were analyzed using a Keyence digital microscope. The statistical approach weighed the variables based on discriminatory value and produced decision trees with an associated outcome error rate of 8.62-17.82%. © 2014 American Academy of Forensic Sciences.

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.

The microscopic structure of an exactly solvable model binary solution that exhibits two closed loops in the phase diagram.

PubMed

Lungu, Radu P; Huckaby, Dale A

2008-07-21

An exactly solvable lattice model describing a binary solution is considered where rodlike molecules of types AA and BB cover the links of a honeycomb lattice, the neighboring molecular ends having three-body and orientation-dependent bonding interactions. At phase coexistence of AA-rich and BB-rich phases, the average fraction of each type of triangle of neighboring molecular ends is calculated exactly. The fractions of the different types of triangles are then used to deduce the local microscopic structure of the coexisting phases for a case of the model that contains two closed loops in the phase diagram.

3D real-time visualization of blood flow in cerebral aneurysms by light field particle image velocimetry

NASA Astrophysics Data System (ADS)

Carlsohn, Matthias F.; Kemmling, André; Petersen, Arne; Wietzke, Lennart

2016-04-01

Cerebral aneurysms require endovascular treatment to eliminate potentially lethal hemorrhagic rupture by hemostasis of blood flow within the aneurysm. Devices (e.g. coils and flow diverters) promote homeostasis, however, measurement of blood flow within an aneurysm or cerebral vessel before and after device placement on a microscopic level has not been possible so far. This would allow better individualized treatment planning and improve manufacture design of devices. For experimental analysis, direct measurement of real-time microscopic cerebrovascular flow in micro-structures may be an alternative to computed flow simulations. An application of microscopic aneurysm flow measurement on a regular basis to empirically assess a high number of different anatomic shapes and the corresponding effect of different devices would require a fast and reliable method at low cost with high throughout assessment. Transparent three dimensional 3D models of brain vessels and aneurysms may be used for microscopic flow measurements by particle image velocimetry (PIV), however, up to now the size of structures has set the limits for conventional 3D-imaging camera set-ups. On line flow assessment requires additional computational power to cope with the processing large amounts of data generated by sequences of multi-view stereo images, e.g. generated by a light field camera capturing the 3D information by plenoptic imaging of complex flow processes. Recently, a fast and low cost workflow for producing patient specific three dimensional models of cerebral arteries has been established by stereo-lithographic (SLA) 3D printing. These 3D arterial models are transparent an exhibit a replication precision within a submillimeter range required for accurate flow measurements under physiological conditions. We therefore test the feasibility of microscopic flow measurements by PIV analysis using a plenoptic camera system capturing light field image sequences. Averaging across a sequence of single double or triple shots of flashed images enables reconstruction of the real-time corpuscular flow through the vessel system before and after device placement. This approach could enable 3D-insight of microscopic flow within blood vessels and aneurysms at submillimeter resolution. We present an approach that allows real-time assessment of 3D particle flow by high-speed light field image analysis including a solution that addresses high computational load by image processing. The imaging set-up accomplishes fast and reliable PIV analysis in transparent 3D models of brain aneurysms at low cost. High throughput microscopic flow assessment of different shapes of brain aneurysms may therefore be possibly required for patient specific device designs.

Direct microscopic image and measurement of the atomization process of a port fuel injector

NASA Astrophysics Data System (ADS)

Esmail, Mohamed; Kawahara, Nobuyuki; Tomita, Eiji; Sumida, Mamoru

2010-07-01

The main objective of this study is to observe and investigate the phenomena of atomization, i.e. the fuel break-up process very close to the nozzle exit of a practical port fuel injector (PFI). In order to achieve this objective, direct microscopic images of the atomization process were obtained using an ultra-high-speed video camera that could record 102 frames at rates of up to 1 Mfps, coupled with a long-distance microscope and Barlow lens. The experiments were carried out using a PFI in a closed chamber at atmospheric pressure. Time-series images of the spray behaviour were obtained with a high temporal resolution using backlighting. The direct microscopic images of a liquid column break-up were compared with experimental results from laser-induced exciplex fluorescence (LIEF), and the wavelength obtained from the experimental results compared with that predicated from the Kelvin-Helmholtz break-up model. The droplet size diameters from a ligament break-up were compared with results predicated from Weber's analysis. Furthermore, experimental results of the mean droplet diameter from a direct microscopic image were compared with the results obtained from phase Doppler anemometry (PDA) experimental results. Three conclusions were obtained from this study. The atomization processes and detailed characterizations of the break-up of a liquid column were identified; the direct microscopic image results were in good agreement with the results obtained from LIEF, experimental results of the wavelength were in good agreement with those from the Kelvin-Helmholtz break-up model. The break-up process of liquid ligaments into droplets was investigated, and Weber's analysis of the predicated droplet diameter from ligament break-up was found to be applicable only at larger wavelengths. Finally, the direct microscopic image method and PDA method give qualitatively similar trends for droplet size distribution and quantitatively similar values of Sauter mean diameter.

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 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.

Study of Fission Barrier Heights of Uranium Isotopes by the Macroscopic-Microscopic Method

NASA Astrophysics Data System (ADS)

Zhong, Chun-Lai; Fan, Tie-Shuan

2014-09-01

Potential energy surfaces of uranium nuclei in the range of mass numbers 229 through 244 are investigated in the framework of the macroscopic-microscopic model and the heights of static fission barriers are obtained in terms of a double-humped structure. The macroscopic part of the nuclear energy is calculated according to Lublin—Strasbourg-drop (LSD) model. Shell and pairing corrections as the microscopic part are calculated with a folded-Yukawa single-particle potential. The calculation is carried out in a five-dimensional parameter space of the generalized Lawrence shapes. In order to extract saddle points on the potential energy surface, a new algorithm which can effectively find an optimal fission path leading from the ground state to the scission point is developed. The comparison of our results with available experimental data and others' theoretical results confirms the reliability of our calculations.

Automatic segmentation of Leishmania parasite in microscopic images using a modified CV level set method

NASA Astrophysics Data System (ADS)

Farahi, Maria; Rabbani, Hossein; Talebi, Ardeshir; Sarrafzadeh, Omid; Ensafi, Shahab

2015-12-01

Visceral Leishmaniasis is a parasitic disease that affects liver, spleen and bone marrow. According to World Health Organization report, definitive diagnosis is possible just by direct observation of the Leishman body in the microscopic image taken from bone marrow samples. We utilize morphological and CV level set method to segment Leishman bodies in digital color microscopic images captured from bone marrow samples. Linear contrast stretching method is used for image enhancement and morphological method is applied to determine the parasite regions and wipe up unwanted objects. Modified global and local CV level set methods are proposed for segmentation and a shape based stopping factor is used to hasten the algorithm. Manual segmentation is considered as ground truth to evaluate the proposed method. This method is tested on 28 samples and achieved 10.90% mean of segmentation error for global model and 9.76% for local model.

Microscopic cascading of second-order molecular nonlinearity: New design principles for enhancing third-order nonlinearity.

PubMed

Baev, Alexander; Autschbach, Jochen; Boyd, Robert W; Prasad, Paras N

2010-04-12

Herein, we develop a phenomenological model for microscopic cascading and substantiate it with ab initio calculations. It is shown that the concept of local microscopic cascading of a second-order nonlinearity can lead to a third-order nonlinearity, without introducing any new loss mechanisms that could limit the usefulness of our approach. This approach provides a new molecular design protocol, in which the current great successes achieved in producing molecules with extremely large second-order nonlinearity can be used in a supra molecular organization in a preferred orientation to generate very large third-order response magnitudes. The results of density functional calculations for a well-known second-order molecule, (para)nitroaniline, show that a head-to-tail dimer configuration exhibits enhanced third-order nonlinearity, in agreement with the phenomenological model which suggests that such an arrangement will produce cascading due to local field effects.

An orientation-independent DIC microscope allows high resolution imaging of epithelial cell migration and wound healing in a Cnidarian model

PubMed Central

Malamy, Jocelyn; Shribak, Michael

2017-01-01

Epithelial cell dynamics can be difficult to study in intact animals or tissues. Here we use the medusa form of the hydrozoan Clytia hemisphaerica, which is covered with a monolayer of epithelial cells, to test the efficacy of an orientation-independent differential interference contrast (OI-DIC) microscope for in vivo imaging of wound healing. OI-DIC provides an unprecedented resolution phase image of epithelial cells closing a wound in a live, non-transgenic animal model. In particular, the OI-DIC microscope equipped with a 40×/0.75NA objective lens and using the illumination light with wavelength 546 nm demonstrated a resolution of 460 nm. The repair of individual cells, the adhesion of cells to close a gap, and the concomitant contraction of these cells during closure is clearly visualized. PMID:29345317

Microscopic observation of magnetic bacteria in the magnetic field of a rotating permanent magnet.

PubMed

Smid, Pieter; Shcherbakov, Valeriy; Petersen, Nikolai

2015-09-01

Magnetotactic bacteria are ubiquitous and can be found in both freshwater and marine environments. Due to intracellular chains of magnetic single domain particles, they behave like swimming compass needles. In external magnetic fields like the Earth's magnetic field, a torque is acting on the chain. This will cause the bacterium to be rotated and aligned with the external field. The swimming direction of magnetotactic bacteria can be controlled with external magnetic fields, which makes it convenient to study them under a light microscope. Usually, a special set of coils arranged around a light microscope is used to control the swimming magnetotactic bacteria. Here, we present a simple mechanical system with a permanent magnet, which produces a rotating magnetic field of nearly constant amplitude in the focal plane of a light microscope. The device is placed beside the light microscope and easily adaptable to almost any microscope and thus convenient for field experiments. To describe the trajectories qualitatively, a theoretical model of the trajectories is presented. This device can be used to control the swimming direction of magnetotactic bacteria and also for studying their magnetic and hydrodynamic properties.

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.

Quantitative characterization of semiconductor structures with a scanning microwave microscope.

PubMed

Korolyov, S A; Reznik, A N

2018-02-01

In this work, our earlier method for measuring resistance R sh of semiconductor films with a near-field scanning microwave microscope [A. N. Reznik and S. A. Korolyov, J. Appl. Phys. 119, 094504 (2016)] is studied in a 0.1 kΩ/sq < R sh < 15 kΩ/sq range. The method is based on a microscope model in the form of a monopole or dipole antenna interacting with an arbitrary layered structure. The model fitting parameters are determined from the data yielded by calibration measurements on a system of etalon samples. The performance of the method was analyzed experimentally, using strip-probe and coaxial-probe microscopes in the frequency range of 1-3 GHz. For test structures, we used doped GaN films on the Al 2 O 3 substrate and also transistor structures based on the AlGaN/GaN heterojunction and AlGaAs/GaAs/InGaAs/GaAs/AlGaAs quantum well with a conducting channel. The obtained microwave microscope data were compared with the results of measurements by the van der Pauw method. At the first stage of the experiment, the calibration etalons were bulk homogeneous samples with different permittivity/conductivity values. In this case, satisfactory agreement between the microscope and the van der Pauw data was obtained with a strip probe on all tested samples in the entire range of R sh . With a coaxial probe, such accordance was observed only in high-ohmic samples with R sh > 1 kΩ/sq. The use of GaN film structures as a calibration system helped to increase the accuracy of the coaxial-probe-aided measurement of R sh to a level of ∼10%.

Quantitative characterization of semiconductor structures with a scanning microwave microscope

NASA Astrophysics Data System (ADS)

Korolyov, S. A.; Reznik, A. N.

2018-02-01

In this work, our earlier method for measuring resistance Rsh of semiconductor films with a near-field scanning microwave microscope [A. N. Reznik and S. A. Korolyov, J. Appl. Phys. 119, 094504 (2016)] is studied in a 0.1 kΩ/sq < Rsh < 15 kΩ/sq range. The method is based on a microscope model in the form of a monopole or dipole antenna interacting with an arbitrary layered structure. The model fitting parameters are determined from the data yielded by calibration measurements on a system of etalon samples. The performance of the method was analyzed experimentally, using strip-probe and coaxial-probe microscopes in the frequency range of 1-3 GHz. For test structures, we used doped GaN films on the Al2O3 substrate and also transistor structures based on the AlGaN/GaN heterojunction and AlGaAs/GaAs/InGaAs/GaAs/AlGaAs quantum well with a conducting channel. The obtained microwave microscope data were compared with the results of measurements by the van der Pauw method. At the first stage of the experiment, the calibration etalons were bulk homogeneous samples with different permittivity/conductivity values. In this case, satisfactory agreement between the microscope and the van der Pauw data was obtained with a strip probe on all tested samples in the entire range of Rsh. With a coaxial probe, such accordance was observed only in high-ohmic samples with Rsh > 1 kΩ/sq. The use of GaN film structures as a calibration system helped to increase the accuracy of the coaxial-probe-aided measurement of Rsh to a level of ˜10%.

Microscopic Study of the 6Li(p, α)3He Reaction at Low Energies

NASA Astrophysics Data System (ADS)

Solovyev, Alexander; Igashov, Sergey

2018-01-01

The 6Li(p, α)3He reaction important for nuclear astrophysics is studied in the framework of a microscopic approach based on a multichannel algebraic version of the resonating group model. Astrophysical S-factor for the reaction is calculated at low energies. The obtained result is compared with experimental data and other theoretical calculations.

Ferromagnetic interaction model of activity level in workplace communication

NASA Astrophysics Data System (ADS)

Akitomi, Tomoaki; Ara, Koji; Watanabe, Jun-ichiro; Yano, Kazuo

2013-03-01

The nature of human-human interaction, specifically, how people synchronize with each other in multiple-participant conversations, is described by a ferromagnetic interaction model of people’s activity levels. We found two microscopic human interaction characteristics from a real-environment face-to-face conversation. The first characteristic is that people quite regularly synchronize their activity level with that of the other participants in a conversation. The second characteristic is that the degree of synchronization increases as the number of participants increases. Based on these microscopic ferromagnetic characteristics, a “conversation activity level” was modeled according to the Ising model. The results of a simulation of activity level based on this model well reproduce macroscopic experimental measurements of activity level. This model will give a new insight into how people interact with each other in a conversation.

Inferring phenomenological models of Markov processes from data

NASA Astrophysics Data System (ADS)

Rivera, Catalina; Nemenman, Ilya

Microscopically accurate modeling of stochastic dynamics of biochemical networks is hard due to the extremely high dimensionality of the state space of such networks. Here we propose an algorithm for inference of phenomenological, coarse-grained models of Markov processes describing the network dynamics directly from data, without the intermediate step of microscopically accurate modeling. The approach relies on the linear nature of the Chemical Master Equation and uses Bayesian Model Selection for identification of parsimonious models that fit the data. When applied to synthetic data from the Kinetic Proofreading process (KPR), a common mechanism used by cells for increasing specificity of molecular assembly, the algorithm successfully uncovers the known coarse-grained description of the process. This phenomenological description has been notice previously, but this time it is derived in an automated manner by the algorithm. James S. McDonnell Foundation Grant No. 220020321.

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.

Strong Inference in Mathematical Modeling: A Method for Robust Science in the Twenty-First Century.

PubMed

Ganusov, Vitaly V

2016-01-01

While there are many opinions on what mathematical modeling in biology is, in essence, modeling is a mathematical tool, like a microscope, which allows consequences to logically follow from a set of assumptions. Only when this tool is applied appropriately, as microscope is used to look at small items, it may allow to understand importance of specific mechanisms/assumptions in biological processes. Mathematical modeling can be less useful or even misleading if used inappropriately, for example, when a microscope is used to study stars. According to some philosophers (Oreskes et al., 1994), the best use of mathematical models is not when a model is used to confirm a hypothesis but rather when a model shows inconsistency of the model (defined by a specific set of assumptions) and data. Following the principle of strong inference for experimental sciences proposed by Platt (1964), I suggest "strong inference in mathematical modeling" as an effective and robust way of using mathematical modeling to understand mechanisms driving dynamics of biological systems. The major steps of strong inference in mathematical modeling are (1) to develop multiple alternative models for the phenomenon in question; (2) to compare the models with available experimental data and to determine which of the models are not consistent with the data; (3) to determine reasons why rejected models failed to explain the data, and (4) to suggest experiments which would allow to discriminate between remaining alternative models. The use of strong inference is likely to provide better robustness of predictions of mathematical models and it should be strongly encouraged in mathematical modeling-based publications in the Twenty-First century.

Agent-based model with multi-level herding for complex financial systems

NASA Astrophysics Data System (ADS)

Chen, Jun-Jie; Tan, Lei; Zheng, Bo

2015-02-01

In complex financial systems, the sector structure and volatility clustering are respectively important features of the spatial and temporal correlations. However, the microscopic generation mechanism of the sector structure is not yet understood. Especially, how to produce these two features in one model remains challenging. We introduce a novel interaction mechanism, i.e., the multi-level herding, in constructing an agent-based model to investigate the sector structure combined with volatility clustering. According to the previous market performance, agents trade in groups, and their herding behavior comprises the herding at stock, sector and market levels. Further, we propose methods to determine the key model parameters from historical market data, rather than from statistical fitting of the results. From the simulation, we obtain the sector structure and volatility clustering, as well as the eigenvalue distribution of the cross-correlation matrix, for the New York and Hong Kong stock exchanges. These properties are in agreement with the empirical ones. Our results quantitatively reveal that the multi-level herding is the microscopic generation mechanism of the sector structure, and provide new insight into the spatio-temporal interactions in financial systems at the microscopic level.

Agent-based model with multi-level herding for complex financial systems

PubMed Central

Chen, Jun-Jie; Tan, Lei; Zheng, Bo

2015-01-01

In complex financial systems, the sector structure and volatility clustering are respectively important features of the spatial and temporal correlations. However, the microscopic generation mechanism of the sector structure is not yet understood. Especially, how to produce these two features in one model remains challenging. We introduce a novel interaction mechanism, i.e., the multi-level herding, in constructing an agent-based model to investigate the sector structure combined with volatility clustering. According to the previous market performance, agents trade in groups, and their herding behavior comprises the herding at stock, sector and market levels. Further, we propose methods to determine the key model parameters from historical market data, rather than from statistical fitting of the results. From the simulation, we obtain the sector structure and volatility clustering, as well as the eigenvalue distribution of the cross-correlation matrix, for the New York and Hong Kong stock exchanges. These properties are in agreement with the empirical ones. Our results quantitatively reveal that the multi-level herding is the microscopic generation mechanism of the sector structure, and provide new insight into the spatio-temporal interactions in financial systems at the microscopic level. PMID:25669427

Spatial-spectral blood cell classification with microscopic hyperspectral imagery

NASA Astrophysics Data System (ADS)

Ran, Qiong; Chang, Lan; Li, Wei; Xu, Xiaofeng

2017-10-01

Microscopic hyperspectral images provide a new way for blood cell examination. The hyperspectral imagery can greatly facilitate the classification of different blood cells. In this paper, the microscopic hyperspectral images are acquired by connecting the microscope and the hyperspectral imager, and then tested for blood cell classification. For combined use of the spectral and spatial information provided by hyperspectral images, a spatial-spectral classification method is improved from the classical extreme learning machine (ELM) by integrating spatial context into the image classification task with Markov random field (MRF) model. Comparisons are done among ELM, ELM-MRF, support vector machines(SVM) and SVMMRF methods. Results show the spatial-spectral classification methods(ELM-MRF, SVM-MRF) perform better than pixel-based methods(ELM, SVM), and the proposed ELM-MRF has higher precision and show more accurate location of cells.

Macroscopic model of scanning force microscope

DOEpatents

Guerra-Vela, Claudio; Zypman, Fredy R.

2004-10-05

A macroscopic version of the Scanning Force Microscope is described. It consists of a cantilever under the influence of external forces, which mimic the tip-sample interactions. The use of this piece of equipment is threefold. First, it serves as direct way to understand the parts and functions of the Scanning Force Microscope, and thus it is effectively used as an instructional tool. Second, due to its large size, it allows for simple measurements of applied forces and parameters that define the state of motion of the system. This information, in turn, serves to compare the interaction forces with the reconstructed ones, which cannot be done directly with the standard microscopic set up. Third, it provides a kinematics method to non-destructively measure elastic constants of materials, such as Young's and shear modules, with special application for brittle materials.

Analysis and comparison of safety models using average daily, average hourly, and microscopic traffic.

PubMed

Wang, Ling; Abdel-Aty, Mohamed; Wang, Xuesong; Yu, Rongjie

2018-02-01

There have been plenty of traffic safety studies based on average daily traffic (ADT), average hourly traffic (AHT), or microscopic traffic at 5 min intervals. Nevertheless, not enough research has compared the performance of these three types of safety studies, and seldom of previous studies have intended to find whether the results of one type of study is transferable to the other two studies. First, this study built three models: a Bayesian Poisson-lognormal model to estimate the daily crash frequency using ADT, a Bayesian Poisson-lognormal model to estimate the hourly crash frequency using AHT, and a Bayesian logistic regression model for the real-time safety analysis using microscopic traffic. The model results showed that the crash contributing factors found by different models were comparable but not the same. Four variables, i.e., the logarithm of volume, the standard deviation of speed, the logarithm of segment length, and the existence of diverge segment, were positively significant in the three models. Additionally, weaving segments experienced higher daily and hourly crash frequencies than merge and basic segments. Then, each of the ADT-based, AHT-based, and real-time models was used to estimate safety conditions at different levels: daily and hourly, meanwhile, the real-time model was also used in 5 min intervals. The results uncovered that the ADT- and AHT-based safety models performed similar in predicting daily and hourly crash frequencies, and the real-time safety model was able to provide hourly crash frequency. Copyright © 2017 Elsevier Ltd. All rights reserved.

Strong Inference in Mathematical Modeling: A Method for Robust Science in the Twenty-First Century

PubMed Central

Ganusov, Vitaly V.

2016-01-01

While there are many opinions on what mathematical modeling in biology is, in essence, modeling is a mathematical tool, like a microscope, which allows consequences to logically follow from a set of assumptions. Only when this tool is applied appropriately, as microscope is used to look at small items, it may allow to understand importance of specific mechanisms/assumptions in biological processes. Mathematical modeling can be less useful or even misleading if used inappropriately, for example, when a microscope is used to study stars. According to some philosophers (Oreskes et al., 1994), the best use of mathematical models is not when a model is used to confirm a hypothesis but rather when a model shows inconsistency of the model (defined by a specific set of assumptions) and data. Following the principle of strong inference for experimental sciences proposed by Platt (1964), I suggest “strong inference in mathematical modeling” as an effective and robust way of using mathematical modeling to understand mechanisms driving dynamics of biological systems. The major steps of strong inference in mathematical modeling are (1) to develop multiple alternative models for the phenomenon in question; (2) to compare the models with available experimental data and to determine which of the models are not consistent with the data; (3) to determine reasons why rejected models failed to explain the data, and (4) to suggest experiments which would allow to discriminate between remaining alternative models. The use of strong inference is likely to provide better robustness of predictions of mathematical models and it should be strongly encouraged in mathematical modeling-based publications in the Twenty-First century. PMID:27499750

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.

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.

Unsteady Crystal Growth Due to Step-Bunch Cascading

NASA Technical Reports Server (NTRS)

Vekilov, Peter G.; Lin, Hong; Rosenberger, Franz

1997-01-01

Based on our experimental findings of growth rate fluctuations during the crystallization of the protein lysozym, we have developed a numerical model that combines diffusion in the bulk of a solution with diffusive transport to microscopic growth steps that propagate on a finite crystal facet. Nonlinearities in layer growth kinetics arising from step interaction by bulk and surface diffusion, and from step generation by surface nucleation, are taken into account. On evaluation of the model with properties characteristic for the solute transport, and the generation and propagation of steps in the lysozyme system, growth rate fluctuations of the same magnitude and characteristic time, as in the experiments, are obtained. The fluctuation time scale is large compared to that of step generation. Variations of the governing parameters of the model reveal that both the nonlinearity in step kinetics and mixed transport-kinetics control of the crystallization process are necessary conditions for the fluctuations. On a microscopic scale, the fluctuations are associated with a morphological instability of the vicinal face, in which a step bunch triggers a cascade of new step bunches through the microscopic interfacial supersaturation distribution.

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.

Kinetic modeling of microscopic processes during electron cyclotron resonance microwave plasma-assisted molecular beam epitaxial growth of GaN/GaAs-based heterostructures

NASA Astrophysics Data System (ADS)

Bandić, Z. Z.; Hauenstein, R. J.; O'Steen, M. L.; McGill, T. C.

1996-03-01

Microscopic growth processes associated with GaN/GaAs molecular beam epitaxy (MBE) are examined through the introduction of a first-order kinetic model. The model is applied to the electron cyclotron resonance microwave plasma-assisted MBE (ECR-MBE) growth of a set of δ-GaNyAs1-y/GaAs strained-layer superlattices that consist of nitrided GaAs monolayers separated by GaAs spacers, and that exhibit a strong decrease of y with increasing T over the range 540-580 °C. This y(T) dependence is quantitatively explained in terms of microscopic anion exchange, and thermally activated N surface-desorption and surface-segregation processes. N surface segregation is found to be significant during GaAs overgrowth of GaNyAs1-y layers at typical GaN ECR-MBE growth temperatures, with an estimated activation energy Es˜0.9 eV. The observed y(T) dependence is shown to result from a combination of N surface segregation/desorption processes.

Thrombus segmentation by texture dynamics from microscopic image sequences

NASA Astrophysics Data System (ADS)

Brieu, Nicolas; Serbanovic-Canic, Jovana; Cvejic, Ana; Stemple, Derek; Ouwehand, Willem; Navab, Nassir; Groher, Martin

2010-03-01

The genetic factors of thrombosis are commonly explored by microscopically imaging the coagulation of blood cells induced by injuring a vessel of mice or of zebrafish mutants. The latter species is particularly interesting since skin transparency permits to non-invasively acquire microscopic images of the scene with a CCD camera and to estimate the parameters characterizing the thrombus development. These parameters are currently determined by manual outlining, which is both error prone and extremely time consuming. Even though a technique for automatic thrombus extraction would be highly valuable for gene analysts, little work can be found, which is mainly due to very low image contrast and spurious structures. In this work, we propose to semi-automatically segment the thrombus over time from microscopic image sequences of wild-type zebrafish larvae. To compensate the lack of valuable spatial information, our main idea consists of exploiting the temporal information by modeling the variations of the pixel intensities over successive temporal windows with a linear Markov-based dynamic texture formalization. We then derive an image from the estimated model parameters, which represents the probability of a pixel to belong to the thrombus. We employ this probability image to accurately estimate the thrombus position via an active contour segmentation incorporating also prior and spatial information of the underlying intensity images. The performance of our approach is tested on three microscopic image sequences. We show that the thrombus is accurately tracked over time in each sequence if the respective parameters controlling prior influence and contour stiffness are correctly chosen.

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.

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...

The microscopic model of BiFeO3

NASA Astrophysics Data System (ADS)

Fishman, R. S.

2018-05-01

Many years and great effort have been spent constructing the microscopic model for the room temperature multiferroic BiFeO3. However, earlier models implicitly assumed that the cycloidal wavevector q was confined to one of the three-fold symmetric axes in the hexagonal plane normal to the electric polarization. Because recent measurements indicate that q can be rotated by a magnetic field, it is essential to properly treat the anisotropy that confines q at low fields. We propose that the anisotropy energy -K3S6sin6 θ cos 6 ϕ confines the wavevectors q to the three-fold axis ϕ = 0 and ± 2 π / 3 within the hexagonal plane with θ = π / 2 .

A combined confocal and magnetic resonance microscope for biological studies

NASA Astrophysics Data System (ADS)

Majors, Paul D.; Minard, Kevin R.; Ackerman, Eric J.; Holtom, Gary R.; Hopkins, Derek F.; Parkinson, Christopher I.; Weber, Thomas J.; Wind, Robert A.

2002-12-01

Complementary data acquired with different microscopy techniques provide a basis for establishing a more comprehensive understanding of cell function in health and disease, particularly when results acquired with different methodologies can be correlated in time and space. In this article, a novel microscope is described for studying live cells simultaneously with both confocal scanning laser fluorescence optical microscopy and magnetic resonance microscopy. The various design considerations necessary for integrating these two complementary techniques are discussed, the layout and specifications of the instrument are given, and examples of confocal and magnetic resonance images of large frog cells and model tumor spheroids obtained with the compound microscope are presented.

Generic Features of Tertiary Chromatin Structure as Detected in Natural Chromosomes

PubMed Central

Müller, Waltraud G.; Rieder, Dietmar; Kreth, Gregor; Cremer, Christoph; Trajanoski, Zlatko; McNally, James G.

2004-01-01

Knowledge of tertiary chromatin structure in mammalian interphase chromosomes is largely derived from artificial tandem arrays. In these model systems, light microscope images reveal fibers or beaded fibers after high-density targeting of transactivators to insertional domains spanning several megabases. These images of fibers have lent support to chromonema fiber models of tertiary structure. To assess the relevance of these studies to natural mammalian chromatin, we identified two different ∼400-kb regions on human chromosomes 6 and 22 and then examined light microscope images of interphase tertiary chromatin structure when the regions were transcriptionally active and inactive. When transcriptionally active, these natural chromosomal regions elongated, yielding images characterized by a series of adjacent puncta or “beads”, referred to hereafter as beaded images. These elongated structures required transcription for their maintenance. Thus, despite marked differences in the density and the mode of transactivation, the natural and artificial systems showed similarities, suggesting that beaded images are generic features of transcriptionally active tertiary chromatin. We show here, however, that these images do not necessarily favor chromonema fiber models but can also be explained by a radial-loop model or even a simple nucleosome affinity, random-chain model. Thus, light microscope images of tertiary structure cannot distinguish among competing models, although they do impose key constraints: chromatin must be clustered to yield beaded images and then packaged within each cluster to enable decondensation into adjacent clusters. PMID:15485905

Nucleon Isovector Pairing in Nuclei: Microscopic Approach, Boson Representation, and Collective Model

NASA Astrophysics Data System (ADS)

Jolos, R. V.; Kartavenko, V. G.; Kolganova, E. A.

2018-03-01

Nucleon pair correlations in atomic nuclei are analyzed within a nuclear microscopic model with residual isovector pairing forces. These are formulated in the boson representation of fermion operators whereby the collective mode of pair excitations can be isolated without restricting the size of the one-particle basis. This method allows one to analyze the fluctuations in the nonsuperfluid phase of nuclear matter, its phase transition to the superfluid phase, and strong pair correlations. The performance of the method is exemplified by numerical results for the nuclei in the vicinity of the doubly magic 56Ni nucleus.

Development of Nomarski microscopy for quantitative determination of surface topography

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

Hartman, J. S.; Gordon, R. L.; Lessor, D. L.

1979-01-01

The use of Nomarski differential interference contrast (DIC) microscopy has been extended to provide nondestructive, quantitative analysis of a sample's surface topography. Theoretical modeling has determined the dependence of the image intensity on the microscope's optical components, the sample's optical properties, and the sample's surface orientation relative to the microscope. Results include expressions to allow the inversion of image intensity data to determine sample surface slopes. A commercial Nomarski system has been modified and characterized to allow the evaluation of the optical model. Data have been recorded with smooth, planar samples that verify the theoretical predictions.

Compact divided-pupil line-scanning confocal microscope for investigation of human tissues

NASA Astrophysics Data System (ADS)

Glazowski, Christopher; Peterson, Gary; Rajadhyaksha, Milind

2013-03-01

Divided-pupil line-scanning confocal microscopy (DPLSCM) can provide a simple and low-cost approach for imaging of human tissues with pathology-like nuclear and cellular detail. Using results from a multidimensional numerical model of DPLSCM, we found optimal pupil configurations for improved axial sectioning, as well as control of speckle noise in the case of reflectance imaging. The modeling results guided the design and construction of a simple (10 component) microscope, packaged within the footprint of an iPhone, and capable of cellular resolution. We present the optical design with experimental video-images of in-vivo human tissues.

A Micro-Mechanism-Based Continuum Corrosion Fatigue Damage Model for Steels

NASA Astrophysics Data System (ADS)

Sun, Bin; Li, Zhaoxia

2018-05-01

A micro-mechanism-based corrosion fatigue damage model is developed for studying the high-cycle corrosion fatigue of steel from multi-scale viewpoint. The developed physical corrosion fatigue damage model establishes micro-macro relationships between macroscopic continuum damage evolution and collective evolution behavior of microscopic pits and cracks, which can be used to describe the multi-scale corrosion fatigue process of steel. As a case study, the model is used to predict continuum damage evolution and number density of the corrosion pit and short crack of steel component in 5% NaCl water under constant stress amplitude at 20 kHz, and the numerical results are compared with experimental results. It shows that the model is effective and can be used to evaluate the continuum macroscopic corrosion fatigue damage and study microscopic corrosion fatigue mechanisms of steel.

A Micro-Mechanism-Based Continuum Corrosion Fatigue Damage Model for Steels

NASA Astrophysics Data System (ADS)

Sun, Bin; Li, Zhaoxia

2018-04-01

A micro-mechanism-based corrosion fatigue damage model is developed for studying the high-cycle corrosion fatigue of steel from multi-scale viewpoint. The developed physical corrosion fatigue damage model establishes micro-macro relationships between macroscopic continuum damage evolution and collective evolution behavior of microscopic pits and cracks, which can be used to describe the multi-scale corrosion fatigue process of steel. As a case study, the model is used to predict continuum damage evolution and number density of the corrosion pit and short crack of steel component in 5% NaCl water under constant stress amplitude at 20 kHz, and the numerical results are compared with experimental results. It shows that the model is effective and can be used to evaluate the continuum macroscopic corrosion fatigue damage and study microscopic corrosion fatigue mechanisms of steel.

Microscopic and macroscopic models for the onset and progression of Alzheimer's disease

NASA Astrophysics Data System (ADS)

Bertsch, Michiel; Franchi, Bruno; Carla Tesi, Maria; Tosin, Andrea

2017-10-01

In the first part of this paper we review a mathematical model for the onset and progression of Alzheimer’s disease (AD) that was developed in subsequent steps over several years. The model is meant to describe the evolution of AD in vivo. In Achdou et al (2013 J. Math. Biol. 67 1369-92) we treated the problem at a microscopic scale, where the typical length scale is a multiple of the size of the soma of a single neuron. Subsequently, in Bertsch et al (2017 Math. Med. Biol. 34 193-214) we concentrated on the macroscopic scale, where brain neurons are regarded as a continuous medium, structured by their degree of malfunctioning. In the second part of the paper we consider the relation between the microscopic and the macroscopic models. In particular we show under which assumptions the kinetic transport equation, which in the macroscopic model governs the evolution of the probability measure for the degree of malfunctioning of neurons, can be derived from a particle-based setting. The models are based on aggregation and diffusion equations for β-Amyloid (Aβ from now on), a protein fragment that healthy brains regularly produce and eliminate. In case of dementia Aβ monomers are no longer properly washed out and begin to coalesce forming eventually plaques. Two different mechanisms are assumed to be relevant for the temporal evolution of the disease: (i) diffusion and agglomeration of soluble polymers of amyloid, produced by damaged neurons; (ii) neuron-to-neuron prion-like transmission. In the microscopic model we consider mechanism (i), modelling it by a system of Smoluchowski equations for the amyloid concentration (describing the agglomeration phenomenon), with the addition of a diffusion term as well as of a source term on the neuronal membrane. At the macroscopic level instead we model processes (i) and (ii) by a system of Smoluchowski equations for the amyloid concentration, coupled to a kinetic-type transport equation for the distribution function of the degree of malfunctioning of the neurons. The transport equation contains an integral term describing the random onset of the disease as a jump process localized in particularly sensitive areas of the brain.

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.

Microscopic modeling of direct pre-equilibrium emission from neutron induced reactions on even and odd actinides

NASA Astrophysics Data System (ADS)

Dupuis, M.; Hilaire, S.; Péru, S.; Bauge, E.; Kerveno, M.; Dessagne, P.; Henning, G.

2017-09-01

Direct inelastic scattering to discrete excitations and pre-equilibrium emission are described within a microscopic model. Nuclear structure information are obtained in the (Quasi) Random Phase Approximation ((Q)RPA) framework implemented with the Gogny force. The relevant optical and transition potentials are build considering the JLM folding model. Various successful applications are shown for (n,n), (n,n'), (n,xn) and (n,xnγ) reactions for spherical and axially deformed even-even or odd targets. The rearrangement corrections to transition potentials and the contribution of unnatural parity excitations to pre-equilibrium emission are discussed. Our model predictions for (n,n'γ) reactions, for intra- and inter-band transitions in 238U, and for the 239Pu(n,2n) cross section are analyzed.

Stripe order in the underdoped region of the two-dimensional Hubbard model

NASA Astrophysics Data System (ADS)

Zheng, Bo-Xiao; Chung, Chia-Min; Corboz, Philippe; Ehlers, Georg; Qin, Ming-Pu; Noack, Reinhard M.; Shi, Hao; White, Steven R.; Zhang, Shiwei; Chan, Garnet Kin-Lic

2017-12-01

Competing inhomogeneous orders are a central feature of correlated electron materials, including the high-temperature superconductors. The two-dimensional Hubbard model serves as the canonical microscopic physical model for such systems. Multiple orders have been proposed in the underdoped part of the phase diagram, which corresponds to a regime of maximum numerical difficulty. By combining the latest numerical methods in exhaustive simulations, we uncover the ordering in the underdoped ground state. We find a stripe order that has a highly compressible wavelength on an energy scale of a few kelvin, with wavelength fluctuations coupled to pairing order. The favored filled stripe order is different from that seen in real materials. Our results demonstrate the power of modern numerical methods to solve microscopic models, even in challenging settings.

