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Displaying 76 - 100 of 159

Letter in response to V. Stodden et al., Science 354, 1240 (2016).

January 2, 2018
Author(s)
Mark W. Maciejewski, Adam D. Schuyler, Michael R. Gryk, Ion I. Moraru, Pedro R. Romero, Eldon L. Ulrich, Hamid R. Eghbalnia, Miron Livny, Frank Delaglio, Jeffrey C. Hoch
Stodden et al. (1) bring welcome attention to the problem of reproducibility of computational analyses, and recommend guidelines for addressing the barriers to reproducibility. However, one important barrier to long-term reproducibility of computational

Modeling, Validation and Verification of Three-Dimensional Cell-Scaffold Contacts from Terabyte- sized Images

December 1, 2017
Author(s)
Peter Bajcsy, Sowon Joy Yoon, Stephen Florczyk, Nathan Hotaling, Mylene H. Simon, Piotr Szczypinski, Nicholas J. Schaub, Carl G. Simon Jr., Mary C. Brady, Ram D. Sriram
Background: Cell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and spun coat, large microfiber, and medium microfiber scaffolds. Our

Model-based Dynamic Scheduling for Multicore Implementation of Image Processing Systems

October 5, 2017
Author(s)
Timothy J. Blattner, Walid Keyrouz, Jiahao Wu, Shuvra S. Bhattacharyya
In this paper, we present a new software tool, called HTGS Model-based Engine (HMBE), for the design and implementation of multicore signal processing applications. HMBE provides complementary capabilities to HTGS (Hybrid Task Graph Scheduler), which is a

MRI Birdcage RF Coil Resonance with Uncertainty and Relative Error Convergence Rates

October 4, 2017
Author(s)
Jeffrey T. Fong, Nathanael A. Heckert, James J. Filliben, Pedro V. Marcal, Robert Rainsberger, Karl F. Stupic, Stephen E. Russek
In a magnetic resonance imaging (MRI) system, it is necessary to excite the nuclei of a patient into coherent precession for imaging. This requires a coupling between the nuclei and a source of radio frequency (RF) power using a transmitter. To receive a

Energy renormalization approach to coarse-graining of polymer dynamics

August 8, 2017
Author(s)
Wenjie Xia, Jake Song, Cheol Jeong, David D. Hsu, Frederick R. Phelan Jr., Jack F. Douglas, Sinan Keten
A major challenge in soft matter science is the bottom-up prediction of the temperature- dependent behavior of amorphous glass-forming (GF) polymers. Coarse-grained (CG) models derived from atomistic simulation data offer chemical specificity and access to

Non-Uniform Sampling for All: More Spectral Quality, Less Measurement Time

June 30, 2017
Author(s)
Frank Delaglio, Gregory S. Walker, Kathleen A. Farley, Raman Sharma, Jeffrey C. Hoch, Luke Arbogast, Robert Brinson, John Marino
Nuclear Magnetic Resonance (NMR) spectroscopy is an indispensable tool in pharmaceutical science, with uses in drug discovery, development, and manufacturing. Non-Uniform Sampling (NUS) is an acquisition method for NMR experiments with two or more

A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows

June 22, 2017
Author(s)
Timothy J. Blattner, Walid Keyrouz, Mary C. Brady, Shuvra S. Bhattacharyya, Milton Halem
Designing applications for scalability is key to improving their performance in hybrid and cluster computing. Scheduling code to utilize parallelism is difficult, particularly when dealing with data dependencies, memory management, data motion, and

NMRbox: A Resource for Biomolecular NMR Computation

May 25, 2017
Author(s)
Mark W. Maciejewski, Adam D. Schuyler, Michael R. Gryk, Ion I. Moraru, Pedro R. Romero, Eldon L. Ulrich, Hamid R. Eghbalnia, Miron Livny, Frank Delaglio, Jeffrey C. Hoch
Advances in computation have been enabling for many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large

A novel measure and significance testing in data analysis of cell image segmentation

April 20, 2017
Author(s)
Jin Chu Wu, Michael W. Halter, Raghu N. Kacker, John T. Elliott, Anne L. Plant
Background: Cell image segmentation (CIS) is an essential part of quantitative imaging of biological cells. Designing a performance measure and conducting significance testing are critical for evaluating and comparing the CIS algorithms for image-based

Open Source Private Cloud Platforms for Big Data

February 10, 2017
Author(s)
Martial Michel, Edmond J. Golden III, Olivier Serres, Ahmad Anbar, Tarek El-Ghazawi
Due to its availability, Cloud computing is the de facto platform of choice for big data, where Big Data as a Service (BDaaS) is believed to be the next best thing. In this book chapter we will first introduce cloud computing, defining the advantages it

