Fat vs. thin threading approach on GPUs: application to stochastic simulation of chemical reactions

We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimise data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximises parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie (J. Phys. Chem, Vol. 81, p. 2340-2361, 1977). In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction system’s size

STOCHSIMGPU Parallel stochastic simulation for the Systems\ud Biology Toolbox 2 for MATLAB

Motivation: The importance of stochasticity in biological systems is becoming increasingly recognised and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU which exploits graphics processing units (GPUs)for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB.\ud \ud Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM), and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user’s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2

Effects of Process Variables and Size Scale on Solidification Microstructure in Laser-Based Solid Freeform Fabrication of Ti-6Al-4V

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Sensor Fusion Algorithm and Calibration for a Gyroscope-free IMU

AbstractThis paper presents a gyroscope-free inertial measurement unit (IMU) that only consists of linear acceleration sensors. Only a simple matrix multiplication has to be performed in order to calculate the complete relative movement of a body. However, the precise positions and orientations of the sensors within the body frame have to be known in order to calculate the exact movement of the body. A simple and effective calibration algorithm developed in this paper can be applied to determine these parameters entirely even without any previous knowledge. Measurements on a 3D-rotation table were carried out to demonstrate the accuracy improvements after the calibration. Thereby, the RMS error of the angular rate was reduced by a factor of 2.8

How to Select the Correct Education Strategy: When Not to Go Online

Screening for intimate partner violence is an important injury prevention strategy. Nurses who develop staff education, to promote screening, need to select a method that is sensitive to learners. Online learning, although convenient, is not well suited to sensitive topics such as screening for intimate partner violence. The purpose of this article is to describe a curriculum for intimate partner violence screening based on self-efficacy theory, which includes a hospital-produced video, a role play, and a discussion

Transition of Experienced and New Graduate Nurses to a Pediatric Hospital

This study reports on the 3-, 6-, 12-, and 18-month outcomes of 118 newly hired registered nurses (RNs) who completed a 12-month transition-to-practice program at a pediatric hospital. Experienced RNs (n = 42) and new graduate RNs (n = 76) showed improved organization, prioritization, communication, and leadership skills over time. The experienced RNs reported better communication and leadership skills than the new graduate nurses. Results inform transition program development for both new and experienced nurses. The American Association of Colleges of Nursing (2012) predicts that, without a multifaceted approach, a national nursing shortage will occur by 2020. Many nurses leave their first position and sometimes the profession within the first year of employment (Baxter, 2010; Welding, 2011). Retaining nurses is a vital component of any approach to averting a nursing shortage. In an attempt to retain nurses, healthcare institutions often provide a transition-to-practice (TTP) or nurse residency program for new graduate nurses (NGN) entering the profession. The Institute of Medicine (2011) in its Future of Nursing report also recommends a transition program for nurses moving to a new specialty or to advanced practice roles. Completing a NGN transition program is associated with a decrease in nurse attrition by as much as 80% (Halfer, Graf, & Sullivan, 2008; Rush, Adamack, Gordon, Lilly, & Janke, 2013; Spector et al., 2015). This reported decrease has led to organizational interest in transition programs to improve retention. The goals of residency programs for the NGN have ranged from increasing new nurse confidence and competence, to increasing satisfaction and retention (Fink, Krugman, Casey, & Goode, 2008; Goode, Lynn, McElroy, Bednash, & Murray, 2013; Institute of Medicine, 2011; Spector et al., 2015). Although literature supports the effectiveness of transition programs for the NGN (Fink et al., 2008; Goode et al., 2013; Spector et al., 2015), there is little evidence on the experienced nurse’s transition to a new specialty practice. Furthermore, most transition programs do not report outcomes beyond the first 12 months of employment. Thus, the purpose of this study is to evaluate nurse stressors and supports during and after a 12-month transition-to-employment program for both new and experienced nurses transitioning to a pediatric practice

ICONGETM v1.0 – flexible NUOPC-driven two-way coupling via ESMF exchange grids between the unstructured-grid atmosphere model ICON and the structured-grid coastal ocean model GETM

Two-way model coupling is important for representing the mutual interactions and feedbacks between atmosphere and ocean dynamics. This work presents the development of the two-way coupled model system ICONGETM, consisting of the atmosphere model ICON and the ocean model GETM. ICONGETM is built on the latest NUOPC coupling software with flexible data exchange and conservative interpolation via ESMF exchange grids. With ICON providing a state-of-the-art kernel for numerical weather prediction on an unstructured mesh and GETM being an established coastal ocean model, ICONGETM is especially suited for high-resolution studies. For demonstration purposes the newly developed model system has been applied to a coastal upwelling scenario in the central Baltic Sea

Numerical issues of the Total Exchange Flow (TEF) analysis framework for quantifying estuarine circulation

For more than a century, estuarine exchange flow has been quantified by means of the Knudsen relations which connect bulk quantities such as inflow and outflow volume fluxes and salinities. These relations are closely linked to estuarine mixing. The recently developed Total Exchange Flow (TEF) analysis framework, which uses salinity coordinates to calculate these bulk quantities, allows an exact formulation of the Knudsen relations in realistic cases. There are however numerical issues, since the original method does not converge to the TEF bulk values for an increasing number of salinity classes. In the present study, this problem is investigated and the method of dividing salinities, described by MacCready et al. (2018), is mathematically introduced. A challenging yet compact analytical scenario for a well-mixed estuarine exchange flow is investigated for both methods, showing the proper convergence of the dividing salinity method. Furthermore, the dividing salinity method is applied to model results of the Baltic Sea to demonstrate the analysis of realistic exchange flows and exchange flows with more than two layers.</p