Ultrawidefield microscope for high-speed fluorescence imaging and targeted optogenetic stimulation.

PubMed

Werley, Christopher A; Chien, Miao-Ping; Cohen, Adam E

2017-12-01

The rapid increase in the number and quality of fluorescent reporters and optogenetic actuators has yielded a powerful set of tools for recording and controlling cellular state and function. To achieve the full benefit of these tools requires improved optical systems with high light collection efficiency, high spatial and temporal resolution, and patterned optical stimulation, in a wide field of view (FOV). Here we describe our 'Firefly' microscope, which achieves these goals in a Ø6 mm FOV. The Firefly optical system is optimized for simultaneous photostimulation and fluorescence imaging in cultured cells. All but one of the optical elements are commercially available, yet the microscope achieves 10-fold higher light collection efficiency at its design magnification than the comparable commercially available microscope using the same objective. The Firefly microscope enables all-optical electrophysiology ('Optopatch') in cultured neurons with a throughput and information content unmatched by other neuronal phenotyping systems. This capability opens possibilities in disease modeling and phenotypic drug screening. We also demonstrate applications of the system to voltage and calcium recordings in human induced pluripotent stem cell derived cardiomyocytes.

Ultrawidefield microscope for high-speed fluorescence imaging and targeted optogenetic stimulation

PubMed Central

Werley, Christopher A.; Chien, Miao-Ping; Cohen, Adam E.

2017-01-01

The rapid increase in the number and quality of fluorescent reporters and optogenetic actuators has yielded a powerful set of tools for recording and controlling cellular state and function. To achieve the full benefit of these tools requires improved optical systems with high light collection efficiency, high spatial and temporal resolution, and patterned optical stimulation, in a wide field of view (FOV). Here we describe our ‘Firefly’ microscope, which achieves these goals in a Ø6 mm FOV. The Firefly optical system is optimized for simultaneous photostimulation and fluorescence imaging in cultured cells. All but one of the optical elements are commercially available, yet the microscope achieves 10-fold higher light collection efficiency at its design magnification than the comparable commercially available microscope using the same objective. The Firefly microscope enables all-optical electrophysiology (‘Optopatch’) in cultured neurons with a throughput and information content unmatched by other neuronal phenotyping systems. This capability opens possibilities in disease modeling and phenotypic drug screening. We also demonstrate applications of the system to voltage and calcium recordings in human induced pluripotent stem cell derived cardiomyocytes. PMID:29296505

Three-dimensional reconstruction of highly complex microscopic samples using scanning electron microscopy and optical flow estimation.

PubMed

Baghaie, Ahmadreza; Pahlavan Tafti, Ahmad; Owen, Heather A; D'Souza, Roshan M; Yu, Zeyun

2017-01-01

Scanning Electron Microscope (SEM) as one of the major research and industrial equipment for imaging of micro-scale samples and surfaces has gained extensive attention from its emerge. However, the acquired micrographs still remain two-dimensional (2D). In the current work a novel and highly accurate approach is proposed to recover the hidden third-dimension by use of multi-view image acquisition of the microscopic samples combined with pre/post-processing steps including sparse feature-based stereo rectification, nonlocal-based optical flow estimation for dense matching and finally depth estimation. Employing the proposed approach, three-dimensional (3D) reconstructions of highly complex microscopic samples were achieved to facilitate the interpretation of topology and geometry of surface/shape attributes of the samples. As a byproduct of the proposed approach, high-definition 3D printed models of the samples can be generated as a tangible means of physical understanding. Extensive comparisons with the state-of-the-art reveal the strength and superiority of the proposed method in uncovering the details of the highly complex microscopic samples.

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.

MTF measurements on real time for performance analysis of electro-optical systems

NASA Astrophysics Data System (ADS)

Stuchi, Jose Augusto; Signoreto Barbarini, Elisa; Vieira, Flavio Pascoal; dos Santos, Daniel, Jr.; Stefani, Mário Antonio; Yasuoka, Fatima Maria Mitsue; Castro Neto, Jarbas C.; Linhari Rodrigues, Evandro Luis

2012-06-01

The need of methods and tools that assist in determining the performance of optical systems is actually increasing. One of the most used methods to perform analysis of optical systems is to measure the Modulation Transfer Function (MTF). The MTF represents a direct and quantitative verification of the image quality. This paper presents the implementation of the software, in order to calculate the MTF of electro-optical systems. The software was used for calculating the MTF of Digital Fundus Camera, Thermal Imager and Ophthalmologic Surgery Microscope. The MTF information aids the analysis of alignment and measurement of optical quality, and also defines the limit resolution of optical systems. The results obtained with the Fundus Camera and Thermal Imager was compared with the theoretical values. For the Microscope, the results were compared with MTF measured of Microscope Zeiss model, which is the quality standard of ophthalmological microscope.

Equilibrating high-molecular-weight symmetric and miscible polymer blends with hierarchical back-mapping.

PubMed

Ohkuma, Takahiro; Kremer, Kurt; Daoulas, Kostas

2018-05-02

Understanding properties of polymer alloys with computer simulations frequently requires equilibration of samples comprised of microscopically described long molecules. We present the extension of an efficient hierarchical backmapping strategy, initially developed for homopolymer melts, to equilibrate high-molecular-weight binary blends. These mixtures present significant interest for practical applications and fundamental polymer physics. In our approach, the blend is coarse-grained into models representing polymers as chains of soft blobs. Each blob stands for a subchain with N b microscopic monomers. A hierarchy of blob-based models with different resolution is obtained by varying N b . First the model with the largest N b is used to obtain an equilibrated blend. This configuration is sequentially fine-grained, reinserting at each step the degrees of freedom of the next in the hierarchy blob-based model. Once the blob-based description is sufficiently detailed, the microscopic monomers are reinserted. The hard excluded volume is recovered through a push-off procedure and the sample is re-equilibrated with molecular dynamics (MD), requiring relaxation on the order of the entanglement time. For the initial method development we focus on miscible blends described on microscopic level through a generic bead-spring model, which reproduces hard excluded volume, strong covalent bonds, and realistic liquid density. The blended homopolymers are symmetric with respect to molecular architecture and liquid structure. To parameterize the blob-based models and validate equilibration of backmapped samples, we obtain reference data from independent hybrid simulations combining MD and identity exchange Monte Carlo moves, taking advantage of the symmetry of the blends. The potential of the backmapping strategy is demonstrated by equilibrating blend samples with different degree of miscibility, containing 500 chains with 1000 monomers each. Equilibration is verified by comparing chain conformations and liquid structure in backmapped blends with the reference data. Possible directions for further methodological developments are discussed.

[Effect of electroacupuncture on cellular structure of hippocampus in splenic asthenia pedo-rats].

PubMed

Yang, Zhuo-xin; Zhuo, Yuan-yuan; Yu, Hai-bo; Wang, Ning

2010-02-01

To observe the effect of electroacupuncture (EA) on hippocampal structure in splenic asthenia pedo-rats. A total of 15 SD male rats were randomly assigned to normal control group (n=5), model group (n=5) and EA group (n=5). Splenic asthenic syndrome model was established by intragastric administration of rhubarb and intraperitoneal injection of Reserpine for 14 d. EA (1 mA, 3 Hz/iS Hz) was applied to bilateral "Zusanli" (ST 36) and "Sanyinjiao" (SP 6) for 20 mm, once a day for 14 days. The cellular structure of hippocampus was observed by light microscope and transmission electron microscope. Optical microscopic observation showed that in normal control group, the cellular nucleus was distinct, and the granular cell layer well-arranged and tight. In model group, the intracellular space was widened, and the granular cell layer was out of order in the arrangement. In EA group, the celluldr nucleus and the granular cell layer were nearly normal. Results of the electronic microscope showed that cells in model group had a karyopyknosis with irregular appearance and clear incisure, and some of them presented dissolving and necrotic phenomena; and those in EA group were milder in injury, had nearly-normal nucleus with visible nucleoli and relatively-intact nuclear membrane. Regarding the cellular plasma, in comparison with rich normal organelles of control group, the mitochondria in model group were swelling, with vague, dissolved and broken cristae, while in EA group, majority of the organelles were well-kept, and slightly dissolved mitochondrial cristae found. In regard to the synaptic structure, in comparison with control group, synaptic apomorphosis and swelling mitochondria were found in model group While in EA group, milder swelling and hydropic degeneration were seen. Different from the distinct pre- and post-synaptic membrane and synaptic vesicles of control group, while those in EA group were nearly-normal. electroacupunture can effectively relieve splenasthenic syndrome induced pathohistological changes of neurons of the hippocampus in the rat.

Equilibrating high-molecular-weight symmetric and miscible polymer blends with hierarchical back-mapping

NASA Astrophysics Data System (ADS)

Ohkuma, Takahiro; Kremer, Kurt; Daoulas, Kostas

2018-05-01

Understanding properties of polymer alloys with computer simulations frequently requires equilibration of samples comprised of microscopically described long molecules. We present the extension of an efficient hierarchical backmapping strategy, initially developed for homopolymer melts, to equilibrate high-molecular-weight binary blends. These mixtures present significant interest for practical applications and fundamental polymer physics. In our approach, the blend is coarse-grained into models representing polymers as chains of soft blobs. Each blob stands for a subchain with N b microscopic monomers. A hierarchy of blob-based models with different resolution is obtained by varying N b. First the model with the largest N b is used to obtain an equilibrated blend. This configuration is sequentially fine-grained, reinserting at each step the degrees of freedom of the next in the hierarchy blob-based model. Once the blob-based description is sufficiently detailed, the microscopic monomers are reinserted. The hard excluded volume is recovered through a push-off procedure and the sample is re-equilibrated with molecular dynamics (MD), requiring relaxation on the order of the entanglement time. For the initial method development we focus on miscible blends described on microscopic level through a generic bead-spring model, which reproduces hard excluded volume, strong covalent bonds, and realistic liquid density. The blended homopolymers are symmetric with respect to molecular architecture and liquid structure. To parameterize the blob-based models and validate equilibration of backmapped samples, we obtain reference data from independent hybrid simulations combining MD and identity exchange Monte Carlo moves, taking advantage of the symmetry of the blends. The potential of the backmapping strategy is demonstrated by equilibrating blend samples with different degree of miscibility, containing 500 chains with 1000 monomers each. Equilibration is verified by comparing chain conformations and liquid structure in backmapped blends with the reference data. Possible directions for further methodological developments are discussed.

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.

Structure of S-shaped growth in innovation diffusion

NASA Astrophysics Data System (ADS)

Shimogawa, Shinsuke; Shinno, Miyuki; Saito, Hiroshi

2012-05-01

A basic question on innovation diffusion is why the growth curve of the adopter population in a large society is often S shaped. From macroscopic, microscopic, and mesoscopic viewpoints, the growth of the adopter population is observed as the growth curve, individual adoptions, and differences among individual adoptions, respectively. The S shape can be explained if an empirical model of the growth curve can be deduced from models of microscopic and mesoscopic structures. However, even the structure of growth curve has not been revealed yet because long-term extrapolations by proposed models of S-shaped curves are unstable and it has been very difficult to predict the long-term growth and final adopter population. This paper studies the S-shaped growth from the viewpoint of social regularities. Simple methods to analyze power laws enable us to extract the structure of the growth curve directly from the growth data of recent basic telecommunication services. This empirical model of growth curve is singular at the inflection point and a logarithmic function of time after this point, which explains the unstable extrapolations obtained using previously proposed models and the difficulty in predicting the final adopter population. Because the empirical S curve can be expressed in terms of two power laws of the regularity found in social performances of individuals, we propose the hypothesis that the S shape represents the heterogeneity of the adopter population, and the heterogeneity parameter is distributed under the regularity in social performances of individuals. This hypothesis is so powerful as to yield models of microscopic and mesoscopic structures. In the microscopic model, each potential adopter adopts the innovation when the information accumulated by the learning about the innovation exceeds a threshold. The accumulation rate of information is heterogeneous among the adopter population, whereas the threshold is a constant, which is the opposite of previously proposed models. In the mesoscopic model, flows of innovation information incoming to individuals are organized as dimorphic and partially clustered. These microscopic and mesoscopic models yield the empirical model of the S curve and explain the S shape as representing the regularities of information flows generated through a social self-organization. To demonstrate the validity and importance of the hypothesis, the models of three level structures are applied to reveal the mechanism determining and differentiating diffusion speeds. The empirical model of S curves implies that the coefficient of variation of the flow rates determines the diffusion speed for later adopters. Based on this property, a model describing the inside of information flow clusters can be given, which provides a formula interconnecting the diffusion speed, cluster populations, and a network topological parameter of the flow clusters. For two recent basic telecommunication services in Japan, the formula represents the variety of speeds in different areas and enables us to explain speed gaps between urban and rural areas and between the two services. Furthermore, the formula provides a method to estimate the final adopter population.

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.

Increasing Student Understanding of Microscope Optics by Building and Testing the Limits of Simple, Hand-Made Model Microscopes†

PubMed Central

Drace, Kevin; Couch, Brett; Keeling, Patrick J.

2012-01-01

The ability to effectively use a microscope to observe microorganisms is a crucial skill required for many disciplines within biology, especially general microbiology and cell biology. A basic understanding of the optical properties of light microscopes is required for students to use microscopes effectively, but this subject can also be a challenge to make personally interesting to students. To explore basic optical principles of magnification and resolving power in a more engaging and hands-on fashion, students constructed handmade lenses and microscopes based on Antony van Leeuwenhoek’s design using simple materials—paper, staples, glass, and adhesive putty. Students determined the power of their lenses using a green laser pointer to magnify a copper grid of known size, which also allowed students to examine variables affecting the power and resolution of a lens such as diameter, working distance, and wavelength of light. To assess the effectiveness of the laboratory’s learning objectives, four sections of a general microbiology course were given a brief pre-activity assessment quiz to determine their background knowledge on the subject. One week after the laboratory activity, students were given the same quiz (unannounced) under similar conditions. Students showed significant gains in their understanding of microscope optics. PMID:23653781

How Confocal Is Confocal Raman Microspectroscopy on the Skin? Impact of Microscope Configuration and Sample Preparation on Penetration Depth Profiles.

PubMed

Lunter, Dominique Jasmin

2016-01-01

The aim of the study was to elucidate the effect of sample preparation and microscope configuration on the results of confocal Raman microspectroscopic evaluation of the penetration of a pharmaceutical active into the skin (depth profiling). Pig ear skin and a hydrophilic formulation containing procaine HCl were used as a model system. The formulation was either left on the skin during the measurement, or was wiped off or washed off prior to the analysis. The microscope configuration was varied with respect to objectives and pinholes used. Sample preparation and microscope configuration had a tremendous effect on the results of depth profiling. Regarding sample preparation, the best results could be observed when the formulation was washed off the skin prior to the analysis. Concerning microscope configuration, the use of a 40 × 0.6 numerical aperture (NA) objective in combination with a 25-µm pinhole or a 100 × 1.25 NA objective in combination with a 50-µm pinhole was found to be advantageous. Complete removal of the sample from the skin before the analysis was found to be crucial. A thorough analysis of the suitability of the chosen microscope configuration should be performed before acquiring concentration depth profiles. © 2016 S. Karger AG, Basel.

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.

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.

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...

Track structure model of microscopic energy deposition by protons and heavy ions in segments of neuronal cell dendrites represented by cylinders or spheres

PubMed Central

Alp, Murat; Cucinotta, Francis A.

2017-01-01

Changes to cognition, including memory, following radiation exposure are a concern for cosmic ray exposures to astronauts and in Hadron therapy with proton and heavy ion beams. The purpose of the present work is to develop computational methods to evaluate microscopic energy deposition (ED) in volumes representative of neuron cell structures, including segments of dendrites and spines, using a stochastic track structure model. A challenge for biophysical models of neuronal damage is the large sizes (>100 μm) and variability in volumes of possible dendritic segments and pre-synaptic elements (spines and filopodia). We consider cylindrical and spherical microscopic volumes of varying geometric parameters and aspect ratios from 0.5 to 5 irradiated by protons, and 3He and 12C particles at energies corresponding to a distance of 1 cm to the Bragg peak, which represent particles of interest in Hadron therapy as well as space radiation exposure. We investigate the optimal axis length of dendritic segments to evaluate microscopic ED and hit probabilities along the dendritic branches at a given macroscopic dose. Because of large computation times to analyze ED in volumes of varying sizes, we developed an analytical method to find the mean primary dose in spheres that can guide numerical methods to find the primary dose distribution for cylinders. Considering cylindrical segments of varying aspect ratio at constant volume, we assess the chord length distribution, mean number of hits and ED profiles by primary particles and secondary electrons (δ-rays). For biophysical modeling applications, segments on dendritic branches are proposed to have equal diameters and axes lengths along the varying diameter of a dendritic branch. PMID:28554507

Track structure model of microscopic energy deposition by protons and heavy ions in segments of neuronal cell dendrites represented by cylinders or spheres

NASA Astrophysics Data System (ADS)

Alp, Murat; Cucinotta, Francis A.

2017-05-01

Changes to cognition, including memory, following radiation exposure are a concern for cosmic ray exposures to astronauts and in Hadron therapy with proton and heavy ion beams. The purpose of the present work is to develop computational methods to evaluate microscopic energy deposition (ED) in volumes representative of neuron cell structures, including segments of dendrites and spines, using a stochastic track structure model. A challenge for biophysical models of neuronal damage is the large sizes (> 100 μm) and variability in volumes of possible dendritic segments and pre-synaptic elements (spines and filopodia). We consider cylindrical and spherical microscopic volumes of varying geometric parameters and aspect ratios from 0.5 to 5 irradiated by protons, and 3He and 12C particles at energies corresponding to a distance of 1 cm to the Bragg peak, which represent particles of interest in Hadron therapy as well as space radiation exposure. We investigate the optimal axis length of dendritic segments to evaluate microscopic ED and hit probabilities along the dendritic branches at a given macroscopic dose. Because of large computation times to analyze ED in volumes of varying sizes, we developed an analytical method to find the mean primary dose in spheres that can guide numerical methods to find the primary dose distribution for cylinders. Considering cylindrical segments of varying aspect ratio at constant volume, we assess the chord length distribution, mean number of hits and ED profiles by primary particles and secondary electrons (δ-rays). For biophysical modeling applications, segments on dendritic branches are proposed to have equal diameters and axes lengths along the varying diameter of a dendritic branch.

Track structure model of microscopic energy deposition by protons and heavy ions in segments of neuronal cell dendrites represented by cylinders or spheres.

PubMed

Alp, Murat; Cucinotta, Francis A

2017-05-01

Changes to cognition, including memory, following radiation exposure are a concern for cosmic ray exposures to astronauts and in Hadron therapy with proton and heavy ion beams. The purpose of the present work is to develop computational methods to evaluate microscopic energy deposition (ED) in volumes representative of neuron cell structures, including segments of dendrites and spines, using a stochastic track structure model. A challenge for biophysical models of neuronal damage is the large sizes (> 100µm) and variability in volumes of possible dendritic segments and pre-synaptic elements (spines and filopodia). We consider cylindrical and spherical microscopic volumes of varying geometric parameters and aspect ratios from 0.5 to 5 irradiated by protons, and 3 He and 12 C particles at energies corresponding to a distance of 1cm to the Bragg peak, which represent particles of interest in Hadron therapy as well as space radiation exposure. We investigate the optimal axis length of dendritic segments to evaluate microscopic ED and hit probabilities along the dendritic branches at a given macroscopic dose. Because of large computation times to analyze ED in volumes of varying sizes, we developed an analytical method to find the mean primary dose in spheres that can guide numerical methods to find the primary dose distribution for cylinders. Considering cylindrical segments of varying aspect ratio at constant volume, we assess the chord length distribution, mean number of hits and ED profiles by primary particles and secondary electrons (δ-rays). For biophysical modeling applications, segments on dendritic branches are proposed to have equal diameters and axes lengths along the varying diameter of a dendritic branch. Copyright © 2017. Published by Elsevier Ltd.

Development of HiLo Microscope and its use in In-Vivo Applications

NASA Astrophysics Data System (ADS)

Patel, Shreyas J.

The functionality of achieving optical sectioning in biomedical research is invaluable as it allows for visualization of a biological sample at different depths while being free of background scattering. Most current microscopy techniques that offer optical sectioning, unfortunately, require complex instrumentation and thus are generally costly. HiLo microscopy, on the other hand, offers the same functionality and advantage at a relatively low cost. Hence, the work described in this thesis involves the design, build, and application of a HiLo microscope. More specifically, a standalone HiLo microscope was built in addition to implementing HiLo microscopy on a standard fluorescence microscope. In HiLo microscopy, optical sectioning is achieved by acquiring two different types of images per focal plane. One image is acquired under uniform illumination and the other is acquired under speckle illumination. These images are processed using an algorithm that extracts in-focus information and removes features and glare that occur as a result of background fluorescence. To show the benefits of the HiLo microscopy, several imaging experiments on various samples were performed under a HiLo microscope and compared against a traditional fluorescence microscope and a confocal microscope, which is considered the gold standard in optical imaging. In-vitro and ex-vivo imaging was performed on a set of pollen grains, and optically cleared mouse brain and heart slices. Each of these experiments showed great reduction in background scattering at different depths under HiLo microscopy. More importantly, HiLo imaging of optically cleared heart slice demonstrated emergence of different vasculature at different depths. Reduction of out-of-focus light increased the spatial resolution and allowed better visualization of capillary vessels. Furthermore, HiLo imaging was tested in an in-vivo model of a rodent dorsal window chamber model. When imaging the same sample under confocal microscope, the results were comparable between the two modalities. Additionally, a method of achieving blood flow maps at different depth using a combination of HiLo and LSI imaging is also discussed. The significance of this combined technique could help categorize blood flow to particular depths; this can help improve outcomes of medical treatments such pulse dye laser and photodynamic therapy treatments.

Investigating Cell-Material Interactions of Magnetospirillum magneticum as an Approach for Probing Submerged Surface Structural Integrity

DTIC Science & Technology

2012-07-01

developed a microscope- based , offset Helmholtz coil system with a custom-designed microcontroller. We have developed a microfabrication approach for...implemented an experimental model system using ferromagnetic beads. We have applied direct and frequency based magnetic fields for controlling magnetotactic...fields. Expanded Accomplishments We have developed a microscope- based , offset Helmholtz coil system with a custom- designed microcontroller. To be

Charge frustration in complex fluids and in electronic systems

NASA Astrophysics Data System (ADS)

Carraro, Carlo

1997-02-01

The idea of charge frustration is applied to describe the properties of such diverse physical systems as oil-water-surfactant mixtures and metal-ammonia solutions. The minimalist charge-frustrated model possesses one energy scale and two length scales. For oil-water-surfactant mixtures, these parameters have been determined starting from the microscopic properties of the physical systems under study. Thus, microscopic properties are successfully related to the observed mesoscopic structure.

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.

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.

Molecular modeling of polycarbonate materials: Glass transition and mechanical properties

NASA Astrophysics Data System (ADS)

Palczynski, Karol; Wilke, Andreas; Paeschke, Manfred; Dzubiella, Joachim

2017-09-01

Linking the experimentally accessible macroscopic properties of thermoplastic polymers to their microscopic static and dynamic properties is a key requirement for targeted material design. Classical molecular dynamics simulations enable us to study the structural and dynamic behavior of molecules on microscopic scales, and statistical physics provides a framework for relating these properties to the macroscopic properties. We take a first step toward creating an automated workflow for the theoretical prediction of thermoplastic material properties by developing an expeditious method for parameterizing a simple yet surprisingly powerful coarse-grained bisphenol-A polycarbonate model which goes beyond previous coarse-grained models and successfully reproduces the thermal expansion behavior, the glass transition temperature as a function of the molecular weight, and several elastic properties.

Upscaling soil saturated hydraulic conductivity from pore throat characteristics

NASA Astrophysics Data System (ADS)

Ghanbarian, Behzad; Hunt, Allen G.; Skaggs, Todd H.; Jarvis, Nicholas

2017-06-01

Upscaling and/or estimating saturated hydraulic conductivity Ksat at the core scale from microscopic/macroscopic soil characteristics has been actively under investigation in the hydrology and soil physics communities for several decades. Numerous models have been developed based on different approaches, such as the bundle of capillary tubes model, pedotransfer functions, etc. In this study, we apply concepts from critical path analysis, an upscaling technique first developed in the physics literature, to estimate saturated hydraulic conductivity at the core scale from microscopic pore throat characteristics reflected in capillary pressure data. With this new model, we find Ksat estimations to be within a factor of 3 of the average measured saturated hydraulic conductivities reported by Rawls et al. (1982) for the eleven USDA soil texture classes.

RIPL - Reference Input Parameter Library for Calculation of Nuclear Reactions and Nuclear Data Evaluations

NASA Astrophysics Data System (ADS)

Capote, R.; Herman, M.; Obložinský, P.; Young, P. G.; Goriely, S.; Belgya, T.; Ignatyuk, A. V.; Koning, A. J.; Hilaire, S.; Plujko, V. A.; Avrigeanu, M.; Bersillon, O.; Chadwick, M. B.; Fukahori, T.; Ge, Zhigang; Han, Yinlu; Kailas, S.; Kopecky, J.; Maslov, V. M.; Reffo, G.; Sin, M.; Soukhovitskii, E. Sh.; Talou, P.

2009-12-01

We describe the physics and data included in the Reference Input Parameter Library, which is devoted to input parameters needed in calculations of nuclear reactions and nuclear data evaluations. Advanced modelling codes require substantial numerical input, therefore the International Atomic Energy Agency (IAEA) has worked extensively since 1993 on a library of validated nuclear-model input parameters, referred to as the Reference Input Parameter Library (RIPL). A final RIPL coordinated research project (RIPL-3) was brought to a successful conclusion in December 2008, after 15 years of challenging work carried out through three consecutive IAEA projects. The RIPL-3 library was released in January 2009, and is available on the Web through http://www-nds.iaea.org/RIPL-3/. This work and the resulting database are extremely important to theoreticians involved in the development and use of nuclear reaction modelling (ALICE, EMPIRE, GNASH, UNF, TALYS) both for theoretical research and nuclear data evaluations. The numerical data and computer codes included in RIPL-3 are arranged in seven segments: MASSES contains ground-state properties of nuclei for about 9000 nuclei, including three theoretical predictions of masses and the evaluated experimental masses of Audi et al. (2003). DISCRETE LEVELS contains 117 datasets (one for each element) with all known level schemes, electromagnetic and γ-ray decay probabilities available from ENSDF in October 2007. NEUTRON RESONANCES contains average resonance parameters prepared on the basis of the evaluations performed by Ignatyuk and Mughabghab. OPTICAL MODEL contains 495 sets of phenomenological optical model parameters defined in a wide energy range. When there are insufficient experimental data, the evaluator has to resort to either global parameterizations or microscopic approaches. Radial density distributions to be used as input for microscopic calculations are stored in the MASSES segment. LEVEL DENSITIES contains phenomenological parameterizations based on the modified Fermi gas and superfluid models and microscopic calculations which are based on a realistic microscopic single-particle level scheme. Partial level densities formulae are also recommended. All tabulated total level densities are consistent with both the recommended average neutron resonance parameters and discrete levels. GAMMA contains parameters that quantify giant resonances, experimental gamma-ray strength functions and methods for calculating gamma emission in statistical model codes. The experimental GDR parameters are represented by Lorentzian fits to the photo-absorption cross sections for 102 nuclides ranging from 51V to 239Pu. FISSION includes global prescriptions for fission barriers and nuclear level densities at fission saddle points based on microscopic HFB calculations constrained by experimental fission cross sections.

RIPL - Reference Input Parameter Library for Calculation of Nuclear Reactions and Nuclear Data Evaluations

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

Capote, R.; Herman, M.; Oblozinsky, P.

We describe the physics and data included in the Reference Input Parameter Library, which is devoted to input parameters needed in calculations of nuclear reactions and nuclear data evaluations. Advanced modelling codes require substantial numerical input, therefore the International Atomic Energy Agency (IAEA) has worked extensively since 1993 on a library of validated nuclear-model input parameters, referred to as the Reference Input Parameter Library (RIPL). A final RIPL coordinated research project (RIPL-3) was brought to a successful conclusion in December 2008, after 15 years of challenging work carried out through three consecutive IAEA projects. The RIPL-3 library was released inmore » January 2009, and is available on the Web through (http://www-nds.iaea.org/RIPL-3/). This work and the resulting database are extremely important to theoreticians involved in the development and use of nuclear reaction modelling (ALICE, EMPIRE, GNASH, UNF, TALYS) both for theoretical research and nuclear data evaluations. The numerical data and computer codes included in RIPL-3 are arranged in seven segments: MASSES contains ground-state properties of nuclei for about 9000 nuclei, including three theoretical predictions of masses and the evaluated experimental masses of Audi et al. (2003). DISCRETE LEVELS contains 117 datasets (one for each element) with all known level schemes, electromagnetic and {gamma}-ray decay probabilities available from ENSDF in October 2007. NEUTRON RESONANCES contains average resonance parameters prepared on the basis of the evaluations performed by Ignatyuk and Mughabghab. OPTICAL MODEL contains 495 sets of phenomenological optical model parameters defined in a wide energy range. When there are insufficient experimental data, the evaluator has to resort to either global parameterizations or microscopic approaches. Radial density distributions to be used as input for microscopic calculations are stored in the MASSES segment. LEVEL DENSITIES contains phenomenological parameterizations based on the modified Fermi gas and superfluid models and microscopic calculations which are based on a realistic microscopic single-particle level scheme. Partial level densities formulae are also recommended. All tabulated total level densities are consistent with both the recommended average neutron resonance parameters and discrete levels. GAMMA contains parameters that quantify giant resonances, experimental gamma-ray strength functions and methods for calculating gamma emission in statistical model codes. The experimental GDR parameters are represented by Lorentzian fits to the photo-absorption cross sections for 102 nuclides ranging from {sup 51}V to {sup 239}Pu. FISSION includes global prescriptions for fission barriers and nuclear level densities at fission saddle points based on microscopic HFB calculations constrained by experimental fission cross sections.« less

RIPL-Reference Input Parameter Library for Calculation of Nuclear Reactions and Nuclear Data Evaluations

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

Capote, R.; Herman, M.; Capote,R.

We describe the physics and data included in the Reference Input Parameter Library, which is devoted to input parameters needed in calculations of nuclear reactions and nuclear data evaluations. Advanced modelling codes require substantial numerical input, therefore the International Atomic Energy Agency (IAEA) has worked extensively since 1993 on a library of validated nuclear-model input parameters, referred to as the Reference Input Parameter Library (RIPL). A final RIPL coordinated research project (RIPL-3) was brought to a successful conclusion in December 2008, after 15 years of challenging work carried out through three consecutive IAEA projects. The RIPL-3 library was released inmore » January 2009, and is available on the Web through http://www-nds.iaea.org/RIPL-3/. This work and the resulting database are extremely important to theoreticians involved in the development and use of nuclear reaction modelling (ALICE, EMPIRE, GNASH, UNF, TALYS) both for theoretical research and nuclear data evaluations. The numerical data and computer codes included in RIPL-3 are arranged in seven segments: MASSES contains ground-state properties of nuclei for about 9000 nuclei, including three theoretical predictions of masses and the evaluated experimental masses of Audi et al. (2003). DISCRETE LEVELS contains 117 datasets (one for each element) with all known level schemes, electromagnetic and {gamma}-ray decay probabilities available from ENSDF in October 2007. NEUTRON RESONANCES contains average resonance parameters prepared on the basis of the evaluations performed by Ignatyuk and Mughabghab. OPTICAL MODEL contains 495 sets of phenomenological optical model parameters defined in a wide energy range. When there are insufficient experimental data, the evaluator has to resort to either global parameterizations or microscopic approaches. Radial density distributions to be used as input for microscopic calculations are stored in the MASSES segment. LEVEL DENSITIES contains phenomenological parameterizations based on the modified Fermi gas and superfluid models and microscopic calculations which are based on a realistic microscopic single-particle level scheme. Partial level densities formulae are also recommended. All tabulated total level densities are consistent with both the recommended average neutron resonance parameters and discrete levels. GAMMA contains parameters that quantify giant resonances, experimental gamma-ray strength functions and methods for calculating gamma emission in statistical model codes. The experimental GDR parameters are represented by Lorentzian fits to the photo-absorption cross sections for 102 nuclides ranging from {sup 51}V to {sup 239}Pu. FISSION includes global prescriptions for fission barriers and nuclear level densities at fission saddle points based on microscopic HFB calculations constrained by experimental fission cross sections.« less

Directional sensitivity of the retina: A layered scattering model of outer-segment photoreceptor pigments

PubMed Central

Vohnsen, Brian

2014-01-01

Photoreceptor outer segments have been modeled as stacked arrays of discs or membrane infoldings containing visual pigments with light-induced dipole moments. Waveguiding has been excluded so fields diffract beyond the physical boundaries of each photoreceptor cell. Optical reciprocity is used to argue for identical radiative and light gathering properties of pigments to model vision. Two models have been introduced: one a macroscopic model that assumes a uniform pigment density across each layer and another microscopic model that includes the spatial location of each pigment molecule within each layer. Both models result in highly similar directionality at the pupil plane which proves to be insensitive to the exact details of the outer-segment packing being predominantly determined by the first and last contributing layers as set by the fraction of bleaching. The versatility of the microscopic model is demonstrated with an array of examples that includes the Stiles-Crawford effect, visibility of a focused beam of light and the role of defocus. PMID:24877016

An analytical model for scanning electron microscope Type I magnetic contrast with energy filtering

NASA Astrophysics Data System (ADS)

Chim, W. K.

1994-02-01

In this article, a theoretical model for type I magnetic contrast calculations in the scanning electron microscope with energy filtering is presented. This model uses an approximate form of the secondary electron (SE) energy distribution by Chung and Everhart [M. S. Chung and T. E. Everhart, J. Appl. Phys. 45, 707 (1974). Closed form analytical expressions for the contrast and quality factors, which take into consideration the work function and field-distance integral of the material being studied, are obtained. This analytical model is compared with that of a more accurate numerical model. Results showed that the contrast and quality factors for the analytical model differed by not more than 20% from the numerical model, with the actual difference depending on the range of filtered SE energies considered. This model has also been extended to the situation of a two-detector (i.e., detector A and B) configuration, in which enhanced magnetic contrast and quality factor can be obtained by operating in the ``A-B'' mode.

Microdose fluorescence imaging of ABY-029 on an operating microscope adapted by custom illumination and imaging modules.

PubMed

Elliott, Jonathan T; Dsouza, Alisha V; Marra, Kayla; Pogue, Brian W; Roberts, David W; Paulsen, Keith D

2016-09-01

Fluorescence guided surgery has the potential to positively impact surgical oncology; current operating microscopes and stand-alone imaging systems are too insensitive or too cumbersome to maximally take advantage of new tumor-specific agents developed through the microdose pathway. To this end, a custom-built illumination and imaging module enabling picomolar-sensitive near-infrared fluorescence imaging on a commercial operating microscope is described. The limits of detection and system specifications are characterized, and in vivo efficacy of the system in detecting ABY-029 is evaluated in a rat orthotopic glioma model following microdose injections, showing the suitability of the device for microdose phase 0 clinical trials.

Microdose fluorescence imaging of ABY-029 on an operating microscope adapted by custom illumination and imaging modules

PubMed Central

Dsouza, Alisha V.; Marra, Kayla; Pogue, Brian W.; Roberts, David W.; Paulsen, Keith D.