From Image Tiles to Web-Based Interactive Measurements in One Stop

January 4, 2017
Author(s)
Antoine Vandecreme, Michael P. Majurski, Joe Chalfoun, Keana Scott, John Henry Scott, Mary C. Brady, Peter Bajcsy
This article aims at introducing readers to a web-based solution useful for interactive measurements of centimeter-sized specimens at nanoscales. Modern imaging technology has enabled nanoscale imaging to become a routine process. As the imaging technology

Cycle Basis Markov Chains for the Ising Model

January 1, 2017
Author(s)
Noah S. Streib, Amanda A. Streib
The ferromagnetic Ising model with zero applied field reduces to sampling even subgraphs X of a graph G with probability proportional to $\lambda^|E(X)|}$, for $\lambda \in [0,1]$. In this paper, we present a class of Markov chains for sampling subgraphs

Architecture for Software-assisted Quantity Calculus

December 2, 2016
Author(s)
David W. Flater
A quantity value, such as 5 kg, consists of a number and a reference (often an International System of Units (SI)unit) that together express the magnitude of a quantity. Many software libraries, packages, and ontologies that implement "quantities and units

MOSAIC: A Modular Single Molecular Analysis Interface for Decoding Multi-state Nanopore Data

October 31, 2016
Author(s)
Jacob H. Forstater, Kyle Briggs, Joseph W. Robertson, Jessica H. Benjamini, Olivier M. Marie-Rose, Canute I. Vaz, John J. Kasianowicz, Vincent Tabard-Cossa, Arvind Balijepalli
Single molecule measurements with nanometer-scale pores are being developed for a wide range of diagnostic and therapeutic applications.  Critical to the method is the ability to accurately and precisely detect the presence of an analyte, quantify its

A Few Selected Contributions to electron and photon collisions with H_2+ and H_2

October 23, 2016
Author(s)
Barry I. Schneider, Lee A. Collins, klaus Bartschat, Xiaoxu Guan, Suxing Hu
We discuss a number of aspects regarding the physics of H_2+ nd H_2. This includes low-energy electron scattering processes and the interaction of both weak (perturbative) and strong (ultrafast/intense) electromagnetic radiation with those systems.

A Library to Enable the Modeling of Optical Imaging of Finite Multi-Line Arrays.

September 30, 2016
Author(s)
Mark Alexander Henn, Bryan M. Barnes
The dataset contains several MATLAB files and input files for the software package JCMsuite that enable the modeling of optical imaging of finite multi-line arrays. (Certain commercial materials are identified in order to specify the experimental procedure

A STATISTICAL APPROACH TO ESTIMATING A 95 % CONFIDENCE LOWER LIMIT FOR THE DESIGN CREEP RUPTURE TIME VS. STRESS CURVE WHEN THE STRESS ESTIMATE HAS AN ERROR UP TO 2 % (*)

July 17, 2016
Author(s)
Jeffrey T. Fong, James J. Filliben, Nathanael A. Heckert, Pedro V. Marcal, Marvin J. Cohn
Recent experimental results on creep-fracture damage with minimum time to failure (minTTF) varying as the 9th power of stress, and a theoretical consequence that the coefficient of variation (CV) of minTTF is necessarily 9 times that of the CV of the

Time Propagation of Partial Differential Equations Using the Short Iterative Lanczos Method and Finite-Element Discrete Variable Representation: An Experiment Using the Intel Phi Coprocessors

July 15, 2016
Author(s)
Barry I. Schneider, klaus Bartschat, Xiaoxu Guan
The Short Iterative Lanczos (SIL) method has been combined with the Finite-Element Discrete Variable Representation (SIL-FEDVR) to yield a powerful approach to solving the time-dependent Schroedinger equation. It has been applied to the interaction of

Acceleration and Parallelization of ZENO/Walk-on-Spheres

June 1, 2016
Author(s)
Derek Juba, Walid Keyrouz, Michael V. Mascagni, Mary C. Brady, Michael Mascagni
This paper describes our on-going work to accelerate ZENO, a software tool based on Monte Carlo methods (MCMs), used for computing material properties at the nanoscale. ZENO employs three main algorithms: (1)Walk on Spheres (WoS), (2)interior sampling, and

Uncertainty Quantification of Stresses in a Cracked Pipe Elbow Weldment Using a Logistic Function Fit, a Nonlinear Least Squares Algorithm, and a Super-Parametric Method

December 30, 2015
Author(s)
Jeffrey T. Fong, James J. Filliben, Nathanael A. Heckert, Pedro V. Marcal, Robert Rainsberger, Li Ma
In a 3-part series of papers, of which this paper is Part II, we investigate the applicability of the fully quadratic hexa-27 element (see Part I) to four problems of interest to the pressure vessels and piping community: (1) The solid-element-based
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