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Current contacts: Benjamin Seibold or Daniel B. Szyld
The Seminar usually takes place on Wednesdays at 4:00 PM in Room 617 on the sixth floor of Wachman Hall. Click on title for abstract.
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The block version of GMRES (BGMRES) is most advantageous over the single right hand side (RHS) counterpart when the cost of communication is high while the cost of floating point operations is not. This is the case on modern Graphics Processing Units(GPUs), while it is generally not the case on traditional Central Processing Units (CPUs). In this talk, experiments on both GPUs and CPUs are shown that compare the performance of BGMRES against GMRES as the number of RHS increases. The experiments indicatethat there are many cases in which BGMRES is slower than GMRES on CPUs, but faster on GPUs. Furthermore, when varying the number of RHS on the GPU, there is an optimal number of RHS where BGMRES is clearly most advantageous over GMRES. A computational modelis developed using hardware specific parameters, showing qualitatively where this optimal number of RHS is, and this model also helps explain the phenomena observed in the experiments.
Rachael Miller Neilan, Duquesne University
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In this talk, I will present an agent-based model (ABM) that simulates the behavior and interactions of neurons in the amygdala for the purpose of studying their impact on pain.
In the ABM, agents represent individual neurons that express either protein kinase C delta (PKC) or somatostatin (SOM). Neurons that express PKC are known to increase pain whereas neurons that express SOM are known to decrease pain. During the model’s initialization, neurons are assigned type-specific parameters based on laboratory data and a location in either the right or left amygdala. A network of directed links is established to allow for the transmission of inhibitory signals between neurons. During each model timestep, neurons accrue damage and the firing rates all of neurons are updated based on the intensity of the external stimulus and the strength of signals transmitted through the network. The ABM outputs an emergent measure of pain, which is calculated in terms of the cumulative pro-nociceptive activity of the PKC neurons and anti-nociceptive activity of the SOM neurons. Results demonstrate the ability of the model to produce changes in pain that are consistent with published studies and highlight the importance of several model parameters.
Undergraduate students contributed to the development and programming of the ABM using NetLogo software.
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Viruses are the most abundant biological entity on Earth and play a pivotal role in regulating the evolution of organisms and the planet's biogeochemistry. Most viruses protect their genome in icosahedral shells made of multiple copies of the same protein. Viral icosahedral shells span two orders of magnitude in size and thousands of different architectures. Yet, the physical mechanisms that have selected such diverse viral structures are unknown. Here, I will share my most recent contributions to this fundamental problem. First, I will introduce the generalized quasi-equivalence theory of icosahedral architectures as a framework to investigate systematically viral architectures and their protein components. Second, I will show how the physical relationship between the protein shell and genome of viruses has opened the door to characterize uncultured viruses, predict the existence of unknown viruses, and engineer new viruses from the environment. Finally, I will discuss a novel physical mechanism that may hold the key to how viruses explore different viral architectures.
Subaerial biofilms (SABs) are thin layers of densely packed microorganisms, that live in self-organized structures on soil and rock surfaces exposed to the air. Microbial life within these ecosystems is very hard and mainly dependent on the availability of liquid water, essential for microbial metabolic activities. That’s why SAB inhabitants are special microorganisms, able to resist long desiccation periods and loosen the thermodynamic constraints to the water vapor condensation into the SAB. Here, I will present a multidisciplinary study on subaerial biofilms. First, I will show some confocal microscopy images of SAB microbial colonies, the result of multiple sampling campaigns conducted on the marble surfaces of the Merchants’ Exchange Building (Philadelphia, USA) and on the stone railing of my house in Naples (Italy). Then, I will present a novel theoretical model to predict liquid water availability via microbially-induced condensation and estimate the maximum SAB thickness thermodynamically supported under specific temperature and humidity conditions. Finally, I will apply the present model to a year-long data campaign about temperature and humidity, conducted on the marble roof of the portico of the Thomas Jefferson Memorial (Washington D.C., USA).
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