2016-01-01

Fluorescence guided surgery has the potential to positively impact surgical oncology; current operating microscopes and stand-alone imaging systems are too insensitive or too cumbersome to maximally take advantage of new tumor-specific agents developed through the microdose pathway. To this end, a custom-built illumination and imaging module enabling picomolar-sensitive near-infrared fluorescence imaging on a commercial operating microscope is described. The limits of detection and system specifications are characterized, and in vivo efficacy of the system in detecting ABY-029 is evaluated in a rat orthotopic glioma model following microdose injections, showing the suitability of the device for microdose phase 0 clinical trials. PMID:27699098

Laws of Large Numbers and Langevin Approximations for Stochastic Neural Field Equations

PubMed Central

2013-01-01

In this study, we consider limit theorems for microscopic stochastic models of neural fields. We show that the Wilson–Cowan equation can be obtained as the limit in uniform convergence on compacts in probability for a sequence of microscopic models when the number of neuron populations distributed in space and the number of neurons per population tend to infinity. This result also allows to obtain limits for qualitatively different stochastic convergence concepts, e.g., convergence in the mean. Further, we present a central limit theorem for the martingale part of the microscopic models which, suitably re-scaled, converges to a centred Gaussian process with independent increments. These two results provide the basis for presenting the neural field Langevin equation, a stochastic differential equation taking values in a Hilbert space, which is the infinite-dimensional analogue of the chemical Langevin equation in the present setting. On a technical level, we apply recently developed law of large numbers and central limit theorems for piecewise deterministic processes taking values in Hilbert spaces to a master equation formulation of stochastic neuronal network models. These theorems are valid for processes taking values in Hilbert spaces, and by this are able to incorporate spatial structures of the underlying model. Mathematics Subject Classification (2000): 60F05, 60J25, 60J75, 92C20. PMID:23343328

Protective effects of Sapindus mukorossi Gaertn against fatty liver disease induced by high fat diet in rats

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

Peng, Qiuxian; Department of Biology, Hong Kong Baptist University, Kowloon Tong; Zhang, Qin

Highlights: • AESM is able to prevent the elevation of ALT and AST, and to decreased LDL-C level. • AESM demonstrates the effects of down-regulating blood fat level and protecting liver. • AESM consistent with the efficacy of simvastatin in NAFLD. - Abstract: Objectives: Study the effects of alcohol extract of Sapindus mukorossi Gaertn (AESM) on the metabolism of blood fat, morphology of fenestrated liver sinusoidal endothelial cells (LSEC), and the ultrastructure of liver cells of the rats with non-alcoholic fatty liver disease (NAFLD). Methods: Divide SD rats into control group, model group, simvastatin (7.2 mg/kg) group, and S.mukorossi Gaertnmore » group with high dosage (0.5 g/kg), moderate dosage (0.1 g/kg), and low dosage (0.05 g/kg). After feeding with fat-rich nutrients for 3 weeks and establishing the model of hepatic adipose, conduct intragastric administration and provide the rats with fat-rich nutrients at the same time. At the 43rd day, take blood sample and measure aminotransferase and different indexes of blood fat; take hepatic tissue for pathological section, and observe the hepatic morphological patterns under light microscope; obtain and fix the hepatic tissue after injecting perfusate into the body, and observe the changes of fenestrated LSEC under scanning electron microscope; observe the ultrastructure of liver cells under transmission electron microscope. Results: High-dosage alcohol extracts of S.mukorossi Gaertn can alleviate the AST, ALT, TC, TG, LDL, γ-GT, and ALP level, as well as raise the HDL and APN level in the serum of NAFLD-rat model. In addition, through the observation from light microscope and electron microscopes, the morphology of the hepatic tissue and liver cells as well as the recovery of the fenestrated LSEC in the treatment group has become normal. Conclusions: Alcohol extracts of S.mukorossi Gaertn can regulate the level of blood fat and improve the pathological changes of the hepatic tissues in NAFLD-rat model, which demonstrates the effects of down-regulating fat level and protecting liver.« less

Modeling brain circuitry over a wide range of scales.

PubMed

Fua, Pascal; Knott, Graham W

2015-01-01

If we are ever to unravel the mysteries of brain function at its most fundamental level, we will need a precise understanding of how its component neurons connect to each other. Electron Microscopes (EM) can now provide the nanometer resolution that is needed to image synapses, and therefore connections, while Light Microscopes (LM) see at the micrometer resolution required to model the 3D structure of the dendritic network. Since both the topology and the connection strength are integral parts of the brain's wiring diagram, being able to combine these two modalities is critically important. In fact, these microscopes now routinely produce high-resolution imagery in such large quantities that the bottleneck becomes automated processing and interpretation, which is needed for such data to be exploited to its full potential. In this paper, we briefly review the Computer Vision techniques we have developed at EPFL to address this need. They include delineating dendritic arbors from LM imagery, segmenting organelles from EM, and combining the two into a consistent representation.

Modeling brain circuitry over a wide range of scales

PubMed Central

Fua, Pascal; Knott, Graham W.

2015-01-01

If we are ever to unravel the mysteries of brain function at its most fundamental level, we will need a precise understanding of how its component neurons connect to each other. Electron Microscopes (EM) can now provide the nanometer resolution that is needed to image synapses, and therefore connections, while Light Microscopes (LM) see at the micrometer resolution required to model the 3D structure of the dendritic network. Since both the topology and the connection strength are integral parts of the brain's wiring diagram, being able to combine these two modalities is critically important. In fact, these microscopes now routinely produce high-resolution imagery in such large quantities that the bottleneck becomes automated processing and interpretation, which is needed for such data to be exploited to its full potential. In this paper, we briefly review the Computer Vision techniques we have developed at EPFL to address this need. They include delineating dendritic arbors from LM imagery, segmenting organelles from EM, and combining the two into a consistent representation. PMID:25904852

Surprises in low dimensional spin 1/2 magnets - from crystal chemistry to microscopic magnetic models of complex oxides

NASA Astrophysics Data System (ADS)

Rosner, Helge

2011-03-01

A microscopic understanding of the structure-properties relation in crystalline materials is a main goal of modern solid state chemistry and physics. Due to their peculiar magnetism, low dimensional spin 1/2 systems are often highly sensitive to structural details. Seemingly unimportant structural details can be crucial for the magnetic ground state of a compound, especially in the case of competing interactions, frustration and near-degeneracy. Here, we present for selected, complex Cu 2+ systems that a first principles based approach can reliably provide the correct magnetic model, especially in cases where the interpretation of experimental data meets serious difficulties or fails. We demonstrate that the magnetism of low dimensional insulators crucially depends on the magnetically active orbitals which are determined by details of the ligand field of the magnetic cation. Our theoretical results are in very good agreement with thermodynamic and spectroscopic data and provide deep microscopic insight into topical low dimensional magnets.

Microscopic optical model potential based on a Dirac Brueckner Hartree Fock approach and the relevant uncertainty analysis

NASA Astrophysics Data System (ADS)

Xu, Ruirui; Ma, Zhongyu; Muether, Herbert; van Dalen, E. N. E.; Liu, Tinjin; Zhang, Yue; Zhang, Zhi; Tian, Yuan

2017-09-01

A relativistic microscopic optical model potential, named CTOM, for nucleon-nucleus scattering is investigated in the framework of Dirac-Brueckner-Hartree-Fock approach. The microscopic feature of CTOM is guaranteed through rigorously adopting the isospin dependent DBHF calculation within the subtracted T matrix scheme. In order to verify its prediction power, a global study n, p+ A scattering are carried out. The predicted scattering observables coincide with experimental data within a good accuracy over a broad range of targets and a large region of energies only with two free items, namely the free-range factor t in the applied improved local density approximation and minor adjustments of the scalar and vector potentials in the low-density region. In addition, to estimate the uncertainty of the theoretical results, the deterministic simple least square approach is preliminarily employed to derive the covariance of predicted angular distributions, which is also briefly contained in this paper.

Defining the macroscopic and microscopic findings of experimental focal brain ischemia in rats from a forensic scientist's point of view.

PubMed

Tatlisumak, Ertugrul; Inan, Sevinc; Asirdizer, Mahmut; Apaydin, Nihal; Hayretdag, Ceyda; Kose, Can; Tekdemir, Ibrahim

2009-03-01

Approximately 10% of all deaths in the world occur as a result of stroke. Determination of the time schedule of the pathologic events in a stroke patient is invaluable for a forensic specialist. The aim of this study was to define the schedule of the macroscopic and microscopic changes that occurred in a rat model of permanent focal ischemia for providing useful clues for the evaluation of stroke patients. Male Wistar rats weighing 250 to 350 g were used in this study. Permanent focal brain ischemia was applied by the suture occlusion method. The animals were divided into 7 experimental groups (n = 6) with time schedules including 1.5, 3, 6, 12, 24, 72 hours, and the sham. Brains were harvested at the end of the determined time schedule. Lesions in the frontoparietal cortex were evaluated macroscopically first and later hematoxylin eosin stained sections from the infarct core were investigated microscopically. Macroscopically, enlargement of the ipsilateral hemisphere was mild at 6 hour, apparent at 12 and 24 hours, and mild again at 72 hours. Microscopically, ischemic changes were apparent even at 1.5 hour. Red neurons and infiltration of the parenchyma with neutrophil leukocytes were observed at 12 hours. Pannecrosis and massive leukocyte infiltration were observed at 72 hours. Macroscopic and microscopic findings obtained from a rat model may provide clues for determination of the time-dependent changes due to brain ischemia in human subjects. Finally, the benefits of determination of time course of pathologic changes in the brain for forensic scientists were discussed.

Resolution and throughput optimized intraoperative spectrally encoded coherence tomography and reflectometry (iSECTR) for multimodal imaging during ophthalmic microsurgery

NASA Astrophysics Data System (ADS)

Malone, Joseph D.; El-Haddad, Mohamed T.; Leeburg, Kelsey C.; Terrones, Benjamin D.; Tao, Yuankai K.

2018-02-01

Limited visualization of semi-transparent structures in the eye remains a critical barrier to improving clinical outcomes and developing novel surgical techniques. While increases in imaging speed has enabled intraoperative optical coherence tomography (iOCT) imaging of surgical dynamics, several critical barriers to clinical adoption remain. Specifically, these include (1) static field-of-views (FOVs) requiring manual instrument-tracking; (2) high frame-rates require sparse sampling, which limits FOV; and (3) small iOCT FOV also limits the ability to co-register data with surgical microscopy. We previously addressed these limitations in image-guided ophthalmic microsurgery by developing microscope-integrated multimodal intraoperative swept-source spectrally encoded scanning laser ophthalmoscopy and optical coherence tomography. Complementary en face images enabled orientation and coregistration with the widefield surgical microscope view while OCT imaging enabled depth-resolved visualization of surgical instrument positions relative to anatomic structures-of-interest. In addition, we demonstrated novel integrated segmentation overlays for augmented-reality surgical guidance. Unfortunately, our previous system lacked the resolution and optical throughput for in vivo retinal imaging and necessitated removal of cornea and lens. These limitations were predominately a result of optical aberrations from imaging through a shared surgical microscope objective lens, which was modeled as a paraxial surface. Here, we present an optimized intraoperative spectrally encoded coherence tomography and reflectometry (iSECTR) system. We use a novel lens characterization method to develop an accurate model of surgical microscope objective performance and balance out inherent aberrations using iSECTR relay optics. Using this system, we demonstrate in vivo multimodal ophthalmic imaging through a surgical microscope

Automated adaptive inference of phenomenological dynamical models.

PubMed

Daniels, Bryan C; Nemenman, Ilya

2015-08-21

Dynamics of complex systems is often driven by large and intricate networks of microscopic interactions, whose sheer size obfuscates understanding. With limited experimental data, many parameters of such dynamics are unknown, and thus detailed, mechanistic models risk overfitting and making faulty predictions. At the other extreme, simple ad hoc models often miss defining features of the underlying systems. Here we develop an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the available data. Such adaptive models produce accurate predictions even when microscopic details are unknown. The approach is computationally tractable, even for a relatively large number of dynamical variables. Using simulated data, it correctly infers the phase space structure for planetary motion, avoids overfitting in a biological signalling system and produces accurate predictions for yeast glycolysis with tens of data points and over half of the interacting species unobserved.

Relating the microscopic rules in coalescence-fragmentation models to the cluster-size distribution

NASA Astrophysics Data System (ADS)

Ruszczycki, B.; Burnett, B.; Zhao, Z.; Johnson, N. F.

2009-11-01

Coalescence-fragmentation problems are now of great interest across the physical, biological, and social sciences. They are typically studied from the perspective of rate equations, at the heart of which are the rules used for coalescence and fragmentation. Here we discuss how changes in these microscopic rules affect the macroscopic cluster-size distribution which emerges from the solution to the rate equation. Our analysis elucidates the crucial role that the fragmentation rule can play in such dynamical grouping models. We focus our discussion on two well-known models whose fragmentation rules lie at opposite extremes. In particular, we provide a range of generalizations and new analytic results for the well-known model of social group formation developed by Eguíluz and Zimmermann, [Phys. Rev. Lett. 85, 5659 (2000)]. We develop analytic perturbation treatments of this original model, and extend the analytic analysis to the treatment of growing and declining populations.

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.

Connections between the dynamical symmetries in the microscopic shell model

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

Georgieva, A. I., E-mail: anageorg@issp.bas.bg; Drumev, K. P.

2016-03-25

The dynamical symmetries of the microscopic shell model appear as the limiting cases of a symmetry adapted Pairing-Plus-Quadrupole Model /PQM/, with a Hamiltonian containing isoscalar and isovector pairing and quadrupole interactions. We establish a correspondence between each of the three types of pairing bases and Elliott’s SU(3) basis, that describes collective rotation of nuclear systems with quadrupole deformation. It is derived from their complementarity to the same LS coupling chain of the shell model number conserving algebra. The probability distribution of the S U(3) basis states within the pairing eigenstates is also obtained through a numerical diagonalization of the PQMmore » Hamiltonian in each limit. We introduce control parameters, which define the phase diagram of the model and determine the role of each term of the Hamiltonian in the correct reproduction of the experimental data for the considered nuclei.« less

Automated adaptive inference of phenomenological dynamical models

PubMed Central

Daniels, Bryan C.; Nemenman, Ilya

2015-01-01

Dynamics of complex systems is often driven by large and intricate networks of microscopic interactions, whose sheer size obfuscates understanding. With limited experimental data, many parameters of such dynamics are unknown, and thus detailed, mechanistic models risk overfitting and making faulty predictions. At the other extreme, simple ad hoc models often miss defining features of the underlying systems. Here we develop an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the available data. Such adaptive models produce accurate predictions even when microscopic details are unknown. The approach is computationally tractable, even for a relatively large number of dynamical variables. Using simulated data, it correctly infers the phase space structure for planetary motion, avoids overfitting in a biological signalling system and produces accurate predictions for yeast glycolysis with tens of data points and over half of the interacting species unobserved. PMID:26293508

SPY: A new scission point model based on microscopic ingredients to predict fission fragments properties

NASA Astrophysics Data System (ADS)

Lemaître, J.-F.; Dubray, N.; Hilaire, S.; Panebianco, S.; Sida, J.-L.

2013-12-01

Our purpose is to determine fission fragments characteristics in a framework of a scission point model named SPY for Scission Point Yields. This approach can be considered as a theoretical laboratory to study fission mechanism since it gives access to the correlation between the fragments properties and their nuclear structure, such as shell correction, pairing, collective degrees of freedom, odd-even effects. Which ones are dominant in final state? What is the impact of compound nucleus structure? The SPY model consists in a statistical description of the fission process at the scission point where fragments are completely formed and well separated with fixed properties. The most important property of the model relies on the nuclear structure of the fragments which is derived from full quantum microscopic calculations. This approach allows computing the fission final state of extremely exotic nuclei which are inaccessible by most of the fission model available on the market.

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.

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...

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.

Computational Neuroscience.

ERIC Educational Resources Information Center

Sejnowski, Terrence J.; And Others

1988-01-01

Describes the use of brain models to connect the microscopic level accessible by molecular and cellular techniques with the systems level accessible by the study of behavior. Discusses classes of brain models, and specific examples of such models. Evaluates the strengths and weaknesses of using brain modelling to understand human brain function.…

Design and Implementation of Harmful Algal Bloom Diagnosis System Based on J2EE Platform

NASA Astrophysics Data System (ADS)

Guo, Chunfeng; Zheng, Haiyong; Ji, Guangrong; Lv, Liang

According to the shortcomings which are time consuming and laborious of the traditional HAB (Harmful Algal Bloom) diagnosis by the experienced experts using microscope, all kinds of methods and technologies to identify HAB emerged such as microscopic images, molecular biology, characteristics of pigments analysis, fluorescence spectra, inherent optical properties, etc. This paper proposes the design and implementation of a web-based diagnosis system integrating the popular methods for HAB identification. This system is designed with J2EE platform based on MVC (Model-View-Controller) model as well as technologies such as JSP, Servlets, EJB and JDBC.

Effects of bulk viscosity and hadronic rescattering in heavy ion collisions at energies available at the BNL Relativistic Heavy Ion Collider and at the CERN Large Hadron Collider

NASA Astrophysics Data System (ADS)

Ryu, Sangwook; Paquet, Jean-François; Shen, Chun; Denicol, Gabriel; Schenke, Björn; Jeon, Sangyong; Gale, Charles

2018-03-01

We describe ultrarelativistic heavy ion collisions at the BNL Relativistic Heavy Ion Collider and the CERN Large Hadron Collider with a hybrid model using the IP-Glasma model for the earliest stage and viscous hydrodynamics and microscopic transport for the later stages of the collision. We demonstrate that within this framework the bulk viscosity of the plasma plays an important role in describing the experimentally observed radial flow and azimuthal anisotropy simultaneously. We further investigate the dependence of observables on the temperature below which we employ the microscopic transport description.

A microscopic model of the Stokes-Einstein relation in arbitrary dimension.

PubMed

Charbonneau, Benoit; Charbonneau, Patrick; Szamel, Grzegorz

2018-06-14

The Stokes-Einstein relation (SER) is one of the most robust and widely employed results from the theory of liquids. Yet sizable deviations can be observed for self-solvation, which cannot be explained by the standard hydrodynamic derivation. Here, we revisit the work of Masters and Madden [J. Chem. Phys. 74, 2450-2459 (1981)], who first solved a statistical mechanics model of the SER using the projection operator formalism. By generalizing their analysis to all spatial dimensions and to partially structured solvents, we identify a potential microscopic origin of some of these deviations. We also reproduce the SER-like result from the exact dynamics of infinite-dimensional fluids.

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.

From atoms to steps: The microscopic origins of crystal evolution

NASA Astrophysics Data System (ADS)

Patrone, Paul N.; Einstein, T. L.; Margetis, Dionisios

2014-07-01

The Burton-Cabrera-Frank (BCF) theory of crystal growth has been successful in describing a wide range of phenomena in surface physics. Typical crystal surfaces are slightly misoriented with respect to a facet plane; thus, the BCF theory views such systems as composed of staircase-like structures of steps separating terraces. Adsorbed atoms (adatoms), which are represented by a continuous density, diffuse on terraces, and steps move by absorbing or emitting these adatoms. Here we shed light on the microscopic origins of the BCF theory by deriving a simple, one-dimensional (1D) version of the theory from an atomistic, kinetic restricted solid-on-solid (KRSOS) model without external material deposition. We define the time-dependent adatom density and step position as appropriate ensemble averages in the KRSOS model, thereby exposing the non-equilibrium statistical mechanics origins of the BCF theory. Our analysis reveals that the BCF theory is valid in a low adatom-density regime, much in the same way that an ideal gas approximation applies to dilute gasses. We find conditions under which the surface remains in a low-density regime and discuss the microscopic origin of corrections to the BCF model.

Towards more accurate and reliable predictions for nuclear applications

NASA Astrophysics Data System (ADS)

Goriely, Stephane; Hilaire, Stephane; Dubray, Noel; Lemaître, Jean-François

2017-09-01

The need for nuclear data far from the valley of stability, for applications such as nuclear astrophysics or future nuclear facilities, challenges the robustness as well as the predictive power of present nuclear models. Most of the nuclear data evaluation and prediction are still performed on the basis of phenomenological nuclear models. For the last decades, important progress has been achieved in fundamental nuclear physics, making it now feasible to use more reliable, but also more complex microscopic or semi-microscopic models in the evaluation and prediction of nuclear data for practical applications. Nowadays mean-field models can be tuned at the same level of accuracy as the phenomenological models, renormalized on experimental data if needed, and therefore can replace the phenomenological inputs in the evaluation of nuclear data. The latest achievements to determine nuclear masses within the non-relativistic HFB approach, including the related uncertainties in the model predictions, are discussed. Similarly, recent efforts to determine fission observables within the mean-field approach are described and compared with more traditional existing models.

Foveal light exposure is increased at the time of removal of silicone oil with the potential for phototoxicity.

PubMed

Dogramaci, Mahmut; Williams, Katie; Lee, Ed; Williamson, Tom H

2013-01-01

There is sudden and dramatic visual function deterioration in 1-10 % of eyes filled with silicone oil at the time of removal of silicon oil. Transmission of high-energy blue light is increased in eyes filled with silicone oil. We sought to identify if increased foveal light exposure is a potential factor in the pathophysiology of the visual loss at the time of removal of silicone oil. A graphic ray tracing computer program and laboratory models were used to determine the effect of the intraocular silicone oil bubble size on the foveal illuminance at the time of removal of silicone oil under direct microscope light. The graphic ray tracing computer program revealed a range of optical vignetting effects created by different sizes of silicone oil bubble within the vitreous cavity giving rise to an uneven macular illumination. The laboratory model was used to quantify the variation of illuminance at the foveal region with different sizes of silicone oil bubble with in the vitreous cavity at the time of removal of silicon oil under direct microscope light. To substantiate the hypothesis of the light toxicity during removal of silicone oil, The outcome of oil removal procedures performed under direct microscope illumination in compared to those performed under blocked illumination. The computer program showed that the optical vignetting effect at the macula was dependent on the size of the intraocular silicone oil bubble. The laboratory eye model showed that the foveal illuminance followed a bell-shaped curve with 70 % greater illuminance demonstrated at with 50-60 % silicone oil fill. The clinical data identified five eyes with unexplained vision loss out of 114 eyes that had the procedure performed under direct microscope illumination compared to none out of 78 eyes that had the procedure under blocked illumination. Foveal light exposure, and therefore the potential for phototoxicity, is transiently increased at the time of removal of silicone oil. This is due to uneven macular illumination resulting from the optical vignetting effect of different silicone oil bubble sizes. The increase in foveal light exposure may be significant when the procedure is performed under bright operating microscope light on already stressed photoreceptors of an eye filled with silicon oil. We advocate the use of precautions, such as central shadow filter on the operating microscope light source to reduce foveal light exposure and the risk of phototoxicity at the time of removal of silicone oil. The graphic ray tracing computer program used in this study shows promise in eye modeling for future studies.

Comparing microscopic activity-based and traditional models of travel demand : an Austin area case study

DOT National Transportation Integrated Search

2007-09-01

Two competing approaches to travel demand modeling exist today. The more traditional 4-step travel demand models rely on aggregate demographic data at a traffic analysis zone (TAZ) level. Activity-based microsimulation methods employ more robus...

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

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.

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.

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....

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.

SPY: a new scission-point model based on microscopic inputs to predict fission fragment properties

NASA Astrophysics Data System (ADS)

Panebianco, Stefano; Dubray, Nöel; Goriely, Stéphane; Hilaire, Stéphane; Lemaître, Jean-François; Sida, Jean-Luc

2014-04-01

Despite the difficulty in describing the whole fission dynamics, the main fragment characteristics can be determined in a static approach based on a so-called scission-point model. Within this framework, a new Scission-Point model for the calculations of fission fragment Yields (SPY) has been developed. This model, initially based on the approach developed by Wilkins in the late seventies, consists in performing a static energy balance at scission, where the two fragments are supposed to be completely separated so that their macroscopic properties (mass and charge) can be considered as fixed. Given the knowledge of the system state density, averaged quantities such as mass and charge yields, mean kinetic and excitation energy can then be extracted in the framework of a microcanonical statistical description. The main advantage of the SPY model is the introduction of one of the most up-to-date microscopic descriptions of the nucleus for the individual energy of each fragment and, in the future, for their state density. These quantities are obtained in the framework of HFB calculations using the Gogny nucleon-nucleon interaction, ensuring an overall coherence of the model. Starting from a description of the SPY model and its main features, a comparison between the SPY predictions and experimental data will be discussed for some specific cases, from light nuclei around mercury to major actinides. Moreover, extensive predictions over the whole chart of nuclides will be discussed, with particular attention to their implication in stellar nucleosynthesis. Finally, future developments, mainly concerning the introduction of microscopic state densities, will be briefly discussed.

Particle Interactions Mediated by Dynamical Networks: Assessment of Macroscopic Descriptions

NASA Astrophysics Data System (ADS)

Barré, J.; Carrillo, J. A.; Degond, P.; Peurichard, D.; Zatorska, E.

2018-02-01

We provide a numerical study of the macroscopic model of Barré et al. (Multiscale Model Simul, 2017, to appear) derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodeling process is very fast, the macroscopic model takes the form of a single aggregation-diffusion equation for the density of particles. The theoretical study of the macroscopic model gives precise criteria for the phase transitions of the steady states, and in the one-dimensional case, we show numerically that the stationary solutions of the microscopic model undergo the same phase transitions and bifurcation types as the macroscopic model. In the two-dimensional case, we show that the numerical simulations of the macroscopic model are in excellent agreement with the predicted theoretical values. This study provides a partial validation of the formal derivation of the macroscopic model from a microscopic formulation and shows that the former is a consistent approximation of an underlying particle dynamics, making it a powerful tool for the modeling of dynamical networks at a large scale.

Particle Interactions Mediated by Dynamical Networks: Assessment of Macroscopic Descriptions.

PubMed

Barré, J; Carrillo, J A; Degond, P; Peurichard, D; Zatorska, E

2018-01-01

We provide a numerical study of the macroscopic model of Barré et al. (Multiscale Model Simul, 2017, to appear) derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodeling process is very fast, the macroscopic model takes the form of a single aggregation-diffusion equation for the density of particles. The theoretical study of the macroscopic model gives precise criteria for the phase transitions of the steady states, and in the one-dimensional case, we show numerically that the stationary solutions of the microscopic model undergo the same phase transitions and bifurcation types as the macroscopic model. In the two-dimensional case, we show that the numerical simulations of the macroscopic model are in excellent agreement with the predicted theoretical values. This study provides a partial validation of the formal derivation of the macroscopic model from a microscopic formulation and shows that the former is a consistent approximation of an underlying particle dynamics, making it a powerful tool for the modeling of dynamical networks at a large scale.

Micro vs. macrodiscectomy: Does use of the microscope reduce complication rates?

PubMed

Murphy, Meghan E; Hakim, Jeffrey S; Kerezoudis, Panagiotis; Alvi, Mohammed Ali; Ubl, Daniel S; Habermann, Elizabeth B; Bydon, Mohamad

2017-01-01

A single level discectomy is one of the most common procedures performed by spine surgeons. While some practitioners utilize the microscope, others do not. We postulate improved visualization with an intraoperative microscope decreases complications and inferior outcomes. A multicenter surgical registry was utilized for this retrospective cohort analysis. Patients with degenerative spinal diagnoses undergoing elective single level discectomies from 2010 to 2014 were included. Univariate analysis was performed comparing demographics, patient characteristics, operative data, and outcomes for discectomies performed with and without a microscope. Multivariable logistic regression analysis was then applied to compare outcomes of micro- and macrodiscectomies. Query of the registry yielded 23,583 patients meeting inclusion criteria. On univariate analysis the microscope was used in a greater proportion of the oldest age group as well as Hispanic white patients. Patients with any functional dependency, history of congestive heart failure, chronic corticosteroid use, or anemia (hematocrit<35%) also had greater proportions of microdiscectomies. Thoracic region discectomies more frequently involved use of the microscope than cervical or lumbar discectomies (25.0% vs. 16.4% and 13.0%, respectively, p<0.001). Median operative time (IQR) was increased in microscope cases [80min (60, 108) vs. 74min (54, 102), p<0.001]. Of the patients that required reoperation within 30days, 2.5% of them had undergone a microdiscectomy compared to 1.9% who had undergone a macrodiscectomy, p=0.044. On multivariable analysis, microdiscectomies were more likely to have an operative time in the top quartile of discectomy operative times, ≥103min (OR 1.256, 95% CI 1.151-1.371, p<0.001). In regards to other multivariable outcome models for any complication, surgical site infection, dural tears, reoperation, and readmission, no significant association with microdiscectomy was found. The use of the microscope was found to significantly increase the odds of longer operative time, but not influence rates of postoperative complications. Thus, without evidence from this study that the microscope decreases complications, the use of the microscope should be at the surgeon's discretion, validating the use of both macro and micro approaches to discectomy as acceptable standards of care. Copyright © 2016 Elsevier B.V. All rights reserved.

Augmented microscopy with near-infrared fluorescence detection

NASA Astrophysics Data System (ADS)

Watson, Jeffrey R.; Martirosyan, Nikolay; Skoch, Jesse; Lemole, G. Michael; Anton, Rein; Romanowski, Marek

2015-03-01

Near-infrared (NIR) fluorescence has become a frequently used intraoperative technique for image-guided surgical interventions. In procedures such as cerebral angiography, surgeons use the optical surgical microscope for the color view of the surgical field, and then switch to an electronic display for the NIR fluorescence images. However, the lack of stereoscopic, real-time, and on-site coregistration adds time and uncertainty to image-guided surgical procedures. To address these limitations, we developed the augmented microscope, whereby the electronically processed NIR fluorescence image is overlaid with the anatomical optical image in real-time within the optical path of the microscope. In vitro, the augmented microscope can detect and display indocyanine green (ICG) concentrations down to 94.5 nM, overlaid with the anatomical color image. We prepared polyacrylamide tissue phantoms with embedded polystyrene beads, yielding scattering properties similar to brain matter. In this model, 194 μM solution of ICG was detectable up to depths of 5 mm. ICG angiography was then performed in anesthetized rats. A dynamic process of ICG distribution in the vascular system overlaid with anatomical color images was observed and recorded. In summary, the augmented microscope demonstrates NIR fluorescence detection with superior real-time coregistration displayed within the ocular of the stereomicroscope. In comparison to other techniques, the augmented microscope retains full stereoscopic vision and optical controls including magnification and focus, camera capture, and multiuser access. Augmented microscopy may find application in surgeries where the use of traditional microscopes can be enhanced by contrast agents and image guided delivery of therapeutics, including oncology, neurosurgery, and ophthalmology.

Comparative study of electronic structure and microscopic model of SrMn3P4O14 and Sr3Cu3(PO4)4

NASA Astrophysics Data System (ADS)

Khanam, Dilruba; Rahaman, Badiur

2018-05-01

We present the first principle density functional calculations to figure out the comparative study of the underlying spin model SrMn3P4O14 and Sr3Cu3(PO4)4. We explicitly discuss the nature of the exchange paths and provide quantitative estimates of magnetic exchange couplings for both compounds. A microscopic modeling based on analysis of the electronic structure of both systems puts them in the interesting class of weakly coupled trimer units, which makes chains S=5/2 for SrMn3P4O14 and S=1/2 for Sr3Cu3(PO4)4 that are in turn weakly coupled to each other.

Scaling of chaos in strongly nonlinear lattices.

PubMed

Mulansky, Mario

2014-06-01

Although it is now understood that chaos in complex classical systems is the foundation of thermodynamic behavior, the detailed relations between the microscopic properties of the chaotic dynamics and the macroscopic thermodynamic observations still remain mostly in the dark. In this work, we numerically analyze the probability of chaos in strongly nonlinear Hamiltonian systems and find different scaling properties depending on the nonlinear structure of the model. We argue that these different scaling laws of chaos have definite consequences for the macroscopic diffusive behavior, as chaos is the microscopic mechanism of diffusion. This is compared with previous results on chaotic diffusion [M. Mulansky and A. Pikovsky, New J. Phys. 15, 053015 (2013)], and a relation between microscopic chaos and macroscopic diffusion is established.

A Tissue Engineered Model of Aging: Interdependence and Cooperative Effects in Failing Tissues.

PubMed

Acun, A; Vural, D C; Zorlutuna, P

2017-07-11

Aging remains a fundamental open problem in modern biology. Although there exist a number of theories on aging on the cellular scale, nearly nothing is known about how microscopic failures cascade to macroscopic failures of tissues, organs and ultimately the organism. The goal of this work is to bridge microscopic cell failure to macroscopic manifestations of aging. We use tissue engineered constructs to control the cellular-level damage and cell-cell distance in individual tissues to establish the role of complex interdependence and interactions between cells in aging tissues. We found that while microscopic mechanisms drive aging, the interdependency between cells plays a major role in tissue death, providing evidence on how cellular aging is connected to its higher systemic consequences.

Tunneling rates in electron transport through double-barrier molecular junctions in a scanning tunneling microscope

PubMed Central

Nazin, G. V.; Wu, S. W.; Ho, W.

2005-01-01

The scanning tunneling microscope enables atomic-scale measurements of electron transport through individual molecules. Copper phthalocyanine and magnesium porphine molecules adsorbed on a thin oxide film grown on the NiAl(110) surface were probed. The single-molecule junctions contained two tunneling barriers, vacuum gap, and oxide film. Differential conductance spectroscopy shows that electron transport occurs via vibronic states of the molecules. The intensity of spectral peaks corresponding to the individual vibronic states depends on the relative electron tunneling rates through the two barriers of the junction, as found by varying the vacuum gap tunneling rate by changing the height of the scanning tunneling microscope tip above the molecule. A simple, sequential tunneling model explains the observed trends. PMID:15956189

Tunneling rates in electron transport through double-barrier molecular junctions in a scanning tunneling microscope.

PubMed

Nazin, G V; Wu, S W; Ho, W

2005-06-21

The scanning tunneling microscope enables atomic-scale measurements of electron transport through individual molecules. Copper phthalocyanine and magnesium porphine molecules adsorbed on a thin oxide film grown on the NiAl(110) surface were probed. The single-molecule junctions contained two tunneling barriers, vacuum gap, and oxide film. Differential conductance spectroscopy shows that electron transport occurs via vibronic states of the molecules. The intensity of spectral peaks corresponding to the individual vibronic states depends on the relative electron tunneling rates through the two barriers of the junction, as found by varying the vacuum gap tunneling rate by changing the height of the scanning tunneling microscope tip above the molecule. A simple, sequential tunneling model explains the observed trends.

Proton scattering by short lived sulfur isotopes

NASA Astrophysics Data System (ADS)

Maréchal, F.; Suomijärvi, T.; Blumenfeld, Y.; Azhari, A.; Bauge, E.; Bazin, D.; Brown, J. A.; Cottle, P. D.; Delaroche, J. P.; Fauerbach, M.; Girod, M.; Glasmacher, T.; Hirzebruch, S. E.; Jewell, J. K.; Kelley, J. H.; Kemper, K. W.; Mantica, P. F.; Morrissey, D. J.; Riley, L. A.; Scarpaci, J. A.; Scheit, H.; Steiner, M.

1999-09-01

Elastic and inelastic proton scattering has been measured in inverse kinematics on the unstable nucleus 40S. A phenomenological distorted wave Born approximation analysis yields a quadrupole deformation parameter β2=0.35+/-0.05 for the 2+1 state. Consistent phenomenological and microscopic proton scattering analyses have been applied to all even-even sulfur isotopes from A=32 to A=40. The second analysis used microscopic collective model densities and a modified Jeukenne-Lejeune-Mahaux nucleon-nucleon effective interaction. This microscopic analysis suggests the presence of a neutron skin in the heavy sulfur isotopes. The analysis is consistent with normalization values for λv and λw of 0.95 for both the real and imaginary parts of the Jeukenne-Lejeune-Mahaux potential.

Scanning electron microscopic appearance of rat otocyst of the twelfth postcoital day: elaboration of a method.

PubMed

Marovitz, W F; Khan, K M

1977-01-01

A method for removal, fixation, microdissection, and drying of early rat otocyst for examination by the scanning electron microscope is elaborated. Tissues were dissected, fixed as for conventional transmission electron microscopy and dried by critical point evaporation using amylacetate as the transitional fluid and carbon dioxide as the pressure head. Otocysts were either dissected at the time of initial fixation, or subsequent to drying. The otocyst of the 12th postcoital day was used as a model system in this preliminary report. Critical point drying retained the overall configuration and the fine ultrastructural detail of the otocyst. The interior otocystic surface was visualized and cilia bearing cells of the luminal surface were identified. Most if not all of these cells had a comspicuous, but short kinocillum which terminated in an ovoid bulb. The scanning electron microscopic appearance was correlated to the transmission electron microscopic image seen in the second paper in this Supplement.

Optical forces, torques, and force densities calculated at a microscopic level using a self-consistent hydrodynamics method

NASA Astrophysics Data System (ADS)

Ding, Kun; Chan, C. T.

2018-04-01

The calculation of optical force density distribution inside a material is challenging at the nanoscale, where quantum and nonlocal effects emerge and macroscopic parameters such as permittivity become ill-defined. We demonstrate that the microscopic optical force density of nanoplasmonic systems can be defined and calculated using the microscopic fields generated using a self-consistent hydrodynamics model that includes quantum, nonlocal, and retardation effects. We demonstrate this technique by calculating the microscopic optical force density distributions and the optical binding force induced by external light on nanoplasmonic dimers. This approach works even in the limit when the nanoparticles are close enough to each other so that electron tunneling occurs, a regime in which classical electromagnetic approach fails completely. We discover that an uneven distribution of optical force density can lead to a light-induced spinning torque acting on individual particles. The hydrodynamics method offers us an accurate and efficient approach to study optomechanical behavior for plasmonic systems at the nanoscale.

In vivo imaging of the Drosophila Melanogaster heart using a novel optical coherence tomography microscope

NASA Astrophysics Data System (ADS)

Izatt, Susan D.; Choma, Michael A.; Israel, Steven; Wessells, Robert J.; Bodmer, Rolf; Izatt, Joseph A.

2005-03-01

Real time in vivo optical coherence tomography (OCT) imaging of the adult fruit fly Drosophila melanogaster heart using a newly designed OCT microscope allows accurate assessment of cardiac anatomy and function. D. melanogaster has been used extensively in genetic research for over a century, but in vivo evaluation of the heart has been limited by available imaging technology. The ability to assess phenotypic changes with micrometer-scale resolution noninvasively in genetic models such as D. melanogaster is needed in the advancing fields of developmental biology and genetics. We have developed a dedicated small animal OCT imaging system incorporating a state-of-the-art, real time OCT scanner integrated into a standard stereo zoom microscope which allows for simultaneous OCT and video imaging. System capabilities include A-scan, B-scan, and M-scan imaging as well as automated 3D volumetric acquisition and visualization. Transverse and sagittal B-mode scans of the four chambered D. melanogaster heart have been obtained with the OCT microscope and are consistent with detailed anatomical studies from the literature. Further analysis by M-mode scanning is currently under way to assess cardiac function as a function of age and sex by determination of shortening fraction and ejection fraction. These studies create control cardiac data on the wild type D. melanogaster, allowing subsequent evaluation of phenotypic cardiac changes in this model after regulated genetic mutation.

Microscopic contact area and friction between medical textiles and skin.

PubMed

Derler, S; Rotaru, G-M; Ke, W; El Issawi-Frischknecht, L; Kellenberger, P; Scheel-Sailer, A; Rossi, R M

2014-10-01

The mechanical contact between medical textiles and skin is relevant in the health care for patients with vulnerable skin or chronic wounds. In order to gain new insights into the skin-textile contact on the microscopic level, the 3D surface topography of a normal and a new hospital bed sheet with a regular surface structure was measured using a digital microscope. The topographic data was analysed concerning material distribution and real contact area against smooth surfaces as a function of surface deformations. For contact conditions that are relevant for the skin of patients lying in a hospital bed it was found that the order of magnitude of the ratio of real and apparent contact area between textiles and skin or a mechanical skin model lies between 0.02 and 0.1 and that surface deformations, i.e. penetration of the textile surface asperities into skin or a mechanical skin model, range from 10 to 50µm. The performed analyses of textile 3D surface topographies and comparisons with previous friction measurement results provided information on the relationship between microscopic surface properties and macroscopic friction behaviour of medical textiles. In particular, the new bed sheet was found to be characterised by a trend towards a smaller microscopic contact area (up to a factor of two) and by a larger free interfacial volume (more than a factor of two) in addition to a 1.5 times lower shear strength when in contact with counter-surfaces. The applied methods can be useful to develop improved and skin-adapted materials and surfaces for medical applications. Copyright © 2014 Elsevier Ltd. All rights reserved.

In vivo cellular imaging with microscopes enabled by MEMS scanners

NASA Astrophysics Data System (ADS)

Ra, Hyejun

High-resolution optical imaging plays an important role in medical diagnosis and biomedical research. Confocal microscopy is a widely used imaging method for obtaining cellular and sub-cellular images of biological tissue in reflectance and fluorescence modes. Its characteristic optical sectioning capability also enables three-dimensional (3-D) image reconstruction. However, its use has mostly been limited to excised tissues due to the requirement of high numerical aperture (NA) lenses for cellular resolution. Microscope miniaturization can enable in vivo imaging to make possible early cancer diagnosis and biological studies in the innate environment. In this dissertation, microscope miniaturization for in vivo cellular imaging is presented. The dual-axes confocal (DAC) architecture overcomes limitations of the conventional single-axis confocal (SAC) architecture to allow for miniaturization with high resolution. A microelectromechanical systems (MEMS) scanner is the central imaging component that is key in miniaturization of the DAC architecture. The design, fabrication, and characterization of the two-dimensional (2-D) MEMS scanner are presented. The gimbaled MEMS scanner is fabricated on a double silicon-on-insulator (SOI) wafer and is actuated by self-aligned vertical electrostatic combdrives. The imaging performance of the MEMS scanner in a DAC configuration is shown in a breadboard microscope setup, where reflectance and fluorescence imaging is demonstrated. Then, the MEMS scanner is integrated into a miniature DAC microscope. The whole imaging system is integrated into a portable unit for research in small animal models of human biology and disease. In vivo 3-D imaging is demonstrated on mouse skin models showing gene transfer and siRNA silencing. The siRNA silencing process is sequentially imaged in one mouse over time.

Interacting Boson Model and nucleons

NASA Astrophysics Data System (ADS)

Otsuka, Takaharu

2012-10-01

An overview on the recent development of the microscopic derivation of the Interacting Boson Model is presented with some remarks not found elsewhere. The OAI mapping is reviewed very briefly, including the basic correspondence from nucleon-pair to boson. The new fermionboson mapping method is introduced, where intrinsic states of nucleons and bosons for a wide variation of shapes play an important role. Nucleon intrinsic states are obtained from mean field models, which is Skyrme model in examples to be shown. This method generates IBM-2 Hamiltonian which can describe and predict various situations of quadrupole collective states, including U(5), SU(3), O(6) and E(5) limits. The method is extended so that rotational response (cranking) can be handled, which enables us to describe rotational bands of strongly deformed nuclei. Thus, we have obtained a unified framework for the microscopic derivation of the IBM covering all known situations of quadrupole collectivity at low energy.

Cellular automaton model for molecular traffic jams

NASA Astrophysics Data System (ADS)

Belitsky, V.; Schütz, G. M.

2011-07-01

We consider the time evolution of an exactly solvable cellular automaton with random initial conditions both in the large-scale hydrodynamic limit and on the microscopic level. This model is a version of the totally asymmetric simple exclusion process with sublattice parallel update and thus may serve as a model for studying traffic jams in systems of self-driven particles. We study the emergence of shocks from the microscopic dynamics of the model. In particular, we introduce shock measures whose time evolution we can compute explicitly, both in the thermodynamic limit and for open boundaries where a boundary-induced phase transition driven by the motion of a shock occurs. The motion of the shock, which results from the collective dynamics of the exclusion particles, is a random walk with an internal degree of freedom that determines the jump direction. This type of hopping dynamics is reminiscent of some transport phenomena in biological systems.

[Histologic study on impeding leukoplakia carcinogenesis of golden hamster cheek pouch about Erigeron breviscapus (Vant) Hand-Mazz].

PubMed

Zhou, C T; Zhong, W J; Hua, L; Hu, H F; Jin, Z G

2000-06-01

To observe the effect of Erigeron breviscapus (Vant) Hand Mazz (HEr) in impeding oral leukoplakia carcinogenesis, and to seek effective Chinese herb medicine that can impede precarcinoma of oral mucosas. 132 golden hamsters were randomly divided into model group (60 animals), HEr group (60 animals), and control group 12 animals. Salley's leukoplakia carcinogenesis model of golden hamster cheek pouch was used in this study. HEr was injected into the stomach to impede evolution of carcinogenesis. Pathological specimens were observed via naked eye and light microscope between model group and HEr group. Results were compared. Observation via naked-eye showed that leukoplakia rate of HEr group (18.2%) was lower than that of model group (27.3%). Observation via light microscope showed that carcinogenesis rate descended one fold and displasia rate descended 0.4 fold in HEr group. HEr has exact effect in impeding leukoplakia carcinogenesis.

ECUT: Energy Conversion and Utilization Technologies program. Heterogeneous catalysis modeling program concept

NASA Technical Reports Server (NTRS)

Voecks, G. E.

1983-01-01

Insufficient theoretical definition of heterogeneous catalysts is the major difficulty confronting industrial suppliers who seek catalyst systems which are more active, selective, and stable than those currently available. In contrast, progress was made in tailoring homogeneous catalysts to specific reactions because more is known about the reaction intermediates promoted and/or stabilized by these catalysts during the course of reaction. However, modeling heterogeneous catalysts on a microscopic scale requires compiling and verifying complex information on reaction intermediates and pathways. This can be achieved by adapting homogeneous catalyzed reaction intermediate species, applying theoretical quantum chemistry and computer technology, and developing a better understanding of heterogeneous catalyst system environments. Research in microscopic reaction modeling is now at a stage where computer modeling, supported by physical experimental verification, could provide information about the dynamics of the reactions that will lead to designing supported catalysts with improved selectivity and stability.

Influence of surface topology and electrostatic potential on water/electrode systems

NASA Astrophysics Data System (ADS)

Siepmann, J. Ilja; Sprik, Michiel

1995-01-01

We have used the classical molecular dynamics technique to simulate the ordering of a water film adsorbed on an atomic model of a tip of a scanning tunneling microscope approaching a planar metal surface. For this purpose, we have developed a classical model for the water-substrate interactions that solely depends on the coordinates of the particles and does not require the definition of geometrically smooth boundary surfaces or image planes. The model includes both an electrostatic induction for the metal atoms (determined by means of an extended Lagrangian technique) and a site-specific treatment of the water-metal chemisorption. As a validation of the model we have investigated the structure of water monolayers on metal substrates of various topology [the (111), (110), and (100) crystallographic faces] and composition (Pt, Ag, Cu, and Ni), and compared the results to experiments. The modeling of the electrostatic induction is compatible with a finite external potential imposed on the metal. This feature is used to investigate the structural rearrangements of the water bilayer between the pair of scanning tunneling microscope electrodes in response to an applied external voltage difference. We find significant asymmetry in the dependence on the sign of the applied voltage. Another result of the calculation is an estimate of the perturbation to the work function caused by the wetting film. For the conditions typical for operation of a scanning tunneling microscope probe, the change in the work function is found to be comparable to the applied voltage (a few hundred millivolts).

Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters.

PubMed

Chapman, Michael S; Trzynka, Andrew; Chapman, Brynmor K

2013-04-01

When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5-2.5 Å at resolutions of 4.5-6 Å. Copyright © 2013 Elsevier Inc. All rights reserved.

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.

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.

Mathematical model of a DIC position sensing system within an optical trap

NASA Astrophysics Data System (ADS)

Wulff, Kurt D.; Cole, Daniel G.; Clark, Robert L.

2005-08-01

The quantitative study of displacements and forces of motor proteins and processes that occur at the microscopic level and below require a high level of sensitivity. For optical traps, two techniques for position sensing have been accepted and used quite extensively: quadrant photodiodes and an interferometric position sensing technique based on DIC imaging. While quadrant photodiodes have been studied in depth and mathematically characterized, a mathematical characterization of the interferometric position sensor has not been presented to the authors' knowledge. The interferometric position sensing method works off of the DIC imaging capabilities of a microscope. Circularly polarized light is sent into the microscope and the Wollaston prism used for DIC imaging splits the beam into its orthogonal components, displacing them by a set distance determined by the user. The distance between the axes of the beams is set so the beams overlap at the specimen plane and effectively share the trapped microsphere. A second prism then recombines the light beams and the exiting laser light's polarization is measured and related to position. In this paper we outline the mathematical characterization of a microsphere suspended in an optical trap using a DIC position sensing method. The sensitivity of this mathematical model is then compared to the QPD model. The mathematical model of a microsphere in an optical trap can serve as a calibration curve for an experimental setup.

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.

Effects of bulk viscosity and hadronic rescattering in heavy ion collisions at energies available at the BNL Relativistic Heavy Ion Collider and at the CERN Large Hadron Collider

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

Ryu, Sangwook; Paquet, Jean-Francois; Shen, Chun

Here, we describe ultrarelativistic heavy ion collisions at the BNL Relativistic Heavy Ion Collider and the CERN Large Hadron Collider with a hybrid model using the IP-Glasma model for the earliest stage and viscous hydrodynamics and microscopic transport for the later stages of the collision. We demonstrate that within this framework the bulk viscosity of the plasma plays an important role in describing the experimentally observed radial flow and azimuthal anisotropy simultaneously. Finally, we further investigate the dependence of observables on the temperature below which we employ the microscopic transport description.

Microscopic models of non-radiative and high-current effects in LEDs: state of the art and future developments

NASA Astrophysics Data System (ADS)

Bertazzi, Francesco; Goano, Michele; Calciati, Marco; Zhou, Xiangyu; Ghione, Giovanni; Bellotti, Enrico

2014-02-01

Auger recombination is at the hearth of the debate on droop, the decline of the internal quantum efficiency at high injection levels. The theory of Auger recombination in quantum wells is reviewed. The proposed microscopic model is based on a full-Brillouin-zone description of the electronic structure obtained by nonlocal empirical pseudopotential calculations and the linear combination of bulk bands. The lack of momentum conservation along the confining direction in InGaN/GaN quantum wells enhances direct (i.e. phononless) Auger transitions, leading to Auger coefficients in the range of those predicted for phonon-dressed processes in bulk InGaN.

A new Brewster angle microscope

NASA Astrophysics Data System (ADS)

Lheveder, C.; Hénon, S.; Mercier, R.; Tissot, G.; Fournet, P.; Meunier, J.

1998-03-01

We present a new Brewster angle microscope for the study of very thin layers as thin as monolayers, using a custom-made objective. This objective avoids the drawbacks of the models existing at the present time. Its optical axis is perpendicular to the studied layer and consequently gives an image in focus in all the plane contrary to the existing models which give images in focus along a narrow strip. The objective allows one to obtain images with a good resolution (less than 1 μm) without scanning the surface, at the video frequency, allowing for dynamic studies. A large frontal distance associated with a very large aperture is obtained by using a large lens at the entrance of the objective.

Multiscale modelling and analysis of collective decision making in swarm robotics.

PubMed

Vigelius, Matthias; Meyer, Bernd; Pascoe, Geoffrey

2014-01-01

We present a unified approach to describing certain types of collective decision making in swarm robotics that bridges from a microscopic individual-based description to aggregate properties. Our approach encompasses robot swarm experiments, microscopic and probabilistic macroscopic-discrete simulations as well as an analytic mathematical model. Following up on previous work, we identify the symmetry parameter, a measure of the progress of the swarm towards a decision, as a fundamental integrated swarm property and formulate its time evolution as a continuous-time Markov process. Contrary to previous work, which justified this approach only empirically and a posteriori, we justify it from first principles and derive hard limits on the parameter regime in which it is applicable.

Effects of bulk viscosity and hadronic rescattering in heavy ion collisions at energies available at the BNL Relativistic Heavy Ion Collider and at the CERN Large Hadron Collider

DOE PAGES

Ryu, Sangwook; Paquet, Jean-Francois; Shen, Chun; ...

2018-03-15

Here, we describe ultrarelativistic heavy ion collisions at the BNL Relativistic Heavy Ion Collider and the CERN Large Hadron Collider with a hybrid model using the IP-Glasma model for the earliest stage and viscous hydrodynamics and microscopic transport for the later stages of the collision. We demonstrate that within this framework the bulk viscosity of the plasma plays an important role in describing the experimentally observed radial flow and azimuthal anisotropy simultaneously. Finally, we further investigate the dependence of observables on the temperature below which we employ the microscopic transport description.

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.

Development of a reactive burn model based on an explicit viscoplastic pore collapse model

NASA Astrophysics Data System (ADS)

Bouton, E.; Lefrançois, A.; Belmas, R.

2017-01-01

The aim of this study is to develop a reactive burn model based upon a microscopic hot spot model to compute the shock-initiation of pressed TATB high explosives. Such a model has been implemented in a lagrangian hydrodynamic code. In our calculations, 8 pore radii, ranging from 40 nm to 0.63 μm, have been taken into account and the porosity fraction associated to each void radius has been deduced from the Ultra-Small-Angle X-ray Scattering measurements (USAXS) for PBX-9502. The last parameter of our model is a burn rate that depends on three variables. The first two are the reaction progress variable and the lead shock pressure, the last one is the chemical reaction site number produced in the flow and calculated by the microscopic model. This burn rate has been calibrated by fitting pressure, velocity profiles and run distances to detonation. As the computed results are in close agreement with the measured ones, this model is able to perform a wide variety of numerical simulations including single, double shock waves and the desensitization phenomenon.

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 ...

Calibration of steady-state car-following models using macroscopic loop detector data.

DOT National Transportation Integrated Search

2010-05-01

The paper develops procedures for calibrating the steady-state component of various car following models using : macroscopic loop detector data. The calibration procedures are developed for a number of commercially available : microscopic traffic sim...

An Affordable Microsurgical Training System for a Beginning Neurosurgeon: How to Realize the Self-Training Laboratory.

PubMed

Chung, Sang-Bong; Ryu, Jiwook; Chung, Yeongu; Lee, Sung Ho; Choi, Seok Keun

2017-09-01

To provide detailed information about how to realize a self-training laboratory with cost-effective microsurgical instruments, especially pertinent for the novice trainee. Our training model is designed to allow the practice of the microsurgery skills in an efficient and cost-effective manner. A used stereoscopic microscope is prepared for microsurgical training. A sufficient working distance for microsurgical practice is obtained by attaching an auxiliary objective lens. The minimum instrument list includes 2 jeweler's forceps, iris scissors, and alligator clips. The iris scissors and alligator clip provide good alternatives to micro-scissors and microvascular clamp. The short time needed to set up the microscope and suture the gauze with micro-forceps makes the training model suitable for daily practice. It takes about 15 minutes to suture 10 neighboring fibers of the gauze with 10-0 nylon; thus, training can be completed more quickly. We have developed an inexpensive and efficient micro-anastomosis training system using a stereoscopic microscope and minimal micro-instruments. Especially useful for novice trainees, this system provides high accessibility for microsurgical training. Copyright © 2017 Elsevier Inc. All rights reserved.

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy.

PubMed Central

Pollanen, M. S.; Markiewicz, P.; Bergeron, C.; Goh, M. C.

1994-01-01

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures. Images Figure 1 PMID:8178938

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy.

PubMed

Pollanen, M S; Markiewicz, P; Bergeron, C; Goh, M C

1994-05-01

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures.

Electron Microscopic Analysis of Hippocampal Axo‐Somatic Synapses in a Chronic Stress Model for Depression

PubMed Central

Csabai, Dávid; Seress, László; Varga, Zsófia; Ábrahám, Hajnalka; Miseta, Attila; Wiborg, Ove

2016-01-01

ABSTRACT Stress can alter the number and morphology of excitatory synapses in the hippocampus, but nothing is known about the effect of stress on inhibitory synapses. Here, we used an animal model for depression, the chronic mild stress model, and quantified the number of perisomatic inhibitory neurons and their synapses. We found reduced density of parvalbumin‐positive (PV+) neurons in response to stress, while the density of cholecystokinin‐immunoreactive (CCK+) neurons was unaffected. We did a detailed electron microscopic analysis to quantify the frequency and morphology of perisomatic inhibitory synapses in the hippocampal CA1 area. We analyzed 1100 CA1 pyramidal neurons and 4800 perisomatic terminals in five control and four chronically stressed rats. In the control animals we observed the following parameters: Number of terminals/soma = 57; Number of terminals/100 µm cell perimeter = 10; Synapse/terminal ratio = 32%; Synapse number/100 terminal = 120; Average terminal length = 920nm. None of these parameters were affected by the stress exposure. Overall, these data indicate that despite the depressive‐like behavior and the decrease in the number of perisomatic PV+ neurons in the light microscopic preparations, the number of perisomatic inhibitory synapses on CA1 pyramidal cells was not affected by stress. In the electron microscope, PV+ neurons and the axon terminals appeared to be normal and we did not find any apoptotic or necrotic cells. This data is in sharp contrast to the remarkable remodeling of the excitatory synapses on spines that has been reported in response to stress and depressive‐like behavior. © 2016 The Authors Hippocampus Published by Wiley Periodicals, Inc. PMID:27571571

Monopole antenna in quantitative near-field microwave microscopy of planar structures

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

Reznik, Alexander N.; Korolyov, Sergey A.

We have developed an analytical model of a near-field microwave microscope based on a coaxial resonator with a sharpened tip probe. The probe interacts with a layered sample that features an arbitrary depth distribution of permittivity. The microscopic tip end with the accumulated charge is regarded as a monopole antenna radiating an electric field in near zone. The impedance of such an antenna is determined within a quasi-static approximation. The proposed model is used for calculating the sample-sensitive parameters of the microscope, specifically, resonance frequency f{sub 0} and quality factor Q{sub 0}, as a function of probe-sample distance h. Themore » theory has been verified experimentally in studies of semiconductor structures, both bulk and thin films. For measurements, we built a ∼2.1 GHz microscope with an effective tip radius of about 100 μm. The theoretical and experimental dependences f{sub 0}(h) and Q{sub 0}(h) were found to be in a good agreement. The developed theory underlies the method for determining sheet resistance R{sub sh} of a semiconductor film on a dielectric substrate proposed in this article. Studies were performed on doped n-GaN films on an Al{sub 2}O{sub 3} substrate. The effective radius and height of the probe determined from calibration measurements of etalon samples were used as the model fitting parameters. For etalon samples, we employed homogeneous sapphire and doped silicon plates. We also performed four-probe dc measurements of R{sub sh}. The corresponding values for samples with R{sub sh} > 1 kΩ were found to be 50% to 100% higher than the microwave results, which are attributed to the presence of microdefects in semiconductor films.« less

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.

Collaborative Research and Development (CR&D). Delivery Order 0051: Atomic Scale Transmission Electron Microscope Image Modeling and Application to Semiconductor Heterointerface Characterization

DTIC Science & Technology

2008-01-01

information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE (DD...microscopy ( AEM ), to characterize a variety of III-V semiconductor thin films. The materials investigated include superlattices based on the InAs- GaSb...technique. TEM observations were performed using a Philips-CM 200 FEG transmission electron microscope equipped with a field emission gun, operated at an

Long-wavelength instabilities in a system of interacting active particles

NASA Astrophysics Data System (ADS)

Fazli, Zahra; Najafi, Ali

2018-02-01

Based on a microscopic model, we develop a continuum description for a suspension of microscopic self-propelled particles. With this continuum description we study the role of long-range interactions in destabilizing macroscopic ordered phases that are developed by short-range interactions. Long-wavelength fluctuations can destabilize both isotropic and symmetry-broken polar phases in a suspension of dipolar particles. The instabilities in a suspension of pullers (pushers) arise from splay (bend) fluctuations. Such instabilities are not seen in a suspension of quadrupolar particles.

Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise

ERIC Educational Resources Information Center

Bindel, Thomas H.

2008-01-01

A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…

Normal stresses in semiflexible polymer hydrogels

NASA Astrophysics Data System (ADS)

Vahabi, M.; Vos, Bart E.; de Cagny, Henri C. G.; Bonn, Daniel; Koenderink, Gijsje H.; MacKintosh, F. C.

2018-03-01

Biopolymer gels such as fibrin and collagen networks are known to develop tensile axial stress when subject to torsion. This negative normal stress is opposite to the classical Poynting effect observed for most elastic solids including synthetic polymer gels, where torsion provokes a positive normal stress. As shown recently, this anomalous behavior in fibrin gels depends on the open, porous network structure of biopolymer gels, which facilitates interstitial fluid flow during shear and can be described by a phenomenological two-fluid model with viscous coupling between network and solvent. Here we extend this model and develop a microscopic model for the individual diagonal components of the stress tensor that determine the axial response of semiflexible polymer hydrogels. This microscopic model predicts that the magnitude of these stress components depends inversely on the characteristic strain for the onset of nonlinear shear stress, which we confirm experimentally by shear rheometry on fibrin gels. Moreover, our model predicts a transient behavior of the normal stress, which is in excellent agreement with the full time-dependent normal stress we measure.

Coherent scattering of near-resonant light by a dense, microscopic cloud of cold two-level atoms: Experiment versus theory

NASA Astrophysics Data System (ADS)

Jennewein, Stephan; Brossard, Ludovic; Sortais, Yvan R. P.; Browaeys, Antoine; Cheinet, Patrick; Robert, Jacques; Pillet, Pierre

2018-05-01

We measure the coherent scattering of low-intensity, near-resonant light by a cloud of laser-cooled two-level rubidium atoms with a size comparable to the wavelength of light. We isolate a two-level atomic structure by applying a 300-G magnetic field. We measure both the temporal and the steady-state coherent optical response of the cloud for various detunings of the laser and for atom numbers ranging from 5 to 100. We compare our results to a microscopic coupled-dipole model and to a multimode, paraxial Maxwell-Bloch model. In the low-intensity regime, both models are in excellent agreement, thus validating the Maxwell-Bloch model. Comparing to the data, the models are found in very good agreement for relatively low densities (n /k3≲0.1 ), while significant deviations start to occur at higher density. This disagreement indicates that light scattering in dense, cold atomic ensembles is still not quantitatively understood, even in pristine experimental conditions.

The generalization of the Mermin-Wagner theorem and the possibility of long-range order in the isotropic discrete one-dimensional quantum Heisenberg model

NASA Astrophysics Data System (ADS)

Rudoy, Yu. G.; Kotelnikova, O. A.

2012-10-01

The problem of existence of long-range order in the isotropic quantum Heisenberg model on the D=1 lattice is reconsidered in view of the possibility of sufficiently slow decaying exchange interaction with infinite effective radius. It is shown that the macrosopic arguments given by Landau and Lifshitz and then supported microscopically by Mermin and Wagner fail for this case so that the non-zero spontaneous magnetization may yet exist. This result was anticipated by Thouless on the grounds of phenomenological analysis, and we give its microscopic foundation, which amounts to the generalization of Mermin-Wagner theorem for the case of the infinite second moment of the exchange interaction. Two well known in lattice statistics models - i.e., Kac-I and Kac-II - illustrate our results.

Computational design of microscopic swimmers and capsules: From directed motion to collective behavior

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

Nikolov, Svetoslav V.; Shum, Henry; Balazs, Anna C.

Systems of motile microscopic particles can exhibit behaviors that resemble those of living microorganisms, including cooperative motion, self-organization, and adaptability to changing environments. Using mesoscale computational modeling, we design synthetic microswimmers and microcapsules that undergo controllable, self-propelled motion in solution. Stimuli-responsive hydrogels are used to actuate the microswimmers and to enable their navigation and chemotaxing behavior. The self-propelled motion of microcapsules on solid surfaces is achieved by the release of encapsulated solutes that alter the surface adhesiveness. These signaling solutes also enable interactions among multiple microcapsules that lead to complex, cooperative behavior. Our findings provide guidelines for creating microscopic devicesmore » and machines able to autonomously move and mimic the communication and chemotaxis of biological microorganisms.« 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 novel grid-based mesoscopic model for evacuation dynamics

NASA Astrophysics Data System (ADS)

Shi, Meng; Lee, Eric Wai Ming; Ma, Yi

2018-05-01

This study presents a novel grid-based mesoscopic model for evacuation dynamics. In this model, the evacuation space is discretised into larger cells than those used in microscopic models. This approach directly computes the dynamic changes crowd densities in cells over the course of an evacuation. The density flow is driven by the density-speed correlation. The computation is faster than in traditional cellular automata evacuation models which determine density by computing the movements of each pedestrian. To demonstrate the feasibility of this model, we apply it to a series of practical scenarios and conduct a parameter sensitivity study of the effect of changes in time step δ. The simulation results show that within the valid range of δ, changing δ has only a minor impact on the simulation. The model also makes it possible to directly acquire key information such as bottleneck areas from a time-varied dynamic density map, even when a relatively large time step is adopted. We use the commercial software AnyLogic to evaluate the model. The result shows that the mesoscopic model is more efficient than the microscopic model and provides more in-situ details (e.g., pedestrian movement pattern) than the macroscopic models.

Continuum mesoscopic framework for multiple interacting species and processes on multiple site types and/or crystallographic planes.

PubMed

Chatterjee, Abhijit; Vlachos, Dionisios G

2007-07-21

While recently derived continuum mesoscopic equations successfully bridge the gap between microscopic and macroscopic physics, so far they have been derived only for simple lattice models. In this paper, general deterministic continuum mesoscopic equations are derived rigorously via nonequilibrium statistical mechanics to account for multiple interacting surface species and multiple processes on multiple site types and/or different crystallographic planes. Adsorption, desorption, reaction, and surface diffusion are modeled. It is demonstrated that contrary to conventional phenomenological continuum models, microscopic physics, such as the interaction potential, determines the final form of the mesoscopic equation. Models of single component diffusion and binary diffusion of interacting particles on single-type site lattice and of single component diffusion on complex microporous materials' lattices consisting of two types of sites are derived, as illustrations of the mesoscopic framework. Simplification of the diffusion mesoscopic model illustrates the relation to phenomenological models, such as the Fickian and Maxwell-Stefan transport models. It is demonstrated that the mesoscopic equations are in good agreement with lattice kinetic Monte Carlo simulations for several prototype examples studied.

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.

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...

Design and Development of a Microscopic Model for Polarization

ERIC Educational Resources Information Center

Petridou, E.; Psillos, D.; Hatzikraniotis, E.; Viiri, J.

2009-01-01

As research shows that the knowledge and use of models and modelling by teachers is limited, particularly for predicting phenomena, we developed and applied a sequence of three representations of a simulated model focusing on polarization and specifically showing the behaviour of an atom, and forces exerted on a dipole and an insulator, when a…

Angle-resolved photoemission spectroscopy with quantum gas microscopes

NASA Astrophysics Data System (ADS)

Bohrdt, A.; Greif, D.; Demler, E.; Knap, M.; Grusdt, F.

2018-03-01

Quantum gas microscopes are a promising tool to study interacting quantum many-body systems and bridge the gap between theoretical models and real materials. So far, they were limited to measurements of instantaneous correlation functions of the form 〈O ̂(t ) 〉 , even though extensions to frequency-resolved response functions 〈O ̂(t ) O ̂(0 ) 〉 would provide important information about the elementary excitations in a many-body system. For example, single-particle spectral functions, which are usually measured using photoemission experiments in electron systems, contain direct information about fractionalization and the quasiparticle excitation spectrum. Here, we propose a measurement scheme to experimentally access the momentum and energy-resolved spectral function in a quantum gas microscope with currently available techniques. As an example for possible applications, we numerically calculate the spectrum of a single hole excitation in one-dimensional t -J models with isotropic and anisotropic antiferromagnetic couplings. A sharp asymmetry in the distribution of spectral weight appears when a hole is created in an isotropic Heisenberg spin chain. This effect slowly vanishes for anisotropic spin interactions and disappears completely in the case of pure Ising interactions. The asymmetry strongly depends on the total magnetization of the spin chain, which can be tuned in experiments with quantum gas microscopes. An intuitive picture for the observed behavior is provided by a slave-fermion mean-field theory. The key properties of the spectra are visible at currently accessible temperatures.

Many-body dynamics of chemically propelled nanomotors

NASA Astrophysics Data System (ADS)

Colberg, Peter H.; Kapral, Raymond

2017-08-01

The collective behavior of chemically propelled sphere-dimer motors made from linked catalytic and noncatalytic spheres in a quasi-two-dimensional confined geometry is studied using a coarse-grained microscopic dynamical model. Chemical reactions at the catalytic spheres that convert fuel to product generate forces that couple to solvent degrees of freedom as a consequence of momentum conservation in the microscopic dynamics. The collective behavior of the many-body system is influenced by direct intermolecular interactions among the motors, chemotactic effects due to chemical gradients, hydrodynamic coupling, and thermal noise. Segregation into high and low density phases and globally homogeneous states with strong fluctuations are investigated as functions of the motor characteristics. Factors contributing to this behavior are discussed in the context of active Brownian models.

Multiscale Modelling and Analysis of Collective Decision Making in Swarm Robotics

PubMed Central

Vigelius, Matthias; Meyer, Bernd; Pascoe, Geoffrey

2014-01-01

We present a unified approach to describing certain types of collective decision making in swarm robotics that bridges from a microscopic individual-based description to aggregate properties. Our approach encompasses robot swarm experiments, microscopic and probabilistic macroscopic-discrete simulations as well as an analytic mathematical model. Following up on previous work, we identify the symmetry parameter, a measure of the progress of the swarm towards a decision, as a fundamental integrated swarm property and formulate its time evolution as a continuous-time Markov process. Contrary to previous work, which justified this approach only empirically and a posteriori, we justify it from first principles and derive hard limits on the parameter regime in which it is applicable. PMID:25369026

Electron-beam-induced potentials in semiconductors: calculation and measurement with an SEM/SPM hybrid system

NASA Astrophysics Data System (ADS)

Thomas, Ch; Joachimsthaler, I.; Heiderhoff, R.; Balk, L. J.

2004-10-01

In this work electron-beam-induced potentials are analysed theoretically and experimentally for semiconductors. A theoretical model is developed to describe the surface potential distribution produced by an electron beam. The distribution of generated carriers is calculated using semiconductor equations. This distribution causes a local change in surface potential, which is derived with the help of quasi-Fermi energies. The potential distribution is simulated using the model developed and measured with a scanning probe microscope (SPM) built inside a scanning electron microscope (SEM), for different samples, for different beam excitations and for different cantilever voltages of SPM. In the end, some fields of application are shown where material properties can be determined using an SEM/SPM hybrid system.

Microscopic few-body and Gaussian-shaped density distributions for the analysis of the 6He exotic nucleus with different target nuclei

NASA Astrophysics Data System (ADS)

Aygun, M.; Kucuk, Y.; Boztosun, I.; Ibraheem, Awad A.

2010-12-01

The elastic scattering angular distributions of 6He projectile on different medium and heavy mass target nuclei including 12C, 27Al, 58Ni, 64Zn, 65Cu, 197Au, 208Pb and 209Bi have been examined by using the few-body and Gaussian-shaped density distributions at various energies. The microscopic real parts of the complex nuclear optical potential have been obtained by using the double-folding model for each of the density distributions and the phenomenological imaginary potentials have been taken as the Woods-Saxon type. Comparative results of the few-body and Gaussian-shaped density distributions together with the experimental data are presented within the framework of the optical model.

The relationship between morphological changes of lens epithelial cells and intraocular lens optic material.

PubMed

Majima, K

1998-01-01

To examine the morphological changes of lens epithelial cells (LECs) occurring directly beneath and at regions contacting various intraocular lens (IOL) optic materials, human LECs were cultured on human anterior lens capsules and were further incubated upon placing above the cells lens optics made of polymethylmethacrylate, silicone, and soft acrylic material. Observations as to the morphological changes of LECs under phase-contrast microscope and scanning electron microscope were performed on the 14th day of incubation. Gatherings of LECs were observed at regions contacting the soft acrylic material under phase-contrast microscope, and gatherings of LECs were observed accurately at the same regions mentioned above under scanning electron microscope. On the other hand, LECs in contact with two other optic materials did not show morphological changes. The results suggest that LECs attached to and proliferated on not only the anterior lens capsules but also the soft acrylic IOL optics. The model used in this study may be useful in studying the relationship between cellular movement of LECs and IOL optic material.

Ionic channels in Langmuir-Blodgett films imaged by a scanning tunneling microscope.

PubMed Central

Kolomytkin, O V; Golubok, A O; Davydov, D N; Timofeev, V A; Vinogradova, S A; Tipisev SYa

1991-01-01

The molecular structure of channels formed by gramicidin A in a lipid membrane was imaged by a scanning tunneling microscope operating in air. The mono- and bimolecular films of lipid with gramicidin A were deposited onto a highly oriented pyrolitic graphite substrate by the Langmuir-Blodgett technique. It has been shown that under high concentration gramicidin A molecules can form in lipid films a quasi-regular, densely packed structure. Single gramicidin A molecules were imaged for the first time as well. The cavity of 0.4 +/- 0.05 nm in halfwidth was found on the scanning tunneling microscopy image of the gramicidin A molecule. The results of direct observation obtained by means of scanning tunneling microscope are in good agreement with the known molecular model of gramicidin A. It was shown that gramicidin A molecules can exist in a lipid monolayer as individual molecules or combined into clusters. The results demonstrate that scanning tunneling microscope can be used for high spatial resolution study of ionic channel structure. Images FIGURE 1 FIGURE 2 FIGURE 4 FIGURE 5 PMID:1712239

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

Composition of Meridiani Hematite-rich Spherules: A Mass-Balance Mixing-Model Approach

NASA Astrophysics Data System (ADS)

Jolliff, B. L.; Athena Science Team

2005-03-01

A mass-balance model using APXS data and microscopic images indicates that the composition of spherules ("blueberries"), found at the Meridiani site by the Mars Exploration Rover Opportunity and thought to be concretions, contain ~45-60 wt% hematite.

Reconstruction of cluster masses using particle based lensing

NASA Astrophysics Data System (ADS)

Deb, Sanghamitra

Clusters of galaxies are among the richest astrophysical data systems, but to truly understand these systems, we need a detailed study of the relationship between observables and the underlying cluster dark matter distribution. Gravitational lensing is the most direct probe of dark matter, but many mass reconstruction techniques assume that cluster light traces mass, or combine different lensing signals in an ad hoc way. In this talk, we will describe "Particle Based Lensing" (PBL), a new method for cluster mass reconstruction, that avoids many of the pitfalls of previous techniques. PBL optimally combines lensing information of varying signal-to-noise, and makes no assumptions about the relationship between mass and light. We will describe mass reconstructions in three very different, but very illuminating cluster systems: the "Bullet Cluster" (lE 0657-56), A901/902 and A1689. The "Bullet Cluster" is a system of merging clusters made famous by the first unambiguous lensing detection of dark matter. A901/902 is a multi-cluster system with four peaks, and provides an ideal laboratory for studying cluster interaction. We are particularly interested in measuring and correlating the dark matter clump ellipticities. A1689 is one of the richest clusters known, and has significant substructure at the core. It is also my first exercise in optimally combining weak and strong gravitational lensing in a cluster reconstruction. We find that the dark matter distribution is significantly clumpier than indicated by X-ray maps of the gas. We conclude by discussing various potential applications of PBL to existing and future data.

Ultracold few fermionic atoms in needle-shaped double wells: spin chains and resonating spin clusters from microscopic Hamiltonians emulated via antiferromagnetic Heisenberg and t-J models

NASA Astrophysics Data System (ADS)

Yannouleas, Constantine; Brandt, Benedikt B.; Landman, Uzi

2016-07-01

Advances with trapped ultracold atoms intensified interest in simulating complex physical phenomena, including quantum magnetism and transitions from itinerant to non-itinerant behavior. Here we show formation of antiferromagnetic ground states of few ultracold fermionic atoms in single and double well (DW) traps, through microscopic Hamiltonian exact diagonalization for two DW arrangements: (i) two linearly oriented one-dimensional, 1D, wells, and (ii) two coupled parallel wells, forming a trap of two-dimensional, 2D, nature. The spectra and spin-resolved conditional probabilities reveal for both cases, under strong repulsion, atomic spatial localization at extemporaneously created sites, forming quantum molecular magnetic structures with non-itinerant character. These findings usher future theoretical and experimental explorations into the highly correlated behavior of ultracold strongly repelling fermionic atoms in higher dimensions, beyond the fermionization physics that is strictly applicable only in the 1D case. The results for four atoms are well described with finite Heisenberg spin-chain and cluster models. The numerical simulations of three fermionic atoms in symmetric DWs reveal the emergent appearance of coupled resonating 2D Heisenberg clusters, whose emulation requires the use of a t-J-like model, akin to that used in investigations of high T c superconductivity. The highly entangled states discovered in the microscopic and model calculations of controllably detuned, asymmetric, DWs suggest three-cold-atom DW quantum computing qubits.

Optically Sectioned Imaging of Microvasculature of In-Vivo and Ex-Vivo Thick Tissue Models with Speckle-illumination HiLo Microscopy and HiLo Image Processing Implementation in MATLAB Architecture

NASA Astrophysics Data System (ADS)

Suen, Ricky Wai

The work described in this thesis covers the conversion of HiLo image processing into MATLAB architecture and the use of speckle-illumination HiLo microscopy for use of ex-vivo and in-vivo imaging of thick tissue models. HiLo microscopy is a wide-field fluorescence imaging technique and has been demonstrated to produce optically sectioned images comparable to confocal in thin samples. The imaging technique was developed by Jerome Mertz and the Boston University Biomicroscopy Lab and has been implemented in our lab as a stand-alone optical setup and a modification to a conventional fluorescence microscope. Speckle-illumination HiLo microscopy combines two images taken under speckle-illumination and standard uniform-illumination to generate an optically sectioned image that reject out-of-focus fluorescence. The evaluated speckle contrast in the images is used as a weighting function where elements that move out-of-focus have a speckle contrast that decays to zero. The experiments shown here demonstrate the capability of our HiLo microscopes to produce optically-sectioned images of the microvasculature of ex-vivo and in-vivo thick tissue models. The HiLo microscope were used to image the microvasculature of ex-vivo mouse heart sections prepared for optical histology and the microvasculature of in-vivo rodent dorsal window chamber models. Studies in label-free surface profiling with HiLo microscopy is also presented.

A numerical analysis of the Born approximation for image formation modeling of differential interference contrast microscopy for human embryos

NASA Astrophysics Data System (ADS)

Trattner, Sigal; Feigin, Micha; Greenspan, Hayit; Sochen, Nir

2008-03-01

The differential interference contrast (DIC) microscope is commonly used for the visualization of live biological specimens. It enables the view of the transparent specimens while preserving their viability, being a non-invasive modality. Fertility clinics often use the DIC microscope for evaluation of human embryos quality. Towards quantification and reconstruction of the visualized specimens, an image formation model for DIC imaging is sought and the interaction of light waves with biological matter is examined. In many image formation models the light-matter interaction is expressed via the first Born approximation. The validity region of this approximation is defined in a theoretical bound which limits its use to very small specimens with low dielectric contrast. In this work the Born approximation is investigated via the Helmholtz equation, which describes the interaction between the specimen and light. A solution on the lens field is derived using the Gaussian Legendre quadrature formulation. This numerical scheme is considered both accurate and efficient and has shortened significantly the computation time as compared to integration methods that required a great amount of sampling for satisfying the Whittaker - Shannon sampling theorem. By comparing the numerical results with the theoretical values it is shown that the theoretical bound is not directly relevant to microscopic imaging and is far too limiting. The numerical exhaustive experiments show that the Born approximation is inappropriate for modeling the visualization of thick human embryos.

Middle School Science Notes

ERIC Educational Resources Information Center

School Science Review, 1976

1976-01-01

Describes a lighted demonstration apparatus for representing the distribution of electrons, protons and neutrons in an atom. Also includes experiments with ice, forces, microscopes, spectra, and geological modeling. (CS)

Measurement of the index of refraction of μm crystals by a confocal laser microscope--potential application for the refractive index mapping of μm scale.

PubMed

Kimura, Keisaku; Sato, Seiichi

2014-05-01

A conventional laser microscope can be used to derive the index of refractivity by the ratio of geometrical height of the transparent platelet to the apparent height of the normal incident light for very small crystals in the wide size range. We demonstrate that the simple method is effective for the samples from 100 μm to 16 μm in size using alkali halide crystals as a model system. The method is also applied for the surface fractured micro-crystals and an inclined crystal with microscopic size regime. Furthermore, we present two-dimensional refractive index mapping as well as two-dimensional height profile for the mixture of three alkali halides, KCl, KI, and NaCl, all are μm in size.

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.

New deconvolution method for microscopic images based on the continuous Gaussian radial basis function interpolation model.

PubMed

Chen, Zhaoxue; Chen, Hao

2014-01-01

A deconvolution method based on the Gaussian radial basis function (GRBF) interpolation is proposed. Both the original image and Gaussian point spread function are expressed as the same continuous GRBF model, thus image degradation is simplified as convolution of two continuous Gaussian functions, and image deconvolution is converted to calculate the weighted coefficients of two-dimensional control points. Compared with Wiener filter and Lucy-Richardson algorithm, the GRBF method has an obvious advantage in the quality of restored images. In order to overcome such a defect of long-time computing, the method of graphic processing unit multithreading or increasing space interval of control points is adopted, respectively, to speed up the implementation of GRBF method. The experiments show that based on the continuous GRBF model, the image deconvolution can be efficiently implemented by the method, which also has a considerable reference value for the study of three-dimensional microscopic image deconvolution.

Knowledge Extraction from Atomically Resolved Images.

PubMed

Vlcek, Lukas; Maksov, Artem; Pan, Minghu; Vasudevan, Rama K; Kalinin, Sergei V

2017-10-24

Tremendous strides in experimental capabilities of scanning transmission electron microscopy and scanning tunneling microscopy (STM) over the past 30 years made atomically resolved imaging routine. However, consistent integration and use of atomically resolved data with generative models is unavailable, so information on local thermodynamics and other microscopic driving forces encoded in the observed atomic configurations remains hidden. Here, we present a framework based on statistical distance minimization to consistently utilize the information available from atomic configurations obtained from an atomically resolved image and extract meaningful physical interaction parameters. We illustrate the applicability of the framework on an STM image of a FeSe x Te 1-x superconductor, with the segregation of the chalcogen atoms investigated using a nonideal interacting solid solution model. This universal method makes full use of the microscopic degrees of freedom sampled in an atomically resolved image and can be extended via Bayesian inference toward unbiased model selection with uncertainty quantification.

Structures of p -shell double-Λ hypernuclei studied with microscopic cluster models

NASA Astrophysics Data System (ADS)

Kanada-En'yo, Yoshiko

2018-03-01

0 s -orbit Λ states in p -shell double-Λ hypernuclei (Z Λ Λ A ), Li Λ Λ 8 , Li Λ Λ 9 , Be Λ Λ 10 ,11 ,12 , B Λ Λ 12 ,13 , and C Λ Λ 14 are investigated. Microscopic cluster models are applied to core nuclear part and a potential model is adopted for Λ particles. The Λ -core potential is a folding potential obtained with effective G -matrix Λ -N interactions, which reasonably reproduce energy spectra of Z Λ A -1 . System dependence of the Λ -Λ binding energies is understood by the core polarization energy from nuclear size reduction. Reductions of nuclear sizes and E 2 transition strengths by Λ particles are also discussed.

Fission properties of Po isotopes in different macroscopic-microscopic models

NASA Astrophysics Data System (ADS)

Bartel, J.; Pomorski, K.; Nerlo-Pomorska, B.; Schmitt, Ch

2015-11-01

Fission-barrier heights of nuclei in the Po isotopic chain are investigated in several macroscopic-microscopic models. Using the Yukawa-folded single-particle potential, the Lublin-Strasbourg drop (LSD) model, the Strutinsky shell-correction method to yield the shell corrections and the BCS theory for the pairing contributions, fission-barrier heights are calculated and found in quite good agreement with the experimental data. This turns out, however, to be only the case when the underlying macroscopic, liquid-drop (LD) type, theory is well chosen. Together with the LSD approach, different LD parametrizations proposed by Moretto et al are tested. Four deformation parameters describing respectively elongation, neck-formation, reflectional-asymmetric, and non-axiality of the nuclear shape thus defining the so called modified Funny Hills shape parametrization are used in the calculation. The present study clearly demonstrates that nuclear fission-barrier heights constitute a challenging and selective tool to discern between such different macroscopic approaches.

Modeling the microscopic electrical properties of thrombin binding aptamer (TBA) for label-free biosensors.

PubMed

Alfinito, Eleonora; Reggiani, Lino; Cataldo, Rosella; De Nunzio, Giorgio; Giotta, Livia; Guascito, Maria Rachele

2017-02-10

Aptamers are chemically produced oligonucleotides, able to bind a variety of targets such as drugs, proteins and pathogens with high sensitivity and selectivity. Therefore, aptamers are largely employed for producing label-free biosensors (aptasensors), with significant applications in diagnostics and drug delivery. In particular, the anti-thrombin aptamers are biomolecules of high interest for clinical use, because of their ability to recognize and bind the thrombin enzyme. Among them, the DNA 15-mer aptamer (TBA), has been widely explored around the possibility of using it in aptasensors. This paper proposes a microscopic model of the electrical properties of TBA and of the aptamer-thrombin complex, combining information from both structure and function, following the issues addressed in an emerging branch of electronics known as proteotronics. The theoretical results are compared and validated with measurements reported in the literature. Finally, the model suggests resistance measurements as a novel tool for testing aptamer-target affinity.

Search for microscopic black holes in pp collisions at $$ \\sqrt{s}=8 $$ TeV

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

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.

2013-07-01

A search for microscopic black holes and string balls is presented, based on a data sample of pp collisions at sqrt(s) = 8 TeV recorded by the CMS experiment at the Large Hadron Collider and corresponding to an integrated luminosity of 12 inverse femtobarns. No excess of events with energetic multiparticle final states, typical of black hole production or of similar new physics processes, is observed. Given the agreement of the observations with the expected standard model background, which is dominated by QCD multijet production, 95% confidence limits are set on the production of semiclassical or quantum black holes, ormore » of string balls, corresponding to the exclusions of masses below 4.3 to 6.2 TeV, depending on model assumptions. In addition, model-independent limits are set on new physics processes resulting in energetic multiparticle final states.« less

Modeling the microscopic electrical properties of thrombin binding aptamer (TBA) for label-free biosensors

NASA Astrophysics Data System (ADS)

Alfinito, Eleonora; Reggiani, Lino; Cataldo, Rosella; De Nunzio, Giorgio; Giotta, Livia; Guascito, Maria Rachele

2017-02-01

Aptamers are chemically produced oligonucleotides, able to bind a variety of targets such as drugs, proteins and pathogens with high sensitivity and selectivity. Therefore, aptamers are largely employed for producing label-free biosensors (aptasensors), with significant applications in diagnostics and drug delivery. In particular, the anti-thrombin aptamers are biomolecules of high interest for clinical use, because of their ability to recognize and bind the thrombin enzyme. Among them, the DNA 15-mer aptamer (TBA), has been widely explored around the possibility of using it in aptasensors. This paper proposes a microscopic model of the electrical properties of TBA and of the aptamer-thrombin complex, combining information from both structure and function, following the issues addressed in an emerging branch of electronics known as proteotronics. The theoretical results are compared and validated with measurements reported in the literature. Finally, the model suggests resistance measurements as a novel tool for testing aptamer-target affinity.

On the molecular mechanisms driving pain perception and emergent collective behaviors

NASA Astrophysics Data System (ADS)

Di Patti, F.; Fanelli, D.

2010-05-01

A stochastic model to investigate the microscopic processes which trigger the sensation of pain is considered. The model, presented in Di Patti and Fanelli [Di Patti F, Fanelli D. Can a microscopic stochastic model explain the emergence of pain cycles in patients? J Stat Mech 2009. doi:10.1088/1742-5468/2009/01/P01004], accounts for the action of analgesic drug and introduces an effect of competition with the inactive species populating the bloodstream. Regular oscillations in the amount of bound receptors are detected, following a resonant amplification of the stochastic component intrinsic to the system. The condition for such oscillations to occur are here studied, resorting to combined numerical and analytical techniques. Extended and connected patches of the admissible parameters space are detected which do correspond to the oscillatory behaviors. These findings are discussed with reference to the existing literature on patients' response to the analgesic treatment.

21 CFR 884.6190 - Assisted reproductive microscopes and microscope accessories.

Code of Federal Regulations, 2010 CFR

2010-04-01

... contrast microscopes, dissecting microscopes and inverted stage microscopes. (b) Classification. Class I... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Assisted reproductive microscopes and microscope... Devices § 884.6190 Assisted reproductive microscopes and microscope accessories. (a) Identification...

Impact of Microscope-Integrated OCT on Ophthalmology Resident Performance of Anterior Segment Surgical Maneuvers in Model Eyes.

PubMed

Todorich, Bozho; Shieh, Christine; DeSouza, Philip J; Carrasco-Zevallos, Oscar M; Cunefare, David L; Stinnett, Sandra S; Izatt, Joseph A; Farsiu, Sina; Mruthyunjaya, Privthi; Kuo, Anthony N; Toth, Cynthia A

2016-07-01

The integration of swept-source optical coherence tomography (SS-OCT) into the operating microscope enables real-time, tissue-level three-dimensional (3D) imaging to aid in ophthalmic microsurgery. In this prospective randomized controlled study, we evaluated the impact of SS microscope-integrated OCT (MI-OCT) on ophthalmology residents' performance of ophthalmic microsurgical maneuvers. Fourteen ophthalmology residents from a single institution were stratified by year of training and randomized to perform four anterior segment surgical maneuvers on porcine eyes with (MI-OCT+) or without (MI-OCT-) direct intraoperative OCT guidance. Subsequently, both groups repeated the same maneuvers without MI-OCT feedback to test whether initial MI-OCT experience affected subsequent surgical performance. Finally, the MI-OCT- group was crossed over and allowed to repeat the same maneuvers with direct MI-OCT guidance. Each resident completed a survey at the completion of the study. With direct MI-OCT feedback, residents demonstrated enhanced performance in depth-based anterior segment maneuvers (corneal suture passes at 50% and 90% depth and corneal laceration repair) compared with the residents operating without MI-OCT. Microscope-integrated OCT+ residents continued to outperform the controls when both groups subsequently operated without MI-OCT. For clear corneal wound geometry, there was no statistically significant effect of MI-OCT as applied in this study. Overall, the resident surgeons rated their subjective experience of using MI-OCT very favorably. Microscope-integrated OCT feedback enhances performance of ophthalmology residents in select anterior segment surgical maneuvers. Microscope-integrated OCT represents a valuable tool in the surgical education of ophthalmology residents.

A surface science compatible epifluorescence microscope for inspection of samples under ultra high vacuum and cryogenic conditions.

PubMed

Marquardt, Christian; Paulheim, Alexander; Rohbohm, Nils; Merkel, Rudolf; Sokolowski, Moritz

2017-08-01

We modified an epi-illumination light microscope and mounted it on an ultra high vacuum chamber for investigating samples used in a surface science experiment. For easy access and bake out, all optical components are placed outside the vacuum and the sample is imaged through a glass window. The microscope can be operated in reflection brightfield or epifluorescence mode to image the sample surface or fluorescent dye molecules adsorbed on it. The homemade sample mounting was made compatible for the use under the microscope; sample temperatures as low as 6 K can be achieved. The performance of the microscope is demonstrated on two model samples: Brightfield-images of a well-prepared Ag(100) surface show a macroscopic corrugation of the surface, although low energy electron diffraction data indicate a highly ordered crystalline surface. The surface shows macroscopic protrusions with flat regions, about 20-200 μm in diameter, in between. Fluorescence images of diluted 3,4,9,10-perylene tetracarboxylicacid dianhydride (PTCDA) molecules adsorbed on an ultrathin epitaxial KCl film on the Ag(100) surface show a shading effect at surface protrusions due to an inclined angle of incidence of the PTCDA beam during deposition. For some preparations, the distribution of the fluorescence intensity is inhomogeneous and shows a dense network of bright patches about 5 μm in diameter related to the macroscopic corrugation of the surface. We propose that such a light microscope can aid many surface science experiments, especially those dealing with epitaxial growth or fluorescent materials.

Integrative advances for OCT-guided ophthalmic surgery and intraoperative OCT: microscope integration, surgical instrumentation, and heads-up display surgeon feedback.

PubMed

Ehlers, Justis P; Srivastava, Sunil K; Feiler, Daniel; Noonan, Amanda I; Rollins, Andrew M; Tao, Yuankai K

2014-01-01

To demonstrate key integrative advances in microscope-integrated intraoperative optical coherence tomography (iOCT) technology that will facilitate adoption and utilization during ophthalmic surgery. We developed a second-generation prototype microscope-integrated iOCT system that interfaces directly with a standard ophthalmic surgical microscope. Novel features for improved design and functionality included improved profile and ergonomics, as well as a tunable lens system for optimized image quality and heads-up display (HUD) system for surgeon feedback. Novel material testing was performed for potential suitability for OCT-compatible instrumentation based on light scattering and transmission characteristics. Prototype surgical instruments were developed based on material testing and tested using the microscope-integrated iOCT system. Several surgical maneuvers were performed and imaged, and surgical motion visualization was evaluated with a unique scanning and image processing protocol. High-resolution images were successfully obtained with the microscope-integrated iOCT system with HUD feedback. Six semi-transparent materials were characterized to determine their attenuation coefficients and scatter density with an 830 nm OCT light source. Based on these optical properties, polycarbonate was selected as a material substrate for prototype instrument construction. A surgical pick, retinal forceps, and corneal needle were constructed with semi-transparent materials. Excellent visualization of both the underlying tissues and surgical instrument were achieved on OCT cross-section. Using model eyes, various surgical maneuvers were visualized, including membrane peeling, vessel manipulation, cannulation of the subretinal space, subretinal intraocular foreign body removal, and corneal penetration. Significant iterative improvements in integrative technology related to iOCT and ophthalmic surgery are demonstrated.

An analytic model for accurate spring constant calibration of rectangular atomic force microscope cantilevers.

PubMed

Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang

2015-10-29

Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.

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.

Development of a Tabletop Model for the Generation of Amorphous/ Microcrystalline Metal Powders

DTIC Science & Technology

1980-04-30

Voltage Characteristics for Wetting (si) and Non-wetting (AZ 4.5% Cu ) EHD Spray 2-57 28 Schematic of the Process of Electrohydrodynamic Droplet...Microscope Image of a Deposit , Fine Powders and "Matrix" Film of Fe-Ni-B-P Metallic Glass Alloy Produced by the EHD Technique 3-9 45 Selected Area...Transmission Electron Microscope Image of a Deposit , Fine Powders and "Matrix" Film of Fe-Ni-B-P Metallic Glass Alloy Produced by the EHD Technique 3-11 xi

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.

Model wavefront sensor for adaptive confocal microscopy

NASA Astrophysics Data System (ADS)

Booth, Martin J.; Neil, Mark A. A.; Wilson, Tony

2000-05-01

A confocal microscope permits 3D imaging of volume objects by the inclusion of a pinhole in the detector path which eliminates out of focus light. This configuration is however very sensitive to aberrations induced by the specimen or the optical system and would therefore benefit from an adaptive optics approach. We present a wavefront sensor capable of measuring directly the Zernike components of an aberrated wavefront and show that it is particularly applicable to the confocal microscope since only those wavefronts originating in the focal region contribute to the measured aberration.

EXPERIMENTAL SUBCUTANEOUS CYSTICERCOSIS BY Taenia crassiceps IN BALB/c AND C57BL/6 MICE

PubMed Central

PEREIRA, Íria Márcia; LIMA, Sarah Buzaim; FREITAS, Aline de Araújo; VINAUD, Marina Clare; JUNIOR, Ruy de Souza LINO

2016-01-01

SUMMARY Human cysticercosis is one of the most severe parasitic infections affecting tissues. Experimental models are needed to understand the host-parasite dynamics involved throughout the course of the infection. The subcutaneous experimental model is the closest to what is observed in human cysticercosis that does not affect the central nervous system. The aim of this study was to evaluate macroscopically and microscopically the experimental subcutaneous cysticercosis caused by Taenia crassiceps cysticerci in BALB/c and C57BL/6 mice. Animals were inoculated in the dorsal subcutaneous region and macroscopic and microscopic aspects of the inflammatory process in the host-parasite interface were evaluated until 90 days after the inoculation (DAI). All the infected animals presented vesicles containing cysticerci in the inoculation site, which was translucent at 7 DAI and then remained opaque throughout the experimental days. The microscopic analysis showed granulation tissue in BALB/c mice since the acute phase of infection evolving to chronicity without cure, presenting 80% of larval stage cysticerci at 90 DAI. While C57BL/6 mice presented 67% of final stage cysticerci at 90 DAI, the parasites were surrounded by neutrophils evolving to the infection control. It is possible to conclude that the genetic features of susceptibility (BALB/c) or resistance (C57BL/6) were confirmed in an experimental subcutaneous model of cysticercosis. PMID:27410915

EXPERIMENTAL SUBCUTANEOUS CYSTICERCOSIS BY Taenia crassiceps IN BALB/c AND C57BL/6 MICE.

PubMed

Pereira, Íria Márcia; Lima, Sarah Buzaim; Freitas, Aline de Araújo; Vinaud, Marina Clare; Junior, Ruy de Souza Lino

2016-07-11

Human cysticercosis is one of the most severe parasitic infections affecting tissues. Experimental models are needed to understand the host-parasite dynamics involved throughout the course of the infection. The subcutaneous experimental model is the closest to what is observed in human cysticercosis that does not affect the central nervous system. The aim of this study was to evaluate macroscopically and microscopically the experimental subcutaneous cysticercosis caused by Taenia crassiceps cysticerci in BALB/c and C57BL/6 mice. Animals were inoculated in the dorsal subcutaneous region and macroscopic and microscopic aspects of the inflammatory process in the host-parasite interface were evaluated until 90 days after the inoculation (DAI). All the infected animals presented vesicles containing cysticerci in the inoculation site, which was translucent at 7 DAI and then remained opaque throughout the experimental days. The microscopic analysis showed granulation tissue in BALB/c mice since the acute phase of infection evolving to chronicity without cure, presenting 80% of larval stage cysticerci at 90 DAI. While C57BL/6 mice presented 67% of final stage cysticerci at 90 DAI, the parasites were surrounded by neutrophils evolving to the infection control. It is possible to conclude that the genetic features of susceptibility (BALB/c) or resistance (C57BL/6) were confirmed in an experimental subcutaneous model of cysticercosis.

Living Matter Observations with a Novel Hyperspectral Supercontinuum Confocal Microscope for VIS to Near-IR Reflectance Spectroscopy

PubMed Central

Bertani, Francesca R.; Ferrari, Luisa; Mussi, Valentina; Botti, Elisabetta; Costanzo, Antonio; Selci, Stefano

2013-01-01

A broad range hyper-spectroscopic microscope fed by a supercontinuum laser source and equipped with an almost achromatic optical layout is illustrated with detailed explanations of the design, implementation and data. The real novelty of this instrument, a confocal spectroscopic microscope capable of recording high resolution reflectance data in the VIS-IR spectral range from about 500 nm to 2.5 μm wavelengths, is the possibility of acquiring spectral data at every physical point as defined by lateral coordinates, X and Y, as well as at a depth coordinate, Z, as obtained by the confocal optical sectioning advantage. With this apparatus we collect each single scanning point as a whole spectrum by combining two linear spectral detector arrays, one CCD for the visible range, and one InGaAs infrared array, simultaneously available at the sensor output channel of the home made instrument. This microscope has been developed for biomedical analysis of human skin and other similar applications. Results are shown illustrating the technical performances of the instrument and the capability in extracting information about the composition and the structure of different parts or compartments in biological samples as well as in solid statematter. A complete spectroscopic fingerprinting of samples at microscopic level is shown possible by using statistical analysis on raw data or analytical reflectance models based on Abelés matrix transfer methods. PMID:24233077

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.

A microscopic solution to the magnetic detwinning mystery in EuFe2As2

NASA Astrophysics Data System (ADS)

Maiwald, J.; Mazin, I. I.; Nandi, S.; Xiao, Y.; Gegenwart, P.

One of the greatest recent advances in studying nematic phenomena in Fe-based superconductors was the mechanical detwinning of the 122-family compounds. Unfortunately, these techniques generate considerable stress in the investigated samples, which contaminates the results. Recently, we observed that a minuscule magnetic field of the order of 0.1 T irreversibly and persistently detwins EuFe2As2, opening an entirely new avenue for addressing nematicity. However, further development was hindered by the absence of a microscopic theory explaining this magnetic detwinning. In fact, Eu2+ has zero orbital moment and does not couple to the lattice, and its exchange coupling with the Fe sublattice cancels by symmetry. Moreover, further increase of the field to 1 T leads to a reorientation of Fe domains, while even larger fields 10 T reorient the domains once again. We will present a new microscopic model, based on a sizable biquadratic coupling between the Fe 3 d and Eu 4 f moments. This model quantitatively explains our old and new magnetization and neutron diffraction data, thus removing the veil of mystery and finally opening the door to full-scale research into magnetic detwinning and nematicity in Fe-based superconductors.

Structure of the low-lying positive parity states in the proton-neutron symplectic model

NASA Astrophysics Data System (ADS)

Ganev, H. G.

2018-05-01

The proton-neutron symplectic model with Sp(12, R) dynamical symmetry is applied for the simultaneous description of the microscopic structure of the low-lying states of the ground state, γ and β bands in 166 Er. For this purpose, the model Hamiltonian is diagonalized in the space of stretched states by exploiting the SUp (3) ⊗ SUn (3) symmetry-adapted basis. The theoretical predictions are compared with experiment and some other microscopic collective models, like the one-component Sp(6, R) symplectic and pseudo-SU(3) models. A good description of the energy levels of the three bands under consideration, as well as the enhanced intraband B(E2) transition strengths between the states of the ground and γ bands is obtained without the use of effective charges. The results show the presence of a good SU(3) dynamical symmetry. It is also shown that, in contrast to the Sp(6, R) case, the lowest excited bands, e.g., the β and γ bands, naturally appear together with the ground state band within a single Sp(12, R) irreducible representation.

Ab initio modeling of steady-state and time-dependent charge transport in hole-only α-NPD devices

NASA Astrophysics Data System (ADS)

Liu, Feilong; Massé, Andrea; Friederich, Pascal; Symalla, Franz; Nitsche, Robert; Wenzel, Wolfgang; Coehoorn, Reinder; Bobbert, Peter A.

2016-12-01

We present an ab initio modeling study of steady-state and time-dependent charge transport in hole-only devices of the amorphous molecular semiconductor α-NPD [N ,N'-Di(1 -naphthyl)-N ,N'-diphenyl-(1 ,1'-biphenyl)-4 ,4'-diamine] . The study is based on the microscopic information obtained from atomistic simulations of the morphology and density functional theory calculations of the molecular hole energies, reorganization energies, and transfer integrals. Using stochastic approaches, the microscopic information obtained in simulation boxes at a length scale of ˜10 nm is expanded and employed in one-dimensional (1D) and three-dimensional (3D) master-equation modeling of the charge transport at the device scale of ˜100 nm. Without any fit parameter, predicted current density-voltage and impedance spectroscopy data obtained with the 3D modeling are in very good agreement with measured data on devices with different α-NPD layer thicknesses in a wide range of temperatures, bias voltages, and frequencies. Similarly good results are obtained with the computationally much more efficient 1D modeling after optimizing a hopping prefactor.

Black holes as quantum gravity condensates

NASA Astrophysics Data System (ADS)

Oriti, Daniele; Pranzetti, Daniele; Sindoni, Lorenzo

2018-03-01

We model spherically symmetric black holes within the group field theory formalism for quantum gravity via generalized condensate states, involving sums over arbitrarily refined graphs (dual to three-dimensional triangulations). The construction relies heavily on both the combinatorial tools of random tensor models and the quantum geometric data of loop quantum gravity, both part of the group field theory formalism. Armed with the detailed microscopic structure, we compute the entropy associated with the black hole horizon, which turns out to be equivalently the Boltzmann entropy of its microscopic degrees of freedom and the entanglement entropy between the inside and outside regions. We recover the area law under very general conditions, as well as the Bekenstein-Hawking formula. The result is also shown to be generically independent of any specific value of the Immirzi parameter.

Physics of Weightlifting

NASA Astrophysics Data System (ADS)

Cohen, Caroline

2014-11-01

In the footsteps of J.B. Keller who determined the optimal strategy to run a race, we investigate weightlifting records. We measure the dynamics of lifting barbells of different masses at Bench Press for different athletes. To understand the shape of experimental results, we need both a macroscopic mechanic model and microscopic description of muscle contraction. We dive into muscle in order to understand the relation between force generated by the muscle and its contraction velocity and draw a capillary analogy of muscle contraction. Finally we use the Deshcherevskii kinetik model and derive the dynamics of the barbell. From the fit between data and predictions, we extract microscopic characteristics of muscles. We consider to apply this protocole to diagnose muscle aging or dysfunctions. C. Cohen, B. Darbois Texier, D. Quere, G. Laffaye, C. Clanet.

Microscopic calculations of liquid and solid neutron star matter

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

Chakravarty, Sudip; Miller, Michael D.; Chia-Wei, Woo

1974-02-01

As the first step to a microscopic determination of the solidification density of neutron star matter, variational calculations are performed for both liquid and solid phases using a very simple model potential. The potential, containing only the repulsive part of the Reid /sup 1/S/sub o/ interaction, together with Boltzmann statistics defines a homework problem'' which several groups involved in solidification calculations have agreed to solve. The results were to be compared for the purpose of checking calculational techniques. For the solid energy good agreement with Canuto and Chitre was found. Both the liquid and solid energies are much lower thanmore » those of Pandharipande. It is shown that for this oversimplified model, neutron star matter will remain solid down to ordinary nuclear matter density.« less

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.

Microscopic prediction of speech intelligibility in spatially distributed speech-shaped noise for normal-hearing listeners.

PubMed

Geravanchizadeh, Masoud; Fallah, Ali

2015-12-01

A binaural and psychoacoustically motivated intelligibility model, based on a well-known monaural microscopic model is proposed. This model simulates a phoneme recognition task in the presence of spatially distributed speech-shaped noise in anechoic scenarios. In the proposed model, binaural advantage effects are considered by generating a feature vector for a dynamic-time-warping speech recognizer. This vector consists of three subvectors incorporating two monaural subvectors to model the better-ear hearing, and a binaural subvector to simulate the binaural unmasking effect. The binaural unit of the model is based on equalization-cancellation theory. This model operates blindly, which means separate recordings of speech and noise are not required for the predictions. Speech intelligibility tests were conducted with 12 normal hearing listeners by collecting speech reception thresholds (SRTs) in the presence of single and multiple sources of speech-shaped noise. The comparison of the model predictions with the measured binaural SRTs, and with the predictions of a macroscopic binaural model called extended equalization-cancellation, shows that this approach predicts the intelligibility in anechoic scenarios with good precision. The square of the correlation coefficient (r(2)) and the mean-absolute error between the model predictions and the measurements are 0.98 and 0.62 dB, respectively.

Study of 11Li and 10,11Be nuclei through elastic scattering and breakup reactions

NASA Astrophysics Data System (ADS)

Gaidarov, M. K.; Lukyanov, V. K.; Kadrev, D. N.; Zemlyanaya, E. V.; Antonov, A. N.; Lukyanov, K. V.; Spasova, K.

2016-01-01

The hybrid model of the microscopic optical potential (OP) is applied to calculate the 11Li+p, 10,11Be+p, and 10,11Be+12C elastic scattering cross sections at energies E < 100 MeV/nucleon. The OP's contain the folding-model real part (ReOP) with the direct and exchange terms included, while its imaginary part (ImOP) is derived within the high-energy approximation (HEA) theory. For the 11Li+p elastic scattering, the microscopic large-scale shell model (LSSM) density of 11Li is used, while the density distributions of 10,11Be nuclei obtained within the quantum Monte Carlo (QMC) model and the generator coordinate method (GCM) are utilized to calculate the microscopic OPs and cross sections of elastic scattering of these nuclei on protons and 12C. The depths of the real and imaginary parts of OP are fitted to the elastic scattering data, being simultaneously adjusted to reproduce the true energy dependence of the corresponding volume integrals. Also, the cluster models, in which 11Li consists of 2n-halo and the 9Li core having its own LSSM form of density and 11Be consists of a n-halo and the 10Be core, are adopted. Within the latter, we give predictions for the longitudinal momentum distributions of 9Li fragments produced in the breakup of 11Li at 62 MeV/nucleon on a proton target. It is shown that our results for the diffraction and stripping reaction cross sections in 11Be scattering on 9Be, 93Nb, 181Ta, and 238U targets at 63 MeV/nucleon are in a good agreement with the available experimental data.

Mesoscopic model for the viscosities of nematic liquid crystals.

PubMed

Chrzanowska, A; Kröger, M; Sellers, S

1999-10-01

Based on the definition of the mesoscopic concept by Blenk et al. [Physica A 174, 119 (1991); J. Noneq. Therm. 16, 67 (1991); Mol. Cryst. Liq. Cryst. 204, 133 (1991)] an approach to calculate the Leslie viscosity coefficients for nematic liquid crystals is presented. The approach rests upon the mesoscopic stress tensor, whose structure is assumed similar to the macroscopic Leslie viscous stress. The proposed form is also the main dissipation part of the mesoscopic Navier-Stokes equation. On the basis of the correspondence between microscopic and mesoscopic scales a mean-field mesoscopic potential is introduced. It allows us to obtain the stress tensor angular velocity of the free rotating molecules with the help of the orientational Fokker-Planck equation. The macroscopic stress tensor is calculated as an average of the mesoscopic counterpart. Appropriate relations among mesoscopic viscosities have been found. The mesoscopic analysis results are shown to be consistent with the diffusional model of Kuzuu-Doi and Osipov-Terentjev with the exception of the shear viscosity alpha(4). In the nematic phase alpha(4) is shown to have two contributions: isotropic and nematic. There exists an indication that the influence of the isotropic part is dominant over the nematic part. The so-called microscopic stress tensor used in the microscopic theories is shown to be the mean-field potential-dependent representation of the mesoscopic stress tensor. In the limiting case of total alignment the Leslie coefficients are estimated for the diffusional and mesoscopic models. They are compared to the results of the affine transformation model of the perfectly ordered systems. This comparison shows disagreement concerning the rotational viscosity, whereas the coefficients characteristic for the symmetric part of the viscous stress tensor remain the same. The difference is caused by the hindered diffusion in the affine model case.

A simple model for cell type recognition using 2D-correlation analysis of FTIR images from breast cancer tissue

NASA Astrophysics Data System (ADS)

Ali, Mohamed H.; Rakib, Fazle; Al-Saad, Khalid; Al-Saady, Rafif; Lyng, Fiona M.; Goormaghtigh, Erik

2018-07-01

Breast cancer is the second most common cancer after lung cancer. So far, in clinical practice, most cancer parameters originating from histopathology rely on the visualization by a pathologist of microscopic structures observed in stained tissue sections, including immunohistochemistry markers. Fourier transform infrared spectroscopy (FTIR) spectroscopy provides a biochemical fingerprint of a biopsy sample and, together with advanced data analysis techniques, can accurately classify cell types. Yet, one of the challenges when dealing with FTIR imaging is the slow recording of the data. One cm2 tissue section requires several hours of image recording. We show in the present paper that 2D covariance analysis singles out only a few wavenumbers where both variance and covariance are large. Simple models could be built using 4 wavenumbers to identify the 4 main cell types present in breast cancer tissue sections. Decision trees provide particularly simple models to reach discrimination between the 4 cell types. The robustness of these simple decision-tree models were challenged with FTIR spectral data obtained using different recording conditions. One test set was recorded by transflection on tissue sections in the presence of paraffin while the training set was obtained on dewaxed tissue sections by transmission. Furthermore, the test set was collected with a different brand of FTIR microscope and a different pixel size. Despite the different recording conditions, separating extracellular matrix (ECM) from carcinoma spectra was 100% successful, underlying the robustness of this univariate model and the utility of covariance analysis for revealing efficient wavenumbers. We suggest that 2D covariance maps using the full spectral range could be most useful to select the interesting wavenumbers and achieve very fast data acquisition on quantum cascade laser infrared imaging microscopes.

Systematic development of small molecules to inhibit specific microscopic steps of Aβ42 aggregation in Alzheimer's disease.

PubMed

Habchi, Johnny; Chia, Sean; Limbocker, Ryan; Mannini, Benedetta; Ahn, Minkoo; Perni, Michele; Hansson, Oskar; Arosio, Paolo; Kumita, Janet R; Challa, Pavan Kumar; Cohen, Samuel I A; Linse, Sara; Dobson, Christopher M; Knowles, Tuomas P J; Vendruscolo, Michele

2017-01-10

The aggregation of the 42-residue form of the amyloid-β peptide (Aβ42) is a pivotal event in Alzheimer's disease (AD). The use of chemical kinetics has recently enabled highly accurate quantifications of the effects of small molecules on specific microscopic steps in Aβ42 aggregation. Here, we exploit this approach to develop a rational drug discovery strategy against Aβ42 aggregation that uses as a read-out the changes in the nucleation and elongation rate constants caused by candidate small molecules. We thus identify a pool of compounds that target specific microscopic steps in Aβ42 aggregation. We then test further these small molecules in human cerebrospinal fluid and in a Caenorhabditis elegans model of AD. Our results show that this strategy represents a powerful approach to identify systematically small molecule lead compounds, thus offering an appealing opportunity to reduce the attrition problem in drug discovery.

Surface conservation laws at microscopically diffuse interfaces.

PubMed

Chu, Kevin T; Bazant, Martin Z

2007-11-01

In studies of interfaces with dynamic chemical composition, bulk and interfacial quantities are often coupled via surface conservation laws of excess surface quantities. While this approach is easily justified for microscopically sharp interfaces, its applicability in the context of microscopically diffuse interfaces is less theoretically well-established. Furthermore, surface conservation laws (and interfacial models in general) are often derived phenomenologically rather than systematically. In this article, we first provide a mathematically rigorous justification for surface conservation laws at diffuse interfaces based on an asymptotic analysis of transport processes in the boundary layer and derive general formulae for the surface and normal fluxes that appear in surface conservation laws. Next, we use nonequilibrium thermodynamics to formulate surface conservation laws in terms of chemical potentials and provide a method for systematically deriving the structure of the interfacial layer. Finally, we derive surface conservation laws for a few examples from diffusive and electrochemical transport.

Spectroscopy of reflection-asymmetric nuclei with relativistic energy density functionals

NASA Astrophysics Data System (ADS)

Xia, S. Y.; Tao, H.; Lu, Y.; Li, Z. P.; Nikšić, T.; Vretenar, D.

2017-11-01

Quadrupole and octupole deformation energy surfaces, low-energy excitation spectra, and transition rates in 14 isotopic chains: Xe, Ba, Ce, Nd, Sm, Gd, Rn, Ra, Th, U, Pu, Cm, Cf, and Fm, are systematically analyzed using a theoretical framework based on a quadrupole-octupole collective Hamiltonian (QOCH), with parameters determined by constrained reflection-asymmetric and axially symmetric relativistic mean-field calculations. The microscopic QOCH model based on the PC-PK1 energy density functional and δ -interaction pairing is shown to accurately describe the empirical trend of low-energy quadrupole and octupole collective states, and predicted spectroscopic properties are consistent with recent microscopic calculations based on both relativistic and nonrelativistic energy density functionals. Low-energy negative-parity bands, average octupole deformations, and transition rates show evidence for octupole collectivity in both mass regions, for which a microscopic mechanism is discussed in terms of evolution of single-nucleon orbitals with deformation.

Experimental metrology to obtain thermal phonon transmission coefficients at solid interfaces

NASA Astrophysics Data System (ADS)

Hua, Chengyun; Chen, Xiangwen; Ravichandran, Navaneetha K.; Minnich, Austin J.

2017-05-01

Interfaces play an essential role in phonon-mediated heat conduction in solids, impacting applications ranging from thermoelectric waste heat recovery to heat dissipation in electronics. From the microscopic perspective, interfacial phonon transport is described by transmission coefficients that link vibrational modes in the materials composing the interface. However, direct experimental determination of these coefficients is challenging because most experiments provide a mode-averaged interface conductance that obscures the microscopic detail. Here, we report a metrology to extract thermal phonon transmission coefficients at solid interfaces using ab initio phonon transport modeling and a thermal characterization technique, time-domain thermoreflectance. In combination with transmission electron microscopy characterization of the interface, our approach allows us to link the atomic structure of an interface to the spectral content of the heat crossing it. Our work provides a useful perspective on the microscopic processes governing interfacial heat conduction.

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.

In Situ Microstructural Control and Mechanical Testing Inside the Transmission Electron Microscope at Elevated Temperatures

NASA Astrophysics Data System (ADS)

Wang, Baoming; Haque, M. A.

2015-08-01

With atomic-scale imaging and analytical capabilities such as electron diffraction and energy-loss spectroscopy, the transmission electron microscope has allowed access to the internal microstructure of materials like no other microscopy. It has been mostly a passive or post-mortem analysis tool, but that trend is changing with in situ straining, heating and electrical biasing. In this study, we design and demonstrate a multi-functional microchip that integrates actuators, sensors, heaters and electrodes with freestanding electron transparent specimens. In addition to mechanical testing at elevated temperatures, the chip can actively control microstructures (grain growth and phase change) of the specimen material. Using nano-crystalline aluminum, nickel and zirconium as specimen materials, we demonstrate these novel capabilities inside the microscope. Our approach of active microstructural control and quantitative testing with real-time visualization can influence mechanistic modeling by providing direct and accurate evidence of the fundamental mechanisms behind materials behavior.

Microscopic Virtual Media (MVM) in Physics Learning: Case Study on Students Understanding of Heat Transfer

NASA Astrophysics Data System (ADS)

Wibowo, F. C.; Suhandi, A.; Rusdiana, D.; Darman, D. R.; Ruhiat, Y.; Denny, Y. R.; Suherman; Fatah, A.

2016-08-01

A Study area in physics learning is purposeful on the effects of various types of learning interventions to help students construct the basic of scientific conception about physics. Microscopic Virtual Media (MVM) are applications for physics learning to support powerful modelling microscopic involving physics concepts and processes. In this study groups (experimental) of 18±20 years old, students were studied to determine the role of MVM in the development of functional understanding of the concepts of thermal expansion in heat transfer. The experimental group used MVM in learning process. The results show that students who learned with virtual media exhibited significantly higher scores in the research tasks. Our findings proved that the MVM may be used as an alternative instructional tool, in order to help students to confront and constructed their basic of scientific conception and developed their understanding.

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.

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.

Low conductive support for thermal insulation of a sample holder of a variable temperature scanning tunneling microscope

NASA Astrophysics Data System (ADS)

Hanzelka, Pavel; Vonka, Jakub; Musilova, Vera

2013-08-01

We have designed a supporting system to fix a sample holder of a scanning tunneling microscope in an UHV chamber at room temperature. The microscope will operate down to a temperature of 20 K. Low thermal conductance, high mechanical stiffness, and small dimensions are the main features of the supporting system. Three sets of four glass balls placed in vertices of a tetrahedron are used for thermal insulation based on small contact areas between the glass balls. We have analyzed the thermal conductivity of the contacts between the balls mutually and between a ball and a metallic plate while the results have been applied to the entire support. The calculation based on a simple model of the setup has been verified with some experimental measurements. In comparison with other feasible supporting structures, the designed support has the lowest thermal conductance.

Low conductive support for thermal insulation of a sample holder of a variable temperature scanning tunneling microscope.

PubMed

Hanzelka, Pavel; Vonka, Jakub; Musilova, Vera

2013-08-01

We have designed a supporting system to fix a sample holder of a scanning tunneling microscope in an UHV chamber at room temperature. The microscope will operate down to a temperature of 20 K. Low thermal conductance, high mechanical stiffness, and small dimensions are the main features of the supporting system. Three sets of four glass balls placed in vertices of a tetrahedron are used for thermal insulation based on small contact areas between the glass balls. We have analyzed the thermal conductivity of the contacts between the balls mutually and between a ball and a metallic plate while the results have been applied to the entire support. The calculation based on a simple model of the setup has been verified with some experimental measurements. In comparison with other feasible supporting structures, the designed support has the lowest thermal conductance.

Irradiation Creep in Graphite

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

Ubic, Rick; Butt, Darryl; Windes, William

2014-03-13

An understanding of the underlying mechanisms of irradiation creep in graphite material is required to correctly interpret experimental data, explain micromechanical modeling results, and predict whole-core behavior. This project will focus on experimental microscopic data to demonstrate the mechanism of irradiation creep. High-resolution transmission electron microscopy should be able to image both the dislocations in graphite and the irradiation-induced interstitial clusters that pin those dislocations. The team will first prepare and characterize nanoscale samples of virgin nuclear graphite in a transmission electron microscope. Additional samples will be irradiated to varying degrees at the Advanced Test Reactor (ATR) facility and similarlymore » characterized. Researchers will record microstructures and crystal defects and suggest a mechanism for irradiation creep based on the results. In addition, the purchase of a tensile holder for a transmission electron microscope will allow, for the first time, in situ observation of creep behavior on the microstructure and crystallographic defects.« less

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

Experimental metrology to obtain thermal phonon transmission coefficients at solid interfaces

DOE PAGES

Hua, Chengyun; Chen, Xiangwen; Ravichandran, Navaneetha K.; ...

2017-05-17

Interfaces play an essential role in phonon-mediated heat conduction in solids, impacting applications ranging from thermoelectric waste heat recovery to heat dissipation in electronics. From the microscopic perspective, interfacial phonon transport is described by transmission coefficients that link vibrational modes in the materials composing the interface. But, direct experimental determination of these coefficients is challenging because most experiments provide a mode-averaged interface conductance that obscures the microscopic detail. Here, we report a metrology to extract thermal phonon transmission coefficients at solid interfaces using ab initio phonon transport modeling and a thermal characterization technique, time-domain thermoreflectance. In combination with transmission electronmore » microscopy characterization of the interface, our approach allows us to link the atomic structure of an interface to the spectral content of the heat crossing it. This work provides a useful perspective on the microscopic processes governing interfacial heat conduction.« less

The Enigmatic Neutrino

ERIC Educational Resources Information Center

Lincoln, Don; Miceli, Tia

2015-01-01

Through a century of work, physicists have refined a model to describe all fundamental particles, the forces they share, and their interactions on a microscopic scale. This masterpiece of science is called the Standard Model. While this theory is incredibly powerful, we know of at least one particle that exhibits behaviors that are outside of its…

Theory of superconductivity and spin excitations in cuprates

NASA Astrophysics Data System (ADS)

Plakida, Nikolay M.

2018-06-01

A microscopic theory of high-temperature superconductivity in strongly correlated systems as cuprates is presented. The two-subband extended Hubbard model is considered where the intersite Coulomb repulsion and electron-phonon interaction are taken into account. The low-energy spin excitations are considered within the t-J model.

Impact of Microscope-Integrated OCT on Ophthalmology Resident Performance of Anterior Segment Surgical Maneuvers in Model Eyes

PubMed Central

Todorich, Bozho; Shieh, Christine; DeSouza, Philip J.; Carrasco-Zevallos, Oscar M.; Cunefare, David L.; Stinnett, Sandra S.; Izatt, Joseph A.; Farsiu, Sina; Mruthyunjaya, Privthi; Kuo, Anthony N.; Toth, Cynthia A.

2016-01-01

Purpose The integration of swept-source optical coherence tomography (SS-OCT) into the operating microscope enables real-time, tissue-level three-dimensional (3D) imaging to aid in ophthalmic microsurgery. In this prospective randomized controlled study, we evaluated the impact of SS microscope-integrated OCT (MI-OCT) on ophthalmology residents' performance of ophthalmic microsurgical maneuvers. Methods Fourteen ophthalmology residents from a single institution were stratified by year of training and randomized to perform four anterior segment surgical maneuvers on porcine eyes with (MI-OCT+) or without (MI-OCT−) direct intraoperative OCT guidance. Subsequently, both groups repeated the same maneuvers without MI-OCT feedback to test whether initial MI-OCT experience affected subsequent surgical performance. Finally, the MI-OCT− group was crossed over and allowed to repeat the same maneuvers with direct MI-OCT guidance. Each resident completed a survey at the completion of the study. Results With direct MI-OCT feedback, residents demonstrated enhanced performance in depth-based anterior segment maneuvers (corneal suture passes at 50% and 90% depth and corneal laceration repair) compared with the residents operating without MI-OCT. Microscope-integrated OCT+ residents continued to outperform the controls when both groups subsequently operated without MI-OCT. For clear corneal wound geometry, there was no statistically significant effect of MI-OCT as applied in this study. Overall, the resident surgeons rated their subjective experience of using MI-OCT very favorably. Conclusions Microscope-integrated OCT feedback enhances performance of ophthalmology residents in select anterior segment surgical maneuvers. Microscope-integrated OCT represents a valuable tool in the surgical education of ophthalmology residents. PMID:27409466

Integrative Advances for OCT-Guided Ophthalmic Surgery and Intraoperative OCT: Microscope Integration, Surgical Instrumentation, and Heads-Up Display Surgeon Feedback

PubMed Central

Ehlers, Justis P.; Srivastava, Sunil K.; Feiler, Daniel; Noonan, Amanda I.; Rollins, Andrew M.; Tao, Yuankai K.

2014-01-01

Purpose To demonstrate key integrative advances in microscope-integrated intraoperative optical coherence tomography (iOCT) technology that will facilitate adoption and utilization during ophthalmic surgery. Methods We developed a second-generation prototype microscope-integrated iOCT system that interfaces directly with a standard ophthalmic surgical microscope. Novel features for improved design and functionality included improved profile and ergonomics, as well as a tunable lens system for optimized image quality and heads-up display (HUD) system for surgeon feedback. Novel material testing was performed for potential suitability for OCT-compatible instrumentation based on light scattering and transmission characteristics. Prototype surgical instruments were developed based on material testing and tested using the microscope-integrated iOCT system. Several surgical maneuvers were performed and imaged, and surgical motion visualization was evaluated with a unique scanning and image processing protocol. Results High-resolution images were successfully obtained with the microscope-integrated iOCT system with HUD feedback. Six semi-transparent materials were characterized to determine their attenuation coefficients and scatter density with an 830 nm OCT light source. Based on these optical properties, polycarbonate was selected as a material substrate for prototype instrument construction. A surgical pick, retinal forceps, and corneal needle were constructed with semi-transparent materials. Excellent visualization of both the underlying tissues and surgical instrument were achieved on OCT cross-section. Using model eyes, various surgical maneuvers were visualized, including membrane peeling, vessel manipulation, cannulation of the subretinal space, subretinal intraocular foreign body removal, and corneal penetration. Conclusions Significant iterative improvements in integrative technology related to iOCT and ophthalmic surgery are demonstrated. PMID:25141340

Acquisition of basic microsurgery skills using home-based simulation training: A randomised control study.

PubMed

Malik, Mohsan M; Hachach-Haram, Nadine; Tahir, Muaaz; Al-Musabi, Musab; Masud, Dhalia; Mohanna, Pari-Naz

2017-04-01

Acquisition of fine motor skills required in microsurgery can be challenging in the current training system. Therefore, there is an increased demand for novel training and assessment methods to optimise learning outside the clinical setting. Here, we present a randomised control trial of three microsurgical training models, namely laboratory tabletop training microscope (Laboratory Microscope, LM), low-cost jewellers microscope (Home Microscope, HM) and iPad trainer (Home Tablet, HT). Thirty-nine participants were allocated to four groups, control n = 9, LM n = 10, HM n = 10 and HT n = 10. The participants performed a chicken femoral artery anastomosis at baseline and at the completion of training. The performance was assessed as follows: structured assessment of microsurgery skills (SAMS) score, time taken to complete anastomosis and time for suture placement. No statistically significant difference was noted between the groups at baseline. There was a statistically significant improvement in all training arms between the baseline and post-training for SAMS score, time taken to complete the anastomosis and time per suture placement. In addition, a reduction was observed in the leak rate. No statistical difference was observed among the training arms. Our study demonstrated that at the early stages of microsurgical skill acquisition, home training using either the jewellers microscope or iPad produces comparable results to laboratory-based training using a tabletop microscope. Therefore, home microsurgical training is a viable, easily accessible cost-effective modality that allows trainees to practice and take ownership of their technical skill development in this area. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

In Silico Modelling of Transdermal and Systemic Kinetics of Topically Applied Solutes: Model Development and Initial Validation for Transdermal Nicotine.

PubMed

Chen, Tao; Lian, Guoping; Kattou, Panayiotis

2016-07-01

The purpose was to develop a mechanistic mathematical model for predicting the pharmacokinetics of topically applied solutes penetrating through the skin and into the blood circulation. The model could be used to support the design of transdermal drug delivery systems and skin care products, and risk assessment of occupational or consumer exposure. A recently reported skin penetration model [Pharm Res 32 (2015) 1779] was integrated with the kinetic equations for dermis-to-capillary transport and systemic circulation. All model parameters were determined separately from the molecular, microscopic and physiological bases, without fitting to the in vivo data to be predicted. Published clinical studies of nicotine were used for model demonstration. The predicted plasma kinetics is in good agreement with observed clinical data. The simulated two-dimensional concentration profile in the stratum corneum vividly illustrates the local sub-cellular disposition kinetics, including tortuous lipid pathway for diffusion and the "reservoir" effect of the corneocytes. A mechanistic model for predicting transdermal and systemic kinetics was developed and demonstrated with published clinical data. The integrated mechanistic approach has significantly extended the applicability of a recently reported microscopic skin penetration model by providing prediction of solute concentration in the blood.

Sensing of Streptococcus mutans by microscopic imaging ellipsometry

NASA Astrophysics Data System (ADS)

Khaleel, Mai Ibrahim; Chen, Yu-Da; Chien, Ching-Hang; Chang, Yia-Chung

2017-05-01

Microscopic imaging ellipsometry is an optical technique that uses an objective and sensing procedure to measure the ellipsometric parameters Ψ and Δ in the form of microscopic maps. This technique is well known for being noninvasive and label-free. Therefore, it can be used to detect and characterize biological species without any impact. Microscopic imaging ellipsometry was used to measure the optical response of dried Streptococcus mutans cells on a glass substrate. The ellipsometric Ψ and Δ maps were obtained with the Optrel Multiskop system for specular reflection in the visible range (λ=450 to 750 nm). The Ψ and Δ images at 500, 600, and 700 nm were analyzed using three different theoretical models with single-bounce, two-bounce, and multibounce light paths to obtain the optical constants and height distribution. The obtained images of the optical constants show different aspects when comparing the single-bounce analysis with the two-bounce or multibounce analysis in detecting S. mutans samples. Furthermore, the height distributions estimated by two-bounce and multibounce analyses of S. mutans samples were in agreement with the thickness values measured by AFM, which implies that the two-bounce and multibounce analyses can provide information complementary to that obtained by a single-bounce light path.

Telecentric 3D profilometry based on phase-shifting fringe projection.

PubMed

Li, Dong; Liu, Chunyang; Tian, Jindong

2014-12-29

Three dimensional shape measurement in the microscopic range becomes increasingly important with the development of micro manufacturing technology. Microscopic fringe projection techniques offer a fast, robust, and full-field measurement for field sizes from approximately 1 mm² to several cm². However, the depth of field is very small due to the imaging of non-telecentric microscope, which is often not sufficient to measure the complete depth of a 3D-object. And the calibration of phase-to-depth conversion is complicated which need a precision translation stage and a reference plane. In this paper, we propose a novel telecentric phase-shifting projected fringe profilometry for small and thick objects. Telecentric imaging extends the depth of field approximately to millimeter order, which is much larger than that of microscopy. To avoid the complicated phase-to-depth conversion in microscopic fringe projection, we develop a new system calibration method of camera and projector based on telecentric imaging model. Based on these, a 3D reconstruction of telecentric imaging is presented with stereovision aided by fringe phase maps. Experiments demonstrated the feasibility and high measurement accuracy of the proposed system for thick object.

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.

The dynamic process and microscopic mechanism of extraordinary terahertz transmission through perforated superconducting films

PubMed Central

Wu, J. B.; Zhang, X.; Jin, B. B.; Liu, H. T.; Chen, Y. H.; Li, Z. Y.; Zhang, C. H.; Kang, L.; Xu, W. W.; Chen, J.; Wang, H. B.; Tonouchi, M.; Wu, P. H.

2015-01-01

Superconductor is a compelling plasmonic medium at terahertz frequencies owing to its intrinsic low Ohmic loss and good tuning property. However, the microscopic physics of the interaction between terahertz wave and superconducting plasmonic structures is still unknown. In this paper, we conducted experiments of the enhanced terahertz transmission through a series of superconducting NbN subwavelength hole arrays, and employed microscopic hybrid wave model in theoretical analysis of the role of hybrid waves in the enhanced transmission. The theoretical calculation provided a good match of experimental data. In particular, we obtained the following results. When the width of the holes is far below wavelength, the enhanced transmission is mainly caused by localized resonance around individual holes. On the contrary, when the holes are large, hybrid waves scattered by the array of holes dominate the extraordinary transmission. The surface plasmon polaritions are proved to be launched on the surface of superconducting film and the excitation efficiency increases when the temperature approaches critical temperature and the working frequency goes near energy gap frequency. This work will enrich our knowledge on the microscopic physics of extraordinary optical transmission at terahertz frequencies and contribute to developing terahertz plasmonic devices. PMID:26498994

Screening and identification of proteins mediating senna induced gastrointestinal motility enhancement in mouse colon

PubMed Central

Wang, Xin; Zhong, Yue-Xia; Lan, Mei; Zhang, Zong-You; Shi, Yong-Quan; Lu, Ju; Ding, Jie; Wu, Kai-Cun; Jin, Jian-Ping; Pan, Bo-Rong; Fan, Dai Min

2002-01-01

AIM: To isolate the proteins involved in pharmacologic action of senna extract (SE) from mouse gastrointestinal tract and to explore the molecular mechanism of gastrointestinal motility change induced by SE. METHODS: SE was administrated to mice by different routes. Gastrointestinal motility of mice was observed using cathartic, gastrointestinal propellant movement experiments and X-ray analysis. Mouse model for gastrointestinal motility enhancement was established through continuous gastric administration of SE at progressively increased dose. At 3 h and week 3, 4, 6 and 10, morphological changes of gastrointestinal tissues were found under light microscope. Ultrastructural changes of intestinal and colonic tissues at week 6 were observed under transmission electron microscope. The colonic proteomic changes in model mice were examined by two-dimension polyacrylamide gel electrophoresis with immobilized pH gradient isoelectric focusing to screen the differentially expressed proteins, and their molecular masses and isoelectric points were determined. Two N-terminal sequences of the samples were also determined by mass spectrometry. RESULTS: SE (0.3 g) caused diarrhea after gastric administration in 1-6 h and enhanced gastrointestinal propellant (65.1% ± 7.5%; 45.8% ± 14.6%,P < 0.01) in mice, but intramuscular and hypodermic injection had no cathartic effect. X-ray analysis of gastrointestinal motility demonstrated that gastric administration of SE enhanced gastric evacuation and gastrointestinal transferring function. At 3 h and week 3 and 4 after gastric administration of SE, light microscopic examination revealed no apparent change in gastrointestinal mucosal tissues, but transmission electron microscopic examination revealed inflammatory changes in whole layer of intestinal and colonic wall. Twenty differential proteins were detected in the colonic tissues of the model mice by two-dimensional electrophoresis, and the N-terminal amino acid sequences of two proteins were determined. CONCLUSION: SE causes diarrhea and enhances gastrointestinal motility through digestive tract administration. Long-term gastric administration of SE induces inflammatory changes and cell damage in the whole gastrointestinal tract. The differential proteins screened from the colonic tissues of the model mice might mediate the enhancing effect of SE on gastrointestinal motility. PMID:11833095

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

Persistent and automatic intraoperative 3D digitization of surfaces under dynamic magnifications of an operating microscope

PubMed Central

Kumar, Ankur N.; Miga, Michael I.; Pheiffer, Thomas S.; Chambless, Lola B.; Thompson, Reid C.; Dawant, Benoit M.

2014-01-01

One of the major challenges impeding advancement in image-guided surgical (IGS) systems is the soft-tissue deformation during surgical procedures. These deformations reduce the utility of the patient’s preoperative images and may produce inaccuracies in the application of preoperative surgical plans. Solutions to compensate for the tissue deformations include the acquisition of intraoperative tomographic images of the whole organ for direct displacement measurement and techniques that combines intraoperative organ surface measurements with computational biomechanical models to predict subsurface displacements. The later solution has the advantage of being less expensive and amenable to surgical workflow. Several modalities such as textured laser scanners, conoscopic holography, and stereo-pair cameras have been proposed for the intraoperative 3D estimation of organ surfaces to drive patient-specific biomechanical models for the intraoperative update of preoperative images. Though each modality has its respective advantages and disadvantages, stereo-pair camera approaches used within a standard operating microscope is the focus of this article. A new method that permits the automatic and near real-time estimation of 3D surfaces (at 1Hz) under varying magnifications of the operating microscope is proposed. This method has been evaluated on a CAD phantom object and on full-length neurosurgery video sequences (~1 hour) acquired intraoperatively by the proposed stereovision system. To the best of our knowledge, this type of validation study on full-length brain tumor surgery videos has not been done before. The method for estimating the unknown magnification factor of the operating microscope achieves accuracy within 0.02 of the theoretical value on a CAD phantom and within 0.06 on 4 clinical videos of the entire brain tumor surgery. When compared to a laser range scanner, the proposed method for reconstructing 3D surfaces intraoperatively achieves root mean square errors (surface-to-surface distance) in the 0.28-0.81mm range on the phantom object and in the 0.54-1.35mm range on 4 clinical cases. The digitization accuracy of the presented stereovision methods indicate that the operating microscope can be used to deliver the persistent intraoperative input required by computational biomechanical models to update the patient’s preoperative images and facilitate active surgical guidance. PMID:25189364

Persistent and automatic intraoperative 3D digitization of surfaces under dynamic magnifications of an operating microscope.

PubMed

Kumar, Ankur N; Miga, Michael I; Pheiffer, Thomas S; Chambless, Lola B; Thompson, Reid C; Dawant, Benoit M

2015-01-01

One of the major challenges impeding advancement in image-guided surgical (IGS) systems is the soft-tissue deformation during surgical procedures. These deformations reduce the utility of the patient's preoperative images and may produce inaccuracies in the application of preoperative surgical plans. Solutions to compensate for the tissue deformations include the acquisition of intraoperative tomographic images of the whole organ for direct displacement measurement and techniques that combines intraoperative organ surface measurements with computational biomechanical models to predict subsurface displacements. The later solution has the advantage of being less expensive and amenable to surgical workflow. Several modalities such as textured laser scanners, conoscopic holography, and stereo-pair cameras have been proposed for the intraoperative 3D estimation of organ surfaces to drive patient-specific biomechanical models for the intraoperative update of preoperative images. Though each modality has its respective advantages and disadvantages, stereo-pair camera approaches used within a standard operating microscope is the focus of this article. A new method that permits the automatic and near real-time estimation of 3D surfaces (at 1 Hz) under varying magnifications of the operating microscope is proposed. This method has been evaluated on a CAD phantom object and on full-length neurosurgery video sequences (∼1 h) acquired intraoperatively by the proposed stereovision system. To the best of our knowledge, this type of validation study on full-length brain tumor surgery videos has not been done before. The method for estimating the unknown magnification factor of the operating microscope achieves accuracy within 0.02 of the theoretical value on a CAD phantom and within 0.06 on 4 clinical videos of the entire brain tumor surgery. When compared to a laser range scanner, the proposed method for reconstructing 3D surfaces intraoperatively achieves root mean square errors (surface-to-surface distance) in the 0.28-0.81 mm range on the phantom object and in the 0.54-1.35 mm range on 4 clinical cases. The digitization accuracy of the presented stereovision methods indicate that the operating microscope can be used to deliver the persistent intraoperative input required by computational biomechanical models to update the patient's preoperative images and facilitate active surgical guidance. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Towards a physics-based multiscale modelling of the electro-mechanical coupling in electro-active polymers.

PubMed

Cohen, Noy; Menzel, Andreas; deBotton, Gal

2016-02-01

Owing to the increasing number of industrial applications of electro-active polymers (EAPs), there is a growing need for electromechanical models which accurately capture their behaviour. To this end, we compare the predicted behaviour of EAPs undergoing homogeneous deformations according to three electromechanical models. The first model is a phenomenological continuum-based model composed of the mechanical Gent model and a linear relationship between the electric field and the polarization. The electrical and the mechanical responses according to the second model are based on the physical structure of the polymer chain network. The third model incorporates a neo-Hookean mechanical response and a physically motivated microstructurally based long-chains model for the electrical behaviour. In the microstructural-motivated models, the integration from the microscopic to the macroscopic levels is accomplished by the micro-sphere technique. Four types of homogeneous boundary conditions are considered and the behaviours determined according to the three models are compared. For the microstructurally motivated models, these analyses are performed and compared with the widely used phenomenological model for the first time. Some of the aspects revealed in this investigation, such as the dependence of the intensity of the polarization field on the deformation, highlight the need for an in-depth investigation of the relationships between the structure and the behaviours of the EAPs at the microscopic level and their overall macroscopic response.

'Blueberry' Exposed

NASA Technical Reports Server (NTRS)

2004-01-01

This three-dimensional model shows a postage-stamp-sized patch of the rock target in the outcrop near the Mars Exploration Rover Opportunity's landing site. A sliced sphere-like particle, or 'blueberry,' can be seen to the far right of the model. The model was created from images taken by the rover's microscopic imager, after the surface of the rock was scraped away with the rock abrasion tool.

Estimation of polydispersity in aggregating red blood cells by quantitative ultrasound backscatter analysis.

PubMed

de Monchy, Romain; Rouyer, Julien; Destrempes, François; Chayer, Boris; Cloutier, Guy; Franceschini, Emilie

2018-04-01

Quantitative ultrasound techniques based on the backscatter coefficient (BSC) have been commonly used to characterize red blood cell (RBC) aggregation. Specifically, a scattering model is fitted to measured BSC and estimated parameters can provide a meaningful description of the RBC aggregates' structure (i.e., aggregate size and compactness). In most cases, scattering models assumed monodisperse RBC aggregates. This study proposes the Effective Medium Theory combined with the polydisperse Structure Factor Model (EMTSFM) to incorporate the polydispersity of aggregate size. From the measured BSC, this model allows estimating three structural parameters: the mean radius of the aggregate size distribution, the width of the distribution, and the compactness of the aggregates. Two successive experiments were conducted: a first experiment on blood sheared in a Couette flow device coupled with an ultrasonic probe, and a second experiment, on the same blood sample, sheared in a plane-plane rheometer coupled to a light microscope. Results demonstrated that the polydisperse EMTSFM provided the best fit to the BSC data when compared to the classical monodisperse models for the higher levels of aggregation at hematocrits between 10% and 40%. Fitting the polydisperse model yielded aggregate size distributions that were consistent with direct light microscope observations at low hematocrits.

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

Singh, Varinderjit; Vadas, J.; Steinbach, T. K.

Measuring the fusion excitation function for an isotopic chain of projectile nuclei provides a stringent test of a microscopic description of fusion. We report the first measurement of the fusion excitation function at near-barrier energies for the 19O+ 12C system. The measured excitation function is compared with the fusion excitation function of 18O+ 12C. A significant enhancement in the fusion probability of 19O ions with a 12C target as compared to 18O ions is observed. As a result, the experimental cross-sections observed at near-barrier energies are compared with a state-of-the-art microscopic model.

Optimal model-based sensorless adaptive optics for epifluorescence microscopy.

PubMed

Pozzi, Paolo; Soloviev, Oleg; Wilding, Dean; Vdovin, Gleb; Verhaegen, Michel

2018-01-01

We report on a universal sample-independent sensorless adaptive optics method, based on modal optimization of the second moment of the fluorescence emission from a point-like excitation. Our method employs a sample-independent precalibration, performed only once for the particular system, to establish the direct relation between the image quality and the aberration. The method is potentially applicable to any form of microscopy with epifluorescence detection, including the practically important case of incoherent fluorescence emission from a three dimensional object, through minor hardware modifications. We have applied the technique successfully to a widefield epifluorescence microscope and to a multiaperture confocal microscope.

Searches for Kaluza-Klein graviton excitations and microscopic black holes with the aid of the CMS detector at the LHC

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

Savina, M. V., E-mail: savina@cern.ch

2015-06-15

A survey of the results of the Compact Muon Solenoid (CMS) experiment that concern searches for massive Kaluza-Klein graviton excitations and microscopic black holes, quantum black holes, and string balls within models of low-energy multidimensional gravity is presented on behalf of the CMS Collaboration. The analysis in question is performed on the basis of a complete sample of data accumulated for proton-proton collisions at the c.m. energies of 7 and 8 TeV at the Large Hadron Collider (LHC) over the period spanning 2010 and 2012.

The petrographic microscope: Evolution of a mineralogical research instrument

USGS Publications Warehouse

Kile, D.E.

2003-01-01

The petrographic microscope, designed to observe and measure the optical properties of minerals as a means of identifying them, has provided a foundation for mineralogical and petrological research for more than 120 years. Much of what is known today in these fields is attributable to this instrument, the development of which paralleled an evolution of fundamental optical theory and its correlation with mineral structure and composition. This instrument and its related accessories have evolved through a range of models and designs, which are in themselves distinctive for their scientific function and elegant construction, and are today prized by collectors of scientific instruments.

Agent based reasoning for the non-linear stochastic models of long-range memory

NASA Astrophysics Data System (ADS)

Kononovicius, A.; Gontis, V.

2012-02-01

We extend Kirman's model by introducing variable event time scale. The proposed flexible time scale is equivalent to the variable trading activity observed in financial markets. Stochastic version of the extended Kirman's agent based model is compared to the non-linear stochastic models of long-range memory in financial markets. The agent based model providing matching macroscopic description serves as a microscopic reasoning of the earlier proposed stochastic model exhibiting power law statistics.

Grade 12 Students' Conceptual Understanding and Mental Models of Galvanic Cells before and after Learning by Using Small-Scale Experiments in Conjunction with a Model Kit

ERIC Educational Resources Information Center

Supasorn, Saksri

2015-01-01

This study aimed to develop the small-scale experiments involving electrochemistry and the galvanic cell model kit featuring the sub-microscopic level. The small-scale experiments in conjunction with the model kit were implemented based on the 5E inquiry learning approach to enhance students' conceptual understanding of electrochemistry. The…

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.

Reaction rates for mesoscopic reaction-diffusion kinetics

DOE PAGES

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2015-02-23

The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In thismore » paper we derive mesoscopic scale-dependent reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a Robin boundary condition at the reaction radius of two molecules. We also establish fundamental limits on the range of mesh resolutions for which this approach yields accurate results and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics. Finally, we show that for mesh sizes below the fundamental lower limit, results are less accurate. Thus, the lower limit determines the mesh size for which we obtain the most accurate results.« less

Reaction rates for mesoscopic reaction-diffusion kinetics

PubMed Central

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2016-01-01

The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In this paper we derive mesoscopic scale-dependent reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a Robin boundary condition at the reaction radius of two molecules. We also establish fundamental limits on the range of mesh resolutions for which this approach yields accurate results and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics. We show that for mesh sizes below the fundamental lower limit, results are less accurate. Thus, the lower limit determines the mesh size for which we obtain the most accurate results. PMID:25768640

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.

Langevin model of low-energy fission

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

Sierk, Arnold John

Since the earliest days of fission, stochastic models have been used to describe and model the process. For a quarter century, numerical solutions of Langevin equations have been used to model fission of highly excited nuclei, where microscopic potential-energy effects have been neglected. In this paper I present a Langevin model for the fission of nuclei with low to medium excitation energies, for which microscopic effects in the potential energy cannot be ignored. I solve Langevin equations in a five-dimensional space of nuclear deformations. The macroscopic-microscopic potential energy from a global nuclear structure model well benchmarked to nuclear masses ismore » tabulated on a mesh of approximately 10 7 points in this deformation space. The potential is defined continuously inside the mesh boundaries by use of a moving five-dimensional cubic spline approximation. Because of reflection symmetry, the effective mesh is nearly twice this size. For the inertia, I use a (possibly scaled) approximation to the inertia tensor defined by irrotational flow. A phenomenological dissipation tensor related to one-body dissipation is used. A normal-mode analysis of the dynamical system at the saddle point and the assumption of quasiequilibrium provide distributions of initial conditions appropriate to low excitation energies, and are extended to model spontaneous fission. A dynamical model of postscission fragment motion including dynamical deformations and separation allows the calculation of final mass and kinetic-energy distributions, along with other interesting quantities. The model makes quantitative predictions for fragment mass and kinetic-energy yields, some of which are very close to measured ones. Varying the energy of the incident neutron for induced fission allows the prediction of energy dependencies of fragment yields and average kinetic energies. With a simple approximation for spontaneous fission starting conditions, quantitative predictions are made for some observables which are close to measurements. In conclusion, this model is able to reproduce several mass and energy yield observables with a small number of physical parameters, some of which do not need to be varied after benchmarking to 235U (n, f) to predict results for other fissioning isotopes.« less

Langevin model of low-energy fission

DOE PAGES

Sierk, Arnold John

2017-09-05

Since the earliest days of fission, stochastic models have been used to describe and model the process. For a quarter century, numerical solutions of Langevin equations have been used to model fission of highly excited nuclei, where microscopic potential-energy effects have been neglected. In this paper I present a Langevin model for the fission of nuclei with low to medium excitation energies, for which microscopic effects in the potential energy cannot be ignored. I solve Langevin equations in a five-dimensional space of nuclear deformations. The macroscopic-microscopic potential energy from a global nuclear structure model well benchmarked to nuclear masses ismore » tabulated on a mesh of approximately 10 7 points in this deformation space. The potential is defined continuously inside the mesh boundaries by use of a moving five-dimensional cubic spline approximation. Because of reflection symmetry, the effective mesh is nearly twice this size. For the inertia, I use a (possibly scaled) approximation to the inertia tensor defined by irrotational flow. A phenomenological dissipation tensor related to one-body dissipation is used. A normal-mode analysis of the dynamical system at the saddle point and the assumption of quasiequilibrium provide distributions of initial conditions appropriate to low excitation energies, and are extended to model spontaneous fission. A dynamical model of postscission fragment motion including dynamical deformations and separation allows the calculation of final mass and kinetic-energy distributions, along with other interesting quantities. The model makes quantitative predictions for fragment mass and kinetic-energy yields, some of which are very close to measured ones. Varying the energy of the incident neutron for induced fission allows the prediction of energy dependencies of fragment yields and average kinetic energies. With a simple approximation for spontaneous fission starting conditions, quantitative predictions are made for some observables which are close to measurements. In conclusion, this model is able to reproduce several mass and energy yield observables with a small number of physical parameters, some of which do not need to be varied after benchmarking to 235U (n, f) to predict results for other fissioning isotopes.« less

Deriving the nuclear shell model from first principles

NASA Astrophysics Data System (ADS)

Barrett, Bruce R.; Dikmen, Erdal; Vary, James P.; Maris, Pieter; Shirokov, Andrey M.; Lisetskiy, Alexander F.

2014-09-01

The results of an 18-nucleon No Core Shell Model calculation, performed in a large basis space using a bare, soft NN interaction, can be projected into the 0 ℏω space, i.e., the sd -shell. Because the 16 nucleons in the 16O core are frozen in the 0 ℏω space, all the correlations of the 18-nucleon system are captured by the two valence, sd -shell nucleons. By the projection, we obtain microscopically the sd -shell 2-body effective interactions, the core energy and the sd -shell s.p. energies. Thus, the input for standard shell-model calculations can be determined microscopically by this approach. If the same procedure is then applied to 19-nucleon systems, the sd -shell 3-body effective interactions can also be obtained, indicating the importance of these 3-body effective interactions relative to the 2-body effective interactions. Applications to A = 19 and heavier nuclei with different intrinsic NN interactions will be presented and discussed. The results of an 18-nucleon No Core Shell Model calculation, performed in a large basis space using a bare, soft NN interaction, can be projected into the 0 ℏω space, i.e., the sd -shell. Because the 16 nucleons in the 16O core are frozen in the 0 ℏω space, all the correlations of the 18-nucleon system are captured by the two valence, sd -shell nucleons. By the projection, we obtain microscopically the sd -shell 2-body effective interactions, the core energy and the sd -shell s.p. energies. Thus, the input for standard shell-model calculations can be determined microscopically by this approach. If the same procedure is then applied to 19-nucleon systems, the sd -shell 3-body effective interactions can also be obtained, indicating the importance of these 3-body effective interactions relative to the 2-body effective interactions. Applications to A = 19 and heavier nuclei with different intrinsic NN interactions will be presented and discussed. Supported by the US NSF under Grant No. 0854912, the US DOE under Grants Nos. DESC0008485 and DE-FG02-87ER40371, the Higher Education Council of Turkey(YOK), and the Ministry of Education and Science of Russian Fed. under contracts P521 and 14.v37.21.1297.

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...

Theoretical investigation on the magnetic and electric properties in TbSb compound through an anisotropic microscopic model

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

Ranke, P. J. von, E-mail: von.ranke@uol.com.br; Ribeiro, P. O.; Alho, B. P.

2016-05-14

We report the strong correlations between the magnetoresistivity and the magnetic entropy change in the cubic antiferromagnetic TbSb compound. The theoretical investigation was performed through a microscopic model which takes into account the crystalline electrical field anisotropy, exchange coupling interactions between the up and down magnetic sublattices, and the Zeeman interaction. The easy magnetization directions changes from 〈001〉 to 〈110〉 and then to 〈111〉 observed experimentally was successfully theoretically described. Also, the calculation of the temperature dependence of electric resistivity showed good agreement with the experimental data. Theoretical predictions were calculated for the temperature dependence of the magnetic entropy andmore » resistivity changes upon magnetic field variation. Besides, the difference in the spin up and down sublattices resistivity was investigated.« less

Geometric model from microscopic theory for nuclear absorption

NASA Technical Reports Server (NTRS)

John, Sarah; Townsend, Lawrence W.; Wilson, John W.; Tripathi, Ram K.

1993-01-01

A parameter-free geometric model for nuclear absorption is derived herein from microscopic theory. The expression for the absorption cross section in the eikonal approximation, taken in integral form, is separated into a geometric contribution that is described by an energy-dependent effective radius and two surface terms that cancel in an asymptotic series expansion. For collisions of light nuclei, an expression for the effective radius is derived from harmonic oscillator nuclear density functions. A direct extension to heavy nuclei with Woods-Saxon densities is made by identifying the equivalent half-density radius for the harmonic oscillator functions. Coulomb corrections are incorporated, and a simplified geometric form of the Bradt-Peters type is obtained. Results spanning the energy range from 1 MeV/nucleon to 1 GeV/nucleon are presented. Good agreement with experimental results is obtained.

Geometric model for nuclear absorption from microscopic theory

NASA Technical Reports Server (NTRS)

John, S.; Townsend, L. W.; Wilson, J. W.; Tripathi, R. K.

1993-01-01

A parameter-free geometric model for nuclear absorption is derived from microscopic theory. The expression for the absorption cross section in the eikonal approximation taken in integral form is separated into a geometric contribution, described by an energy-dependent effective radius, and two surface terms which are shown to cancel in an asymptotic series expansion. For collisions of light nuclei, an expression for the effective radius is derived using harmonic-oscillator nuclear density functions. A direct extension to heavy nuclei with Woods-Saxon densities is made by identifying the equivalent half density radius for the harmonic-oscillator functions. Coulomb corrections are incorporated and a simplified geometric form of the Bradt-Peters type obtained. Results spanning the energy range of 1 MeV/nucleon to 1 GeV/nucleon are presented. Good agreement with experimental results are obtained.

Effects of micro-structure on aerodynamics of Coccinella septempunctata elytra (ladybird) in forward flight as assessed via electron microscopy.

PubMed

Xiang, Jinwu; Liu, Kai; Li, Daochun; Du, Jianxun

2017-11-01

The effects of micro-structure on aerodynamics of Coccinella septempunctata (Coleoptera: Coccinellidae) elytra in forward flight were investigated. The micro-structure was examined by a scanning electron microscope and a digital microscope. Based on the experimental results, five elytron models were constructed to separately investigate the effects of the camber and the local corrugation in both leading edge and trailing edge on aerodynamics. Computational fluid dynamic simulations of five elytron models were conducted by solving the Reynolds-Averaged Navier-Stokes equations with the Reynolds number of 245. The results show that camber and the local corrugation in the leading edge play significant roles in improving the aerodynamic performance, while the local corrugation in the trailing edge has little effect on aerodynamics. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Radiative heat transfer in low-dimensional systems -- microscopic mode

NASA Astrophysics Data System (ADS)

Woods, Lilia; Phan, Anh; Drosdoff, David

2013-03-01

Radiative heat transfer between objects can increase dramatically at sub-wavelength scales. Exploring ways to modulate such transport between nano-systems is a key issue from fundamental and applied points of view. We advance the theoretical understanding of radiative heat transfer between nano-objects by introducing a microscopic model, which takes into account the individual atoms and their atomic polarizabilities. This approach is especially useful to investigate nano-objects with various geometries and give a detailed description of the heat transfer distribution. We employ this model to study the heat exchange in graphene nanoribbon/substrate systems. Our results for the distance separations, substrates, and presence of extended or localized defects enable making predictions for tailoring the radiative heat transfer at the nanoscale. Financial support from the Department of Energy under Contract No. DE-FG02-06ER46297 is acknowledged.

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.

Kinetic Roughening and Energetics of Tetragonal Lysozyme Crystal Growth: A Preliminary Atomic Force Microscopy Investigation

NASA Technical Reports Server (NTRS)

Gorti, Sridhar; Forsythe, Elizabeth L.; Pusey, Marc L.

2004-01-01

We examined particulars of crystal growth from measurements obtained at both microscopic and molecular levels. The crystal growth measurements performed at the microscopic level are well characterized by a model that balances the flux of macromolecules towards the crystal surface with the flux of the crystal surface. Numerical evaluation of model with measurements of crystal growth, in time, provided accurate estimates for the average growth velocities. Growth velocities thus obtained were also interpreted using well-established phenomenological theories. Moreover, we find that microscopic measurements of growth velocity measurements obtained as a function of temperature best characterizes changes in crystal growth modes, when present. We also examined the possibility of detecting a change in crystal growth modes at the molecular level using atomic force microscopy, AFM. From preliminary AFM measurements performed at various supersaturations, we find that magnitude of surface height fluctuations, h(x), increases with supersaturation. Further examination of surface height fluctuations using methods established for fluctuation spectroscopy also enabled the discovery of the existence of a characteristic length, c, which may possibly determine the mode of crystal growth. Although the results are preliminary, we establish the non- critical divergence of 5 and the root-mean-square (rms) magnitude of height-height fluctuations as the kinetic roughening transition temperatures are approached. Moreover, we also examine approximate models for interpreting the non-critical behavior of both 6 and rms magnitude of height-height fluctuations, as the solution supersaturation is increased towards the kinetic roughening supersaturation.

Monte Carlo simulation of electron thermalization in scintillator materials: Implications for scintillator nonproportionality

DOE PAGES

Prange, Micah P.; Xie, YuLong; Campbell, Luke W.; ...

2017-12-20

The lack of reliable quantitative estimates of the length and time scales associated with hot electron thermalization after a gamma-ray induced energy cascade obscures the interplay of various microscopic processes controlling scintillator performance and hampers the search for improved detector materials. We apply a detailed microscopic kinetic Monte Carlo model of the creation and subsequent thermalization of hot electrons produced by gamma irradiation of six important scintillating crystals to determine the spatial extent of the cloud of excitations produced by gamma rays and the time required for the cloud to thermalize with the host lattice. The main ingredients of themore » model are ensembles of microscopic track structures produced upon gamma excitation (including the energy distribution of the excited carriers), numerical estimates of electron-phonon scattering rates, and a calculated particle dispersion to relate the speed and energy of excited carriers. All these ingredients are based on first-principles density functional theory calculations of the electronic and phonon band structures of the materials. The details of the Monte Carlo model are presented along with the results for thermalization time and distance distributions. Here, these results are discussed in light of previous work. It is found that among the studied materials, calculated thermalization distances are positively correlated with measured nonproportionality. In the important class of halide scintillators, the particle dispersion is found to be more influential than the largest phonon energy in determining the thermalization distance.« less

Generation of dense statistical connectomes from sparse morphological data

PubMed Central

Egger, Robert; Dercksen, Vincent J.; Udvary, Daniel; Hege, Hans-Christian; Oberlaender, Marcel

2014-01-01

Sensory-evoked signal flow, at cellular and network levels, is primarily determined by the synaptic wiring of the underlying neuronal circuitry. Measurements of synaptic innervation, connection probabilities and subcellular organization of synaptic inputs are thus among the most active fields of research in contemporary neuroscience. Methods to measure these quantities range from electrophysiological recordings over reconstructions of dendrite-axon overlap at light-microscopic levels to dense circuit reconstructions of small volumes at electron-microscopic resolution. However, quantitative and complete measurements at subcellular resolution and mesoscopic scales to obtain all local and long-range synaptic in/outputs for any neuron within an entire brain region are beyond present methodological limits. Here, we present a novel concept, implemented within an interactive software environment called NeuroNet, which allows (i) integration of sparsely sampled (sub)cellular morphological data into an accurate anatomical reference frame of the brain region(s) of interest, (ii) up-scaling to generate an average dense model of the neuronal circuitry within the respective brain region(s) and (iii) statistical measurements of synaptic innervation between all neurons within the model. We illustrate our approach by generating a dense average model of the entire rat vibrissal cortex, providing the required anatomical data, and illustrate how to measure synaptic innervation statistically. Comparing our results with data from paired recordings in vitro and in vivo, as well as with reconstructions of synaptic contact sites at light- and electron-microscopic levels, we find that our in silico measurements are in line with previous results. PMID:25426033

Monte Carlo simulation of electron thermalization in scintillator materials: Implications for scintillator nonproportionality

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

Prange, Micah P.; Xie, YuLong; Campbell, Luke W.

2017-12-21

The lack of reliable quantitative estimates of the length and time scales associated with hot electron thermalization after a gamma-ray induced energy cascade obscures the interplay of various microscopic processes controlling scintillator performance and hampers the search for improved detector materials. We apply a detailed microscopic kinetic Monte Carlo model of the creation and subsequent thermalization of hot electrons produced by gamma irradiation of six important scintillating crystals to determine the spatial extent of the cloud of excitations produced by gamma rays and the time required for the cloud to thermalize with the host lattice. The main ingredients of themore » model are ensembles of microscopic track structures produced upon gamma excitation (including the energy distribution of the excited carriers), numerical estimates of electron-phonon scattering rates, and a calculated particle dispersion to relate the speed and energy of excited carriers. All these ingredients are based on first-principles density functional theory calculations of the electronic and phonon band structures of the materials. Details of the Monte Carlo model are presented along with results for thermalization time and distance distributions. These results are discussed in light of previous work. It is found that among the studied materials, calculated thermalization distances are positively correlated with measured nonproportionality. In the important class of halide scintillators, the particle dispersion is found to be more influential than the largest phonon energy in determining the thermalization distance.« less

3-D Teaching Models for All

ERIC Educational Resources Information Center

Bradley, Joan; Farland-Smith, Donna

2010-01-01

Allowing a student to "see" through touch what other students see through a microscope can be a challenging task. Therefore, author Joan Bradley created three-dimensional (3-D) models with one student's visual impairment in mind. They are meant to benefit all students and can be used to teach common high school biology topics, including the…

Edge-defined film-fed growth of thin silicon sheets

NASA Technical Reports Server (NTRS)

Ettouney, H. M.; Kalejs, J. P.

1984-01-01

Finite element analysis was used on two length scales to understand crystal growth of thin silicon sheets. Thermal-capillary models of entire ribbon growth systems were developed. Microscopic modeling of morphological structure of melt/solid interfaces beyond the point of linear instability was carried out. The application to silicon system is discussed.

Visualizing the Entropy Change of a Thermal Reservoir

ERIC Educational Resources Information Center

Langbeheim, Elon; Safran, Samuel A.; Yerushalmi, Edit

2014-01-01

When a system exchanges energy with a constant-temperature environment, the entropy of the surroundings changes. A lattice model of a fluid thermal reservoir can provide a visualization of the microscopic changes that occur in the surroundings upon energy transfer from the system. This model can be used to clarify the consistency of phenomena such…

Coffee Cup Atomic Force Microscopy

ERIC Educational Resources Information Center

Ashkenaz, David E.; Hall, W. Paige; Haynes, Christy L.; Hicks, Erin M.; McFarland, Adam D.; Sherry, Leif J.; Stuart, Douglas A.; Wheeler, Korin E.; Yonzon, Chanda R.; Zhao, Jing; Godwin, Hilary A.; Van Duyne, Richard P.

2010-01-01

In this activity, students use a model created from a coffee cup or cardstock cutout to explore the working principle of an atomic force microscope (AFM). Students manipulate a model of an AFM, using it to examine various objects to retrieve topographic data and then graph and interpret results. The students observe that movement of the AFM…

Flocking from a quantum analogy: spin-orbit coupling in an active fluid

NASA Astrophysics Data System (ADS)

Loewe, Benjamin; Souslov, Anton; Goldbart, Paul M.

2018-01-01

Systems composed of strongly interacting self-propelled particles can form a spontaneously flowing polar active fluid. The study of the connection between the microscopic dynamics of a single such particle and the macroscopic dynamics of the fluid can yield insights into experimentally realizable active flows, but this connection is well understood in only a few select cases. We introduce a model of self-propelled particles based on an analogy with the motion of electrons that have strong spin-orbit coupling. We find that, within our model, self-propelled particles are subject to an analog of the Heisenberg uncertainty principle that relates translational and rotational noise. Furthermore, by coarse-graining this microscopic model, we establish expressions for the coefficients of the Toner-Tu equations—the hydrodynamic equations that describe an active fluid composed of these ‘active spins.’ The connection between stochastic self-propelled particles and quantum particles with spin may help realize exotic phases of matter using active fluids via analogies with systems composed of strongly correlated electrons.

Some new results on the Levy, Levy and Solomon microscopic stock market model

NASA Astrophysics Data System (ADS)

Zschischang, Elmar; Lux, Thomas

2001-03-01

We report some findings from our simulations of the Levy, Levy and Solomon microscopic stock market model. Our results cast doubts on some of the results published in the original papers (i.e., chaotic stock price movements). We also point out the possibility of sensitive dependence on initial conditions of the emerging wealth distribution among agents. Extensions of the model set-up show that with varying degrees of risk aversion, the less risk averse traders will tend to dominate the market. Similarly, when introducing a new trader group (or even a single trader) with a constant share of stocks in their portfolio, the latter will eventually take over and marginalize the other groups. The better performance of the more sober investors is in accordance with traditional perceptions in financial economics. Hence, the survival of ‘noise traders’ looking at short-term trends and patterns remains as much of a puzzle in this framework as in the traditional Efficient Market Theory.

The Gram-positive model organism Bacillus subtilis does not form microscopically detectable cardiolipin-specific lipid domains.

PubMed

Pogmore, Alex-Rose; Seistrup, Kenneth H; Strahl, Henrik

2018-04-01

Rather than being homogenous diffusion-dominated structures, biological membranes can exhibit areas with distinct composition and characteristics, commonly termed as lipid domains. Arguably the most comprehensively studied examples in bacteria are domains formed by cardiolipin, which have been functionally linked to protein targeting, the cell division process and the mode of action of membrane-targeting antimicrobials. Cardiolipin domains were originally identified in the Gram-negative model organism Escherichia coli based on preferential staining by the fluorescent membrane dye nonylacridine orange (NAO), and later reported to also exist in other Gram-negative and -positive bacteria. Recently, the lipid-specificity of NAO has been questioned based on studies conducted in E. coli. This prompted us to reanalyse cardiolipin domains in the Gram-positive model organism Bacillus subtilis. Here we show that logarithmically growing B. subtilis does not form microscopically detectable cardiolipin-specific lipid domains, and that NAO is not a specific stain for cardiolipin in this organism.

Modeling of ultrashort pulse generation in mode-locked VECSELs

NASA Astrophysics Data System (ADS)

Kilen, I.; Koch, S. W.; Hader, J.; Moloney, J. V.

2016-03-01

We present a study of various models for the mode-locked pulse dynamics in a vertical external-cavity surface emitting laser with a saturable absorber. The semiconductor Bloch equations are used to model microscopically the light-matter interaction and the carrier dynamics. Maxwell's equations describe the pulse propagation. Scattering contributions due to higher order correlation effects are approximated using effective rates that are found from a comparison to solving the microscopic scattering equations on the second Born-Markov level. It is shown that the simulations result in the same mode-locked final state whether the system is initialized with a test pulse close to the final mode-locked pulse or the full field build-up from statistical noise is considered. The influence of the cavity design is studied. The longest pulses are found for a standard V-cavity while a linear cavity and a V-cavity with an high reflectivity mirror in the middle are shown to produce similar, much shorter pulses.

Environmental research program. 1995 Annual report

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

Brown, N.J.

1996-06-01

The objective of the Environmental Research Program is to enhance the understanding of, and mitigate the effects of pollutants on health, ecological systems, global and regional climate, and air quality. The program is multidisciplinary and includes fundamental research and development in efficient and environmentally benign combustion, pollutant abatement and destruction, and novel methods of detection and analysis of criteria and noncriteria pollutants. This diverse group conducts investigations in combustion, atmospheric and marine processes, flue-gas chemistry, and ecological systems. Combustion chemistry research emphasizes modeling at microscopic and macroscopic scales. At the microscopic scale, functional sensitivity analysis is used to explore themore » nature of the potential-to-dynamics relationships for reacting systems. Rate coefficients are estimated using quantum dynamics and path integral approaches. At the macroscopic level, combustion processes are modelled using chemical mechanisms at the appropriate level of detail dictated by the requirements of predicting particular aspects of combustion behavior. Parallel computing has facilitated the efforts to use detailed chemistry in models of turbulent reacting flow to predict minor species concentrations.« less

Differentiating Amino Acid Residues and Side Chain Orientations in Peptides Using Scanning Tunneling Microscopy

PubMed Central

Claridge, Shelley A.; Thomas, John C.; Silverman, Miles A.; Schwartz, Jeffrey J.; Yang, Yanlian; Wang, Chen; Weiss, Paul S.

2014-01-01

Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structure at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer’s and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level. PMID:24219245

Modeling of Yb3+/Er3+-codoped microring resonators

NASA Astrophysics Data System (ADS)

Vallés, Juan A.; Gălătuş, Ramona

2015-03-01

The performance of a highly Yb3+/Er3+-codoped phosphate glass add-drop microring resonator is numerically analyzed. The model assumes resonant behaviour of both pump and signal powers and the dependences of pump intensity build-up inside the microring resonator and of the signal transfer functions to the device through and drop ports are evaluated. Detailed equations for the evolution of the rare-earth ions levels population densities and the propagation of the optical powers inside the microring resonator are included in the model. Moreover, due to the high dopant concentrations considered, the microscopic statistical formalism based on the statistical average of the excitation probability of the Er3+ ion in a microscopic level has been used to describe energy-transfer inter-atomic mechanisms. Realistic parameters and working conditions are used for the calculations. Requirements to achieve amplification and laser oscillation within these devices are obtainable as a function of rare earth ions concentration and coupling losses.

Mushy zone modeling

NASA Astrophysics Data System (ADS)

Glicksman, Martin E.; Smith, Richard N.; Marsh, Steven P.; Kuklinski, Robert

A key element of mushy zone modeling is the description of the microscopic evolution of the lengthscales within the mushy zone and the influence of macroscopic transport processes. This paper describes some recent progress in developing a mean-field statistical theory of phase coarsening in adiabatic mushy zones. The main theoretical predictions are temporal scaling laws that indicate that average lengthscale increases as time 1/3, a self-similar distribution of mushy zone lengthscales based on spherical solid particle shapes, and kinetic rate constants which provide the dependences of the coarsening process on material parameters and the volume fraction of the solid phase. High precision thermal decay experiments are described which verify aspects of the theory in pure material mushy zones held under adiabatic conditions. The microscopic coarsening theory is then integrated within a macroscopic heat transfer model of one-dimensional alloy solidification, using the Double Integral Method. The method demonstrates an ability to predict the influence of macroscopic heat transfer on the evolution of primary and secondary dendrite arm spacings in Al-Cu alloys. Finally, some suggestions are made for future experimental and theoretical studies required in developing comprehensive solidification processing models.

Comb model for the anomalous diffusion with dual-phase-lag constitutive relation

NASA Astrophysics Data System (ADS)

Liu, Lin; Zheng, Liancun; Fan, Yu; Chen, Yanping; Liu, Fawang

2018-10-01

As a development of the Fick's model, the dual-phase-lag constitutive relationship with macroscopic and microscopic relaxation characteristics is introduced to describe the anomalous diffusion in comb model. The Dirac delta function in the formulated governing equation represents the special spatial structure of comb model that the horizontal current only exists on the x axis. Solutions are obtained by analytical method with Laplace transform and Fourier transform. The dependence of concentration field and mean square displacement on different parameters are presented and discussed. Results show that the macroscopic and microscopic relaxation parameters have opposite effects on the particle distribution and mean square displacement. Furthermore, four significant results with constant 1/2 are concluded, namely the product of the particle number and the mean square displacement on the x axis equals to 1/2, the exponent of mean square displacement is 1/2 at the special case τq= τP, an asymptotic form of mean square displacement (MSD∼t1/2 as t→0, ∞) is obtained as well at the short time behavior and the long time behavior.

Thermodynamics of transport through the ammonium transporter Amt-1 investigated with free energy calculations.

PubMed

Ullmann, R Thomas; Andrade, Susana L A; Ullmann, G Matthias

2012-08-16

Amt-1 from Archaeoglobus fulgidus (AfAmt-1) belongs to the Amt/Rh family of ammonium/ammonia transporting membrane proteins. The transport mode and the precise microscopic permeation mechanism utilized by these proteins are intensely debated. Open questions concern the identity of the transported substrate (ammonia and/or ammonium) and whether the transport is passive or active. To address these questions, we studied the overall thermodynamics of the different transport modes as a function of the environmental conditions. Then, we investigated the thermodynamics of the underlying microscopic transport mechanisms with free energy calculations within a continuum electrostatics model. The formalism developed for this purpose is of general utility in the calculation of binding free energies for ligands with multiple protonation forms or other binding forms. The results of our calculations are compared to the available experimental and theoretical data on Amt/Rh proteins and discussed in light of the current knowledge on the physiological conditions experienced by microorganisms and plants. We found that microscopic models of electroneutral and electrogenic transport modes are in principle thermodynamically viable. However, only the electrogenic variants have a net thermodynamic driving force under the physiological conditions experienced by microorganisms and plants. Thus, the transport mechanism of AfAmt-1 is most likely electrogenic.

Gross domestic product growth rates as confined Lévy flights: Towards a unifying theory of economic growth rate fluctuations

NASA Astrophysics Data System (ADS)

Lera, Sandro Claudio; Sornette, Didier

2018-01-01

A model that combines economic growth rate fluctuations at the microscopic and macroscopic levels is presented. At the microscopic level, firms are growing at different rates while also being exposed to idiosyncratic shocks at the firm and sector levels. We describe such fluctuations as independent Lévy-stable fluctuations, varying over multiple orders of magnitude. These fluctuations are aggregated and measured at the macroscopic level in averaged economic output quantities such as GDP. A fundamental question is thereby to what extent individual firm size fluctuations can have a noticeable impact on the overall economy. We argue that this question can be answered by considering the Lévy fluctuations as embedded in a steep confining potential well, ensuring nonlinear mean-reversal behavior, without having to rely on microscopic details of the system. The steepness of the potential well directly controls the extent to which idiosyncratic shocks to firms and sectors are damped at the level of the economy. Additionally, the theory naturally accounts for business cycles, represented in terms of a bimodal economic output distribution and thus connects two so far unrelated fields in economics. By analyzing 200 years of U.S. gross domestic product growth rates, we find that the model is in good agreement with the data.

Gross domestic product growth rates as confined Lévy flights: Towards a unifying theory of economic growth rate fluctuations.

PubMed

Lera, Sandro Claudio; Sornette, Didier

2018-01-01

A model that combines economic growth rate fluctuations at the microscopic and macroscopic levels is presented. At the microscopic level, firms are growing at different rates while also being exposed to idiosyncratic shocks at the firm and sector levels. We describe such fluctuations as independent Lévy-stable fluctuations, varying over multiple orders of magnitude. These fluctuations are aggregated and measured at the macroscopic level in averaged economic output quantities such as GDP. A fundamental question is thereby to what extent individual firm size fluctuations can have a noticeable impact on the overall economy. We argue that this question can be answered by considering the Lévy fluctuations as embedded in a steep confining potential well, ensuring nonlinear mean-reversal behavior, without having to rely on microscopic details of the system. The steepness of the potential well directly controls the extent to which idiosyncratic shocks to firms and sectors are damped at the level of the economy. Additionally, the theory naturally accounts for business cycles, represented in terms of a bimodal economic output distribution and thus connects two so far unrelated fields in economics. By analyzing 200 years of U.S. gross domestic product growth rates, we find that the model is in good agreement with the data.

Fluorescence-guided resection of intracranial VX2 tumor in a preclinical model using 5-aminolevulinic acid (ALA): preliminary results

NASA Astrophysics Data System (ADS)

Bogaards, Arjen; Varma, Abhay; Moriyama, Eduardo H.; Lin, Annie; Giles, Anoja; Bisland, Stuart K.; Lilge, Lothar D.; Bilbao, G. M.; Muller, Paul J.; Wilson, Brian C.

2003-06-01

Fluorescence-guided brain tumor resection may help the neurosurgeon to identify tumor margins that merge imperceptibly into the normal brain tissue and are difficult to identify under white light illumination even using an operating microscope. We compared the amount of residual tumor after white light resection using an operating microscope versus that after fluorescnece-guided resection of an intracranial VX2 tumor in a preclinical model using our previously developed co-axial fluorscence imaging and spectroscopy system, exciting and detecting PpIX fluorescence at 405nm and 635nm respectively. Preliminary results: No fluorescence was present in 3 non-tumor-bearing animals. Fluorescence was present in all 15 tumor-bearing animals after white light resection was completed. To date in 4 rabbits, a decrease in residual tumor was found when using additional fluorescence guided resection compared to white light resection only. Conclusions: ALA induced PpIX fluorescence detects tumor margins not seen under an operation microscope using while light. Using fluorescence imaging to guide tumor resection resulted in a 3-fold decrease in the amount of residual timor. However, these preliminary results indicate that also an additional amount of normal brain is resected, which will be further investigated.

Extreme ultraviolet patterned mask inspection performance of advanced projection electron microscope system for 11nm half-pitch generation

NASA Astrophysics Data System (ADS)

Hirano, Ryoichi; Iida, Susumu; Amano, Tsuyoshi; Watanabe, Hidehiro; Hatakeyama, Masahiro; Murakami, Takeshi; Suematsu, Kenichi; Terao, Kenji

2016-03-01

Novel projection electron microscope optics have been developed and integrated into a new inspection system named EBEYE-V30 ("Model EBEYE" is an EBARA's model code) , and the resulting system shows promise for application to half-pitch (hp) 16-nm node extreme ultraviolet lithography (EUVL) patterned mask inspection. To improve the system's inspection throughput for 11-nm hp generation defect detection, a new electron-sensitive area image sensor with a high-speed data processing unit, a bright and stable electron source, and an image capture area deflector that operates simultaneously with the mask scanning motion have been developed. A learning system has been used for the mask inspection tool to meet the requirements of hp 11-nm node EUV patterned mask inspection. Defects are identified by the projection electron microscope system using the "defectivity" from the characteristics of the acquired image. The learning system has been developed to reduce the labor and costs associated with adjustment of the detection capability to cope with newly-defined mask defects. We describe the integration of the developed elements into the inspection tool and the verification of the designed specification. We have also verified the effectiveness of the learning system, which shows enhanced detection capability for the hp 11-nm node.

Possibility of microscopic liquid water formation at landing sites on Mars and their observational potential

NASA Astrophysics Data System (ADS)

Pál, B.; Kereszturi, Á.

2017-01-01

Microscopic liquid brines, especially calcium-perchlorate could emerge by deliquescence on Mars during night time hours. Using climate model computations and orbital humidity observations, the ideal periods and their annual plus daily characteristics at various past, current and future landing sites were compared. Such results provide context for future analysis and targeting the related observations by the next missions for Mars. Based on the analysis, at most (but not all) past missions' landing sites, microscopic brine could emerge during night time for different durations. Analysing the conditions at ExoMars rover's primary landing site at Oxia Planum, the best annual period was found to be between Ls 115-225, and in Local Time 2-5, after midnight. In an ideal case, 4 h of continuous liquid phase can emerge there. Local conditions might cause values to differ from those estimated by the model. Thermal inertia could especially make such differences (low TI values favour fast cooling and H2O cold trapping at loose surfaces) and the concentration of calcium-perchlorate salt in the regolith also influences the process (it might occur preferentially at long-term exposed surfaces without recent loose dust coverage). These factors should be taken into account while targeting future liquid water observations on Mars.

Determination of Poisson Ratio of Bovine Extraocular Muscle by Computed X-Ray Tomography

PubMed Central

Kim, Hansang; Yoo, Lawrence; Shin, Andrew; Demer, Joseph L.

2013-01-01

The Poisson ratio (PR) is a fundamental mechanical parameter that approximates the ratio of relative change in cross sectional area to tensile elongation. However, the PR of extraocular muscle (EOM) is almost never measured because of experimental constraints. The problem was overcome by determining changes in EOM dimensions using computed X-ray tomography (CT) at microscopic resolution during tensile elongation to determine transverse strain indicated by the change in cross-section. Fresh bovine EOM specimens were prepared. Specimens were clamped in a tensile fixture within a CT scanner (SkyScan, Belgium) with temperature and humidity control and stretched up to 35% of initial length. Sets of 500–800 contiguous CT images were obtained at 10-micron resolution before and after tensile loading. Digital 3D models were then built and discretized into 6–8-micron-thick elements. Changes in longitudinal thickness of each microscopic element were determined to calculate strain. Green's theorem was used to calculate areal strain in transverse directions orthogonal to the stretching direction. The mean PR from discretized 3D models for every microscopic element in 14 EOM specimens averaged 0.457 ± 0.004 (SD). The measured PR of bovine EOM is thus near the limit of incompressibility. PMID:23484091

Delineation of the Species Haemophilus influenzae by Phenotype, Multilocus Sequence Phylogeny, and Detection of Marker Genes▿ †

PubMed Central

Nørskov-Lauritsen, Niels; Overballe, Merete D.; Kilian, Mogens

2009-01-01

To obtain more information on the much-debated definition of prokaryotic species, we investigated the borders of Haemophilus influenzae by comparative analysis of H. influenzae reference strains with closely related bacteria including strains assigned to Haemophilus haemolyticus, cryptic genospecies biotype IV, and the never formally validated species “Haemophilus intermedius”. Multilocus sequence phylogeny based on six housekeeping genes separated a cluster encompassing the type and the reference strains of H. influenzae from 31 more distantly related strains. Comparison of 16S rRNA gene sequences supported this delineation but was obscured by a conspicuously high number of polymorphic sites in many of the strains that did not belong to the core group of H. influenzae strains. The division was corroborated by the differential presence of genes encoding H. influenzae adhesion and penetration protein, fuculokinase, and Cu,Zn-superoxide dismutase, whereas immunoglobulin A1 protease activity or the presence of the iga gene was of limited discriminatory value. The existence of porphyrin-synthesizing strains (“H. intermedius”) closely related to H. influenzae was confirmed. Several chromosomally encoded hemin biosynthesis genes were identified, and sequence analysis showed these genes to represent an ancestral genotype rather than recent transfers from, e.g., Haemophilus parainfluenzae. Strains previously assigned to H. haemolyticus formed several separate lineages within a distinct but deeply branching cluster, intermingled with strains of “H. intermedius” and cryptic genospecies biotype IV. Although H. influenzae is phenotypically more homogenous than some other Haemophilus species, the genetic diversity and multicluster structure of strains traditionally associated with H. influenzae make it difficult to define the natural borders of that species. PMID:19060144

OMEGA - OSIRIS Mapping of Emission-line Galaxies in A901/2 - II. Environmental influence on integrated star formation properties and AGN activity

NASA Astrophysics Data System (ADS)

Rodríguez del Pino, Bruno; Aragón-Salamanca, Alfonso; Chies-Santos, Ana L.; Weinzirl, Tim; Bamford, Steven P.; Gray, Meghan E.; Böhm, Asmus; Wolf, Christian; Maltby, David T.

2017-06-01

We present a study of the star formation and AGN activity for galaxies in CP 15051 the Abell 901/2 multicluster system at z ˜ 0.167 as part of the OSIRIS Mapping of Emission-line Galaxies in A901/2 (OMEGA) survey. Using Tuneable Filter data obtained with the OSIRIS instrument at the Gran Telescopio Canarias, we produce spectra covering the Hα and [N II] spectral lines for more than 400 galaxies. Using optical emission-line diagnostics, we identify a significant number of galaxies hosting AGN, which tend to have high masses and a broad range of morphologies. Moreover, within the environmental densities probed by our study, we find no environmental dependence on the fraction of galaxies hosting AGN. The analysis of the integrated Hα emission shows that the specific star formation rates of a majority of the cluster galaxies are below the field values for a given stellar mass. We interpret this result as evidence for a slow decrease in the star formation activity of star-forming galaxies as they fall into higher density regions, contrary to some previous studies that suggested a rapid truncation of star formation. We find that most of the intermediate- and high-mass spiral galaxies go through a phase in which their star formation is suppressed but still retain significant star formation activity. During this phase, these galaxies tend to retain their spiral morphology while their colours become redder. The presence of this type of galaxies in high-density regions indicates that the physical mechanism responsible for suppressing star formation affects mainly the gas component of the galaxies, suggesting that ram-pressure stripping or starvation is potentially responsible.

Assessing microscope image focus quality with deep learning.

PubMed

Yang, Samuel J; Berndl, Marc; Michael Ando, D; Barch, Mariya; Narayanaswamy, Arunachalam; Christiansen, Eric; Hoyer, Stephan; Roat, Chris; Hung, Jane; Rueden, Curtis T; Shankar, Asim; Finkbeiner, Steven; Nelson, Philip

2018-03-15

Large image datasets acquired on automated microscopes typically have some fraction of low quality, out-of-focus images, despite the use of hardware autofocus systems. Identification of these images using automated image analysis with high accuracy is important for obtaining a clean, unbiased image dataset. Complicating this task is the fact that image focus quality is only well-defined in foreground regions of images, and as a result, most previous approaches only enable a computation of the relative difference in quality between two or more images, rather than an absolute measure of quality. We present a deep neural network model capable of predicting an absolute measure of image focus on a single image in isolation, without any user-specified parameters. The model operates at the image-patch level, and also outputs a measure of prediction certainty, enabling interpretable predictions. The model was trained on only 384 in-focus Hoechst (nuclei) stain images of U2OS cells, which were synthetically defocused to one of 11 absolute defocus levels during training. The trained model can generalize on previously unseen real Hoechst stain images, identifying the absolute image focus to within one defocus level (approximately 3 pixel blur diameter difference) with 95% accuracy. On a simpler binary in/out-of-focus classification task, the trained model outperforms previous approaches on both Hoechst and Phalloidin (actin) stain images (F-scores of 0.89 and 0.86, respectively over 0.84 and 0.83), despite only having been presented Hoechst stain images during training. Lastly, we observe qualitatively that the model generalizes to two additional stains, Hoechst and Tubulin, of an unseen cell type (Human MCF-7) acquired on a different instrument. Our deep neural network enables classification of out-of-focus microscope images with both higher accuracy and greater precision than previous approaches via interpretable patch-level focus and certainty predictions. The use of synthetically defocused images precludes the need for a manually annotated training dataset. The model also generalizes to different image and cell types. The framework for model training and image prediction is available as a free software library and the pre-trained model is available for immediate use in Fiji (ImageJ) and CellProfiler.

Correction to verdonck and tuerlinckx (2014).

PubMed

2015-01-01

Reports an error in "The Ising Decision Maker: A binary stochastic network for choice response time" by Stijn Verdonck and Francis Tuerlinckx (Psychological Review, 2014[Jul], Vol 121[3], 422-462). An inaccurate assumption in Appendix B (provided in the erratum) led to an oversimplified result in Equation 18 (the diffusion equations associated with the microscopically defined dynamics). The authors sincerely thank Rani Moran for making them aware of the problem. Only the expression of the diffusion coefficient D is incorrect, and should be changed, as indicated in the erratum. Both the cause of the problem and the solution are also explained in the erratum. (The following abstract of the original article appeared in record 2014-31650-006.) The Ising Decision Maker (IDM) is a new formal model for speeded two-choice decision making derived from the stochastic Hopfield network or dynamic Ising model. On a microscopic level, it consists of 2 pools of binary stochastic neurons with pairwise interactions. Inside each pool, neurons excite each other, whereas between pools, neurons inhibit each other. The perceptual input is represented by an external excitatory field. Using methods from statistical mechanics, the high-dimensional network of neurons (microscopic level) is reduced to a two-dimensional stochastic process, describing the evolution of the mean neural activity per pool (macroscopic level). The IDM can be seen as an abstract, analytically tractable multiple attractor network model of information accumulation. In this article, the properties of the IDM are studied, the relations to existing models are discussed, and it is shown that the most important basic aspects of two-choice response time data can be reproduced. In addition, the IDM is shown to predict a variety of observed psychophysical relations such as Piéron's law, the van der Molen-Keuss effect, and Weber's law. Using Bayesian methods, the model is fitted to both simulated and real data, and its performance is compared to the Ratcliff diffusion model. (PsycINFO Database Record (c) 2015 APA, all rights reserved).

Microscopic description of elastic and direct inelastic nucleon scattering off spherical nuclei

NASA Astrophysics Data System (ADS)

Dupuis, M.

2017-05-01

The purpose of this study is to improve the modeling of nucleon direct inelastic scattering to the continuum using a microscopic and parameter-free approach. For the first time, direct elastic scattering, inelastic scattering to discrete excitations and to the continuum are described within a microscopic approach without adjustable parameters. Proton scattering off 90Zr and 208Pb are the reactions used as test case examples of the calculations. The model uses the Melbourne g-matrix and the Random Phase Approximation description of nuclear states, implemented with the Gogny D1S interaction. The relevant optical and transition potentials in a finite nucleus are calculated within a local density approximation. As we use the nuclear matter approach we limit our study to incident energies above 40 MeV. We first checked that this model provides an accurate account of measured cross sections for elastic scattering and inelastic scattering to discrete states. It is then applied to the direct inelastic scattering to the continuum considering all one-phonon excitations predicted within the RPA approach. This accounts for a part of the direct pre-equilibrium emission, often labeled as the one-step direct process in quantum-based approaches. Our approach provides a very accurate description of angular distributions where the one-step process dominates. The impact of collective excitations is shown to be non negligible for energy transfer to the target up to 20 MeV, decreasing as the incident energy increases. For incident energies above 80 MeV, our modeling provides a good account of direct proton emission for an energy transfer to the target up to 30 MeV. However, the proton emission we predict underestimates the measured cross sections for incident energies below 80 MeV. We compare our prediction to those of the phenomenological exciton model to help interpret this result. Directions that may improve our modeling 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

Simulation of Ectopic Pacemakers in the Heart: Multiple Ectopic Beats Generated by Reentry inside Fibrotic Regions

PubMed Central

Gouvêa de Barros, Bruno; Weber dos Santos, Rodrigo; Alonso, Sergio

2015-01-01

The inclusion of nonconducting media, mimicking cardiac fibrosis, in two models of cardiac tissue produces the formation of ectopic beats. The fraction of nonconducting media in comparison with the fraction of healthy myocytes and the topological distribution of cells determines the probability of ectopic beat generation. First, a detailed subcellular microscopic model that accounts for the microstructure of the cardiac tissue is constructed and employed for the numerical simulation of action potential propagation. Next, an equivalent discrete model is implemented, which permits a faster integration of the equations. This discrete model is a simplified version of the microscopic model that maintains the distribution of connections between cells. Both models produce similar results when describing action potential propagation in homogeneous tissue; however, they slightly differ in the generation of ectopic beats in heterogeneous tissue. Nevertheless, both models present the generation of reentry inside fibrotic tissues. This kind of reentry restricted to microfibrosis regions can result in the formation of ectopic pacemakers, that is, regions that will generate a series of ectopic stimulus at a fast pacing rate. In turn, such activity has been related to trigger fibrillation in the atria and in the ventricles in clinical and animal studies. PMID:26583127

Numerical studies on the electromagnetic properties of the nonlinear Lorentz Computational model for the dielectric media

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

Abe, H.; Okuda, H.

We study linear and nonlinear properties of a new computer simulation model developed to study the propagation of electromagnetic waves in a dielectric medium in the linear and nonlinear regimes. The model is constructed by combining a microscopic model used in the semi-classical approximation for the dielectric media and the particle model developed for the plasma simulations. It is shown that the model may be useful for studying linear and nonlinear wave propagation in the dielectric media.

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...

Non-equilibrium processes in p + Ag collisions at GeV energies

NASA Astrophysics Data System (ADS)

Fidelus, M.; Filges, D.; Goldenbaum, F.; Jarczyk, L.; Kamys, B.; Kistryn, M.; Kistryn, St.; Kozik, E.; Kulessa, P.; Machner, H.; Magiera, A.; Piskor-Ignatowicz, B.; Pysz, K.; Rudy, Z.; Sharma, Sushil K.; Siudak, R.; Wojciechowski, M.; PISA Collaboration

2017-12-01

The double differential spectra d2σ /d Ω d E of p , d , t , 3,4,6He, 6,7,8,9Li, 7,9,10Be, and 10,11,12B were measured at seven scattering angles, 15.6∘, 20∘, 35∘, 50∘, 65∘, 80∘, and 100∘, in the laboratory system for proton induced reactions on a silver target. Measurements were done for three proton energies: 1.2, 1.9, and 2.5 GeV. The experimental data were compared to calculations performed by means of two-step theoretical microscopic models. The first step of the reaction was described by the intranuclear cascade model incl4.6 and the second one by four different models (ABLA07, GEM2, gemini++, and SMM) using their standard parameter settings. Systematic deviations of the data from predictions of the models were observed. The deviations were especially large for the forward scattering angles and for the kinetic energy of emitted particles in the range from about 50 to 150 MeV. This suggests that some important non-equilibrium mechanism is lacking in the present day microscopic models of proton-nucleus collisions in the studied beam energy range.

Structure models: From shell model to ab initio methods. A brief introduction to microscopic theories for exotic nuclei

NASA Astrophysics Data System (ADS)

Bacca, Sonia

2016-04-01

A brief review of models to describe nuclear structure and reactions properties is presented, starting from the historical shell model picture and encompassing modern ab initio approaches. A selection of recent theoretical results on observables for exotic light and medium-mass nuclei is shown. Emphasis is given to the comparison with experiment and to what can be learned about three-body forces and continuum properties.

Model based control of dynamic atomic force microscope.

PubMed

Lee, Chibum; Salapaka, Srinivasa M

2015-04-01

A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H(∞) control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments.

Electric Conduction in Solids: a Pedagogical Approach Supported by Laboratory Measurements and Computer Modelling Environments

NASA Astrophysics Data System (ADS)

Bonura, A.; Capizzo, M. C.; Fazio, C.; Guastella, I.

2008-05-01

In this paper we present a pedagogic approach aimed at modeling electric conduction in semiconductors, built by using NetLogo, a programmable modeling environment for building and exploring multi-agent systems. `Virtual experiments' are implemented to confront predictions of different microscopic models with real measurements of electric properties of matter, such as resistivity. The relations between these electric properties and other physical variables, like temperature, are, then, analyzed.

History-dependent friction and slow slip from time-dependent microscopic junction laws studied in a statistical framework

NASA Astrophysics Data System (ADS)

Thøgersen, Kjetil; Trømborg, Jørgen Kjoshagen; Sveinsson, Henrik Andersen; Malthe-Sørenssen, Anders; Scheibert, Julien

2014-05-01

To study how macroscopic friction phenomena originate from microscopic junction laws, we introduce a general statistical framework describing the collective behavior of a large number of individual microjunctions forming a macroscopic frictional interface. Each microjunction can switch in time between two states: a pinned state characterized by a displacement-dependent force and a slipping state characterized by a time-dependent force. Instead of tracking each microjunction individually, the state of the interface is described by two coupled distributions for (i) the stretching of pinned junctions and (ii) the time spent in the slipping state. This framework allows for a whole family of microjunction behavior laws, and we show how it represents an overarching structure for many existing models found in the friction literature. We then use this framework to pinpoint the effects of the time scale that controls the duration of the slipping state. First, we show that the model reproduces a series of friction phenomena already observed experimentally. The macroscopic steady-state friction force is velocity dependent, either monotonic (strengthening or weakening) or nonmonotonic (weakening-strengthening), depending on the microscopic behavior of individual junctions. In addition, slow slip, which has been reported in a wide variety of systems, spontaneously occurs in the model if the friction contribution from junctions in the slipping state is time weakening. Next, we show that the model predicts a nontrivial history dependence of the macroscopic static friction force. In particular, the static friction coefficient at the onset of sliding is shown to increase with increasing deceleration during the final phases of the preceding sliding event. We suggest that this form of history dependence of static friction should be investigated in experiments, and we provide the acceleration range in which this effect is expected to be experimentally observable.

Proxy-SU(3) symmetry in heavy deformed nuclei

NASA Astrophysics Data System (ADS)

Bonatsos, Dennis; Assimakis, I. E.; Minkov, N.; Martinou, Andriana; Cakirli, R. B.; Casten, R. F.; Blaum, K.

2017-06-01

Background: Microscopic calculations of heavy nuclei face considerable difficulties due to the sizes of the matrices that need to be solved. Various approximation schemes have been invoked, for example by truncating the spaces, imposing seniority limits, or appealing to various symmetry schemes such as pseudo-SU(3). This paper proposes a new symmetry scheme also based on SU(3). This proxy-SU(3) can be applied to well-deformed nuclei, is simple to use, and can yield analytic predictions. Purpose: To present the new scheme and its microscopic motivation, and to test it using a Nilsson model calculation with the original shell model orbits and with the new proxy set. Method: We invoke an approximate, analytic, treatment of the Nilsson model, that allows the above vetting and yet is also transparent in understanding the approximations involved in the new proxy-SU(3). Results: It is found that the new scheme yields a Nilsson diagram for well-deformed nuclei that is very close to the original Nilsson diagram. The specific levels of approximation in the new scheme are also shown, for each major shell. Conclusions: The new proxy-SU(3) scheme is a good approximation to the full set of orbits in a major shell. Being able to replace a complex shell model calculation with a symmetry-based description now opens up the possibility to predict many properties of nuclei analytically and often in a parameter-free way. The new scheme works best for heavier nuclei, precisely where full microscopic calculations are most challenged. Some cases in which the new scheme can be used, often analytically, to make specific predictions, are shown in a subsequent paper.

History-dependent friction and slow slip from time-dependent microscopic junction laws studied in a statistical framework.

PubMed

Thøgersen, Kjetil; Trømborg, Jørgen Kjoshagen; Sveinsson, Henrik Andersen; Malthe-Sørenssen, Anders; Scheibert, Julien

2014-05-01

To study how macroscopic friction phenomena originate from microscopic junction laws, we introduce a general statistical framework describing the collective behavior of a large number of individual microjunctions forming a macroscopic frictional interface. Each microjunction can switch in time between two states: a pinned state characterized by a displacement-dependent force and a slipping state characterized by a time-dependent force. Instead of tracking each microjunction individually, the state of the interface is described by two coupled distributions for (i) the stretching of pinned junctions and (ii) the time spent in the slipping state. This framework allows for a whole family of microjunction behavior laws, and we show how it represents an overarching structure for many existing models found in the friction literature. We then use this framework to pinpoint the effects of the time scale that controls the duration of the slipping state. First, we show that the model reproduces a series of friction phenomena already observed experimentally. The macroscopic steady-state friction force is velocity dependent, either monotonic (strengthening or weakening) or nonmonotonic (weakening-strengthening), depending on the microscopic behavior of individual junctions. In addition, slow slip, which has been reported in a wide variety of systems, spontaneously occurs in the model if the friction contribution from junctions in the slipping state is time weakening. Next, we show that the model predicts a nontrivial history dependence of the macroscopic static friction force. In particular, the static friction coefficient at the onset of sliding is shown to increase with increasing deceleration during the final phases of the preceding sliding event. We suggest that this form of history dependence of static friction should be investigated in experiments, and we provide the acceleration range in which this effect is expected to be experimentally observable.

Sci-Thur AM: YIS – 06: A Monte Carlo study of macro- and microscopic dose descriptors and the microdosimetric spread using detailed cellular models

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

Oliver, Patricia; Thomson, Rowan

2016-08-15

Purpose: To develop Monte Carlo models of cell clusters to investigate the relationships between macro- and microscopic dose descriptors, quantify the microdosimetric spread in energy deposition for subcellular targets, and determine how these results depend on the computational model. Methods: Microscopic tissue structure is modelled as clusters of 13 to 150 cells, with cell (nuclear) radii between 5 and 10 microns (2 and 9 microns). Energy imparted per unit mass (specific energy or dose) is scored in the nucleus (D{sub nuc}) and cytoplasm (D{sub cyt}) for incident photon energies from 20 to 370 keV. Dose-to-water (D{sub w,m}) and dose-to-medium (D{submore » m,m}) are compared to D{sub nuc} and D{sub cyt}. Single cells and single nuclear cavities are also simulated. Results: D{sub nuc} and D{sub cyt} are sensitive to the surrounding environment with deviations of up to 13% for a single nucleus/cell compared with a multicellular cluster. These dose descriptors vary with cell and nucleus size by up to 10%. D{sub nuc} and D{sub cyt} differ from D{sub w,m} and D{sub m,m} by up to 32%. The microdosimetric spread is sensitive to whether cells are arranged randomly or in a hexagonal lattice, and whether subcellular compartment sizes are sampled from a normal distribution or are constant throughout the cluster. Conclusions: D{sub nuc} and D{sub cyt} are sensitive to cell morphology, elemental composition and the presence of surrounding cells. The microdosimetric spread was investigated using realistic elemental compositions for the nucleus and cytoplasm, and depends strongly on subcellular compartment size, source energy and dose.« less

Preclinical evaluation and intraoperative human retinal imaging with a high-resolution microscope-integrated spectral domain optical coherence tomography device.

PubMed

Hahn, Paul; Migacz, Justin; O'Donnell, Rachelle; Day, Shelley; Lee, Annie; Lin, Phoebe; Vann, Robin; Kuo, Anthony; Fekrat, Sharon; Mruthyunjaya, Prithvi; Postel, Eric A; Izatt, Joseph A; Toth, Cynthia A

2013-01-01

The authors have recently developed a high-resolution microscope-integrated spectral domain optical coherence tomography (MIOCT) device designed to enable OCT acquisition simultaneous with surgical maneuvers. The purpose of this report is to describe translation of this device from preclinical testing into human intraoperative imaging. Before human imaging, surgical conditions were fully simulated for extensive preclinical MIOCT evaluation in a custom model eye system. Microscope-integrated spectral domain OCT images were then acquired in normal human volunteers and during vitreoretinal surgery in patients who consented to participate in a prospective institutional review board-approved study. Microscope-integrated spectral domain OCT images were obtained before and at pauses in surgical maneuvers and were compared based on predetermined diagnostic criteria to images obtained with a high-resolution spectral domain research handheld OCT system (HHOCT; Bioptigen, Inc) at the same time point. Cohorts of five consecutive patients were imaged. Successful end points were predefined, including ≥80% correlation in identification of pathology between MIOCT and HHOCT in ≥80% of the patients. Microscope-integrated spectral domain OCT was favorably evaluated by study surgeons and scrub nurses, all of whom responded that they would consider participating in human intraoperative imaging trials. The preclinical evaluation identified significant improvements that were made before MIOCT use during human surgery. The MIOCT transition into clinical human research was smooth. Microscope-integrated spectral domain OCT imaging in normal human volunteers demonstrated high resolution comparable to tabletop scanners. In the operating room, after an initial learning curve, surgeons successfully acquired human macular MIOCT images before and after surgical maneuvers. Microscope-integrated spectral domain OCT imaging confirmed preoperative diagnoses, such as full-thickness macular hole and vitreomacular traction, and demonstrated postsurgical changes in retinal morphology. Two cohorts of five patients were imaged. In the second cohort, the predefined end points were exceeded with ≥80% correlation between microscope-mounted OCT and HHOCT imaging in 100% of the patients. This report describes high-resolution MIOCT imaging using the prototype device in human eyes during vitreoretinal surgery, with successful achievement of predefined end points for imaging. Further refinements and investigations will be directed toward fully integrating MIOCT with vitreoretinal and other ocular surgery to image surgical maneuvers in real time.

Application of confocal surface wave microscope to self-calibrated attenuation coefficient measurement by Goos-Hänchen phase shift modulation.

PubMed

Pechprasarn, Suejit; Chow, Terry W K; Somekh, Michael G

2018-06-04

In this paper, we present a direct method to measure surface wave attenuation arising from both ohmic and coupling losses using our recently developed phase spatial light modulator (phase-SLM) based confocal surface plasmon microscope. The measurement is carried out in the far-field using a phase-SLM to impose an artificial surface wave phase profile in the back focal plane (BFP) of a microscope objective. In other words, we effectively provide an artificially engineered backward surface wave by modulating the Goos Hänchen (GH) phase shift of the surface wave. Such waves with opposing phase and group velocities are well known in acoustics and electromagnetic metamaterials but usually require structured or layered surfaces, here the effective wave is produced externally in the microscope illumination path. Key features of the technique developed here are that it (i) is self-calibrating and (ii) can distinguish between attenuation arising from ohmic loss (k″ Ω ) and coupling (reradiation) loss (k″ c ). This latter feature has not been achieved with existing methods. In addition to providing a unique measurement the measurement occurs of over a localized region of a few microns. The results were then validated against the surface plasmons (SP) dip measurement in the BFP and a theoretical model based on a simplified Green's function.

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.

A next generation positron microscope and a survey of candidate samples for future positron studies

NASA Astrophysics Data System (ADS)

Dull, Terry Lou

A positron microscope has been constructed and is nearing the conclusion of its assembly and testing. The instrument is designed to perform positron and electron microscopy in both scanning and magnifying modes. In scanning mode, a small beam of particles is rastered across the target and the amplitude of a positron or electron related signal is recorded as a function of position. For positrons this signal may come from Doppler Broadening Spectroscopy, Reemitted Positron Spectroscopy or Positron Annihilation Lifetime Spectroscopy. For electrons this signal may come from the number of secondary electrons or Auger Electron Spectroscopy. In magnifying mode an incident beam of particles is directed onto the target and emitted particles, either secondary electrons or reemitted positrons, are magnified to form an image. As a positron microscope the instrument will primarily operate in magnifying mode, as a positron reemission microscope. As an electron microscope the instrument will be able to operate in both magnifying and scanning modes. Depth-profiled Doppler Broadening Spectroscopy studies using a non-microscopic low-energy positron beam have also been performed on a series of samples to ascertain the applicability of positron spectroscopies and/or microscopy to their study. All samples have sub-micron film and/or feature size and thus are only susceptible to positron study with low-energy beams. Several stoichiometries and crystallinities of chalcogenide thin films (which can be optically reversibly switched between crystalline states) were studied and a correlation was found to exist between the amorphous/FCC S-parameter difference and the amorphous/FCC switching time. Amorphous silicon films were studied in an attempt to observe the well-established Staebler-Wronski effect as well as the more controversial photodilatation effect. However, DBS was not able to detect either effect. The passive oxide films on titanium and aluminum were studied in an attempt to verify the Point Defect Model, a detailed, but as yet microscopically unconfirmed, theory of the corrosive breakdown of passive films. DBS results supportive of the PDM were observed. Graphitic carbon fibers were also studied and DBS indicated the presence of a 200 nm thick outer fiber skin possibly characterized by a high degree of graphitic crystallite alignment.

Physics of Neutron Star Crusts.

PubMed

Chamel, Nicolas; Haensel, Pawel

2008-01-01

The physics of neutron star crusts is vast, involving many different research fields, from nuclear and condensed matter physics to general relativity. This review summarizes the progress, which has been achieved over the last few years, in modeling neutron star crusts, both at the microscopic and macroscopic levels. The confrontation of these theoretical models with observations is also briefly discussed.

Systematic development of small molecules to inhibit specific microscopic steps of Aβ42 aggregation in Alzheimer’s disease

PubMed Central

Habchi, Johnny; Chia, Sean; Limbocker, Ryan; Mannini, Benedetta; Ahn, Minkoo; Perni, Michele; Hansson, Oskar; Arosio, Paolo; Kumita, Janet R.; Challa, Pavan Kumar; Cohen, Samuel I. A.; Dobson, Christopher M.; Knowles, Tuomas P. J.; Vendruscolo, Michele

2017-01-01

The aggregation of the 42-residue form of the amyloid-β peptide (Aβ42) is a pivotal event in Alzheimer’s disease (AD). The use of chemical kinetics has recently enabled highly accurate quantifications of the effects of small molecules on specific microscopic steps in Aβ42 aggregation. Here, we exploit this approach to develop a rational drug discovery strategy against Aβ42 aggregation that uses as a read-out the changes in the nucleation and elongation rate constants caused by candidate small molecules. We thus identify a pool of compounds that target specific microscopic steps in Aβ42 aggregation. We then test further these small molecules in human cerebrospinal fluid and in a Caenorhabditis elegans model of AD. Our results show that this strategy represents a powerful approach to identify systematically small molecule lead compounds, thus offering an appealing opportunity to reduce the attrition problem in drug discovery. PMID:28011763

Macroscopic and microscopic spectral properties of brain networks during local and global synchronization

NASA Astrophysics Data System (ADS)

Maksimenko, Vladimir A.; Lüttjohann, Annika; Makarov, Vladimir V.; Goremyko, Mikhail V.; Koronovskii, Alexey A.; Nedaivozov, Vladimir; Runnova, Anastasia E.; van Luijtelaar, Gilles; Hramov, Alexander E.; Boccaletti, Stefano

2017-07-01

We introduce a practical and computationally not demanding technique for inferring interactions at various microscopic levels between the units of a network from the measurements and the processing of macroscopic signals. Starting from a network model of Kuramoto phase oscillators, which evolve adaptively according to homophilic and homeostatic adaptive principles, we give evidence that the increase of synchronization within groups of nodes (and the corresponding formation of synchronous clusters) causes also the defragmentation of the wavelet energy spectrum of the macroscopic signal. Our methodology is then applied to getting a glance into the microscopic interactions occurring in a neurophysiological system, namely, in the thalamocortical neural network of an epileptic brain of a rat, where the group electrical activity is registered by means of multichannel EEG. We demonstrate that it is possible to infer the degree of interaction between the interconnected regions of the brain during different types of brain activities and to estimate the regions' participation in the generation of the different levels of consciousness.

Learning a cost function for microscope image segmentation.

PubMed

Nilufar, Sharmin; Perkins, Theodore J

2014-01-01

Quantitative analysis of microscopy images is increasingly important in clinical researchers' efforts to unravel the cellular and molecular determinants of disease, and for pathological analysis of tissue samples. Yet, manual segmentation and measurement of cells or other features in images remains the norm in many fields. We report on a new system that aims for robust and accurate semi-automated analysis of microscope images. A user interactively outlines one or more examples of a target object in a training image. We then learn a cost function for detecting more objects of the same type, either in the same or different images. The cost function is incorporated into an active contour model, which can efficiently determine optimal boundaries by dynamic programming. We validate our approach and compare it to some standard alternatives on three different types of microscopic images: light microscopy of blood cells, light microscopy of muscle tissue sections, and electron microscopy cross-sections of axons and their myelin sheaths.

Volumetric Light-field Encryption at the Microscopic Scale

PubMed Central

Li, Haoyu; Guo, Changliang; Muniraj, Inbarasan; Schroeder, Bryce C.; Sheridan, John T.; Jia, Shu

2017-01-01

We report a light-field based method that allows the optical encryption of three-dimensional (3D) volumetric information at the microscopic scale in a single 2D light-field image. The system consists of a microlens array and an array of random phase/amplitude masks. The method utilizes a wave optics model to account for the dominant diffraction effect at this new scale, and the system point-spread function (PSF) serves as the key for encryption and decryption. We successfully developed and demonstrated a deconvolution algorithm to retrieve both spatially multiplexed discrete data and continuous volumetric data from 2D light-field images. Showing that the method is practical for data transmission and storage, we obtained a faithful reconstruction of the 3D volumetric information from a digital copy of the encrypted light-field image. The method represents a new level of optical encryption, paving the way for broad industrial and biomedical applications in processing and securing 3D data at the microscopic scale. PMID:28059149

Mie scattering off coated microbubbles

NASA Astrophysics Data System (ADS)

Nelissen, Radboud; Koene, Elmer; Hilgenfeldt, Sascha; Versluis, Michel

2002-11-01

The acoustic behavior of coated microbubbles depends on parameters of the shell coating, which are in turn dependent on bubble size. More intimate knowledge of this size dependence is required for an improved modeling of a distribution of coated microbubbles such as found in ultrasound contrast agents (UCA). Here a setup is designed to simultaneously measure the optical and acoustic response of an ultrasound-driven single bubble contained in a capillary or levitated by the pressure field of a focused transducer. Optical detection is done by Mie scattering through an inverted microscope. Acoustical detection of the single bubble by a receiving transducer is made possible because of the large working distance of the microscope. For Mie scattering investigation of excited bubbles, two regimes can be distinguished, which require different detection techniques: Conventional wide-angle detection through the microscope objective is sufficient for bubbles of radius exceeding 10 mum. For smaller bubbles, two narrow-aperture detectors are used to reconstruct the bubble dynamics from the complex angle-dependence of the scattered light.

Dynamic Contact Angle at the Nanoscale: A Unified View.

PubMed

Lukyanov, Alex V; Likhtman, Alexei E

2016-06-28

Generation of a dynamic contact angle in the course of wetting is a fundamental phenomenon of nature. Dynamic wetting processes have a direct impact on flows at the nanoscale, and therefore, understanding them is exceptionally important to emerging technologies. Here, we reveal the microscopic mechanism of dynamic contact angle generation. It has been demonstrated using large-scale molecular dynamics simulations of bead-spring model fluids that the main cause of local contact angle variations is the distribution of microscopic force acting at the contact line region. We were able to retrieve this elusive force with high accuracy. It has been directly established that the force distribution can be solely predicted on the basis of a general friction law for liquid flow at solid surfaces by Thompson and Troian. The relationship with the friction law provides both an explanation of the phenomenon of dynamic contact angle and a methodology for future predictions. The mechanism is intrinsically microscopic, universal, and irreducible and is applicable to a wide range of problems associated with wetting phenomena.

Contour metrology using critical dimension atomic force microscopy

NASA Astrophysics Data System (ADS)

Orji, Ndubuisi G.; Dixson, Ronald G.; Vladár, András E.; Ming, Bin; Postek, Michael T.

2012-03-01

The critical dimension atomic force microscope (CD-AFM), which is used as a reference instrument in lithography metrology, has been proposed as a complementary instrument for contour measurement and verification. Although data from CD-AFM is inherently three dimensional, the planar two-dimensional data required for contour metrology is not easily extracted from the top-down CD-AFM data. This is largely due to the limitations of the CD-AFM method for controlling the tip position and scanning. We describe scanning techniques and profile extraction methods to obtain contours from CD-AFM data. We also describe how we validated our technique, and explain some of its limitations. Potential sources of error for this approach are described, and a rigorous uncertainty model is presented. Our objective is to show which data acquisition and analysis methods could yield optimum contour information while preserving some of the strengths of CD-AFM metrology. We present comparison of contours extracted using our technique to those obtained from the scanning electron microscope (SEM), and the helium ion microscope (HIM).

Nanometric depth resolution from multi-focal images in microscopy.

PubMed

Dalgarno, Heather I C; Dalgarno, Paul A; Dada, Adetunmise C; Towers, Catherine E; Gibson, Gavin J; Parton, Richard M; Davis, Ilan; Warburton, Richard J; Greenaway, Alan H

2011-07-06

We describe a method for tracking the position of small features in three dimensions from images recorded on a standard microscope with an inexpensive attachment between the microscope and the camera. The depth-measurement accuracy of this method is tested experimentally on a wide-field, inverted microscope and is shown to give approximately 8 nm depth resolution, over a specimen depth of approximately 6 µm, when using a 12-bit charge-coupled device (CCD) camera and very bright but unresolved particles. To assess low-flux limitations a theoretical model is used to derive an analytical expression for the minimum variance bound. The approximations used in the analytical treatment are tested using numerical simulations. It is concluded that approximately 14 nm depth resolution is achievable with flux levels available when tracking fluorescent sources in three dimensions in live-cell biology and that the method is suitable for three-dimensional photo-activated localization microscopy resolution. Sub-nanometre resolution could be achieved with photon-counting techniques at high flux levels.

Nanometric depth resolution from multi-focal images in microscopy

PubMed Central

Dalgarno, Heather I. C.; Dalgarno, Paul A.; Dada, Adetunmise C.; Towers, Catherine E.; Gibson, Gavin J.; Parton, Richard M.; Davis, Ilan; Warburton, Richard J.; Greenaway, Alan H.

2011-01-01

We describe a method for tracking the position of small features in three dimensions from images recorded on a standard microscope with an inexpensive attachment between the microscope and the camera. The depth-measurement accuracy of this method is tested experimentally on a wide-field, inverted microscope and is shown to give approximately 8 nm depth resolution, over a specimen depth of approximately 6 µm, when using a 12-bit charge-coupled device (CCD) camera and very bright but unresolved particles. To assess low-flux limitations a theoretical model is used to derive an analytical expression for the minimum variance bound. The approximations used in the analytical treatment are tested using numerical simulations. It is concluded that approximately 14 nm depth resolution is achievable with flux levels available when tracking fluorescent sources in three dimensions in live-cell biology and that the method is suitable for three-dimensional photo-activated localization microscopy resolution. Sub-nanometre resolution could be achieved with photon-counting techniques at high flux levels. PMID:21247948

Hybrid multiphoton volumetric functional imaging of large-scale bioengineered neuronal networks

NASA Astrophysics Data System (ADS)

Dana, Hod; Marom, Anat; Paluch, Shir; Dvorkin, Roman; Brosh, Inbar; Shoham, Shy

2014-06-01

Planar neural networks and interfaces serve as versatile in vitro models of central nervous system physiology, but adaptations of related methods to three dimensions (3D) have met with limited success. Here, we demonstrate for the first time volumetric functional imaging in a bioengineered neural tissue growing in a transparent hydrogel with cortical cellular and synaptic densities, by introducing complementary new developments in nonlinear microscopy and neural tissue engineering. Our system uses a novel hybrid multiphoton microscope design combining a 3D scanning-line temporal-focusing subsystem and a conventional laser-scanning multiphoton microscope to provide functional and structural volumetric imaging capabilities: dense microscopic 3D sampling at tens of volumes per second of structures with mm-scale dimensions containing a network of over 1,000 developing cells with complex spontaneous activity patterns. These developments open new opportunities for large-scale neuronal interfacing and for applications of 3D engineered networks ranging from basic neuroscience to the screening of neuroactive substances.

Volumetric Light-field Encryption at the Microscopic Scale

NASA Astrophysics Data System (ADS)

Li, Haoyu; Guo, Changliang; Muniraj, Inbarasan; Schroeder, Bryce C.; Sheridan, John T.; Jia, Shu

2017-01-01

We report a light-field based method that allows the optical encryption of three-dimensional (3D) volumetric information at the microscopic scale in a single 2D light-field image. The system consists of a microlens array and an array of random phase/amplitude masks. The method utilizes a wave optics model to account for the dominant diffraction effect at this new scale, and the system point-spread function (PSF) serves as the key for encryption and decryption. We successfully developed and demonstrated a deconvolution algorithm to retrieve both spatially multiplexed discrete data and continuous volumetric data from 2D light-field images. Showing that the method is practical for data transmission and storage, we obtained a faithful reconstruction of the 3D volumetric information from a digital copy of the encrypted light-field image. The method represents a new level of optical encryption, paving the way for broad industrial and biomedical applications in processing and securing 3D data at the microscopic scale.

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.

Controlling molecular condensation/diffusion of copper phthalocyanine by local electric field induced with scanning tunneling microscope tip

NASA Astrophysics Data System (ADS)

Nagaoka, Katsumi; Yaginuma, Shin; Nakayama, Tomonobu

2018-02-01

We have discovered the condensation/diffusion phenomena of copper phthalocyanine (CuPc) molecules controlled with a pulsed electric field induced by the scanning tunneling microscope tip. This behavior is not explained by the conventional induced dipole model. In order to understand the mechanism, we have measured the electronic structure of the molecule by tunneling spectroscopy and also performed theoretical calculations on molecular orbitals. These data clearly indicate that the molecule is positively charged owing to charge transfer to the substrate, and that hydrogen bonding exists between CuPc molecules, which makes the molecular island stable.

Fusion enhancement at near and sub-barrier energies in 19O + 12C

DOE PAGES

Singh, Varinderjit; Vadas, J.; Steinbach, T. K.; ...

2016-12-12

Measuring the fusion excitation function for an isotopic chain of projectile nuclei provides a stringent test of a microscopic description of fusion. We report the first measurement of the fusion excitation function at near-barrier energies for the 19O+ 12C system. The measured excitation function is compared with the fusion excitation function of 18O+ 12C. A significant enhancement in the fusion probability of 19O ions with a 12C target as compared to 18O ions is observed. As a result, the experimental cross-sections observed at near-barrier energies are compared with a state-of-the-art microscopic model.

Pulse-modulated second harmonic imaging microscope quantitatively demonstrates marked increase of collagen in tumor after chemotherapy

NASA Astrophysics Data System (ADS)

Raja, Anju M.; Xu, Shuoyu; Sun, Wanxin; Zhou, Jianbiao; Tai, Dean C. S.; Chen, Chien-Shing; Rajapakse, Jagath C.; So, Peter T. C.; Yu, Hanry

2010-09-01

Pulse-modulated second harmonic imaging microscopes (PM-SHIMs) exhibit improved signal-to-noise ratio (SNR) over conventional SHIMs on sensitive imaging and quantification of weak collagen signals inside tissues. We quantify the spatial distribution of sparse collagen inside a xenograft model of human acute myeloid leukemia (AML) tumor specimens treated with a new drug against receptor tyrosine kinase (ABT-869), and observe a significant increase in collagen area percentage, collagen fiber length, fiber width, and fiber number after chemotherapy. This finding reveals new insights into tumor responses to chemotherapy and suggests caution in developing new drugs and therapeutic regimens against cancers.