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Mathematical models play an important role in biochemical engineering. For example, the models developed in the field of systems biology have been used to identify drug targets to treat pathogens such as Pseudomonas aeruginosa in biofilms. In addition, competitive binding models for chromatography processes have been developed to predict expanded bed breakthrough of a recombinant protein expressed in a high cell density fermentation. Numerical computing tools such as MATLAB can facilitate the development of these models in biochemical engineering. Compared to other computational tools and programming languages, such as C++ and Java, MATLAB is easier for students to learn since it has a large library of functions and toolboxes, including some developed in systems biology. Basic MATLAB modeling techniques have been introduced in advanced engineering courses to enhance student learning experiences. However, a nationwide survey conducted by Villanova University showed that only 28.5% of schools in United States provide training in MATLAB in graduate-level courses in biochemical engineering. Instructors in this survey also indicated they would have a strong interest in using MATLAB modules, if the modules were readily available, in courses such as systems biology. To address the need for MATLAB education in biochemical engineering, Villanova University has developed MATLAB modules and integrated them in the course CHE8663 Systems Biology (Fall semester 2012 & 2013). The teaching modules as well as the teaching strategies for MATLAB are provided here for a course that was offered to in class students as well as distance-learning (i.e., e-learning) students.

It is essential to support real-time communication in networked control systems, such as automotive systems or smart factories. Several studies have been conducted to schedule real-time flows by adjusting their priorities using software-defined networking (SDN). However, because its architecture was not initially designed for real-time communication, unexpected challenges may occur if it is not utilized carefully. In particular, because SDN does not provide an atomic method for priority adjustment, some flows may violate their timing constraints by receiving additional interference during priority adjustment. In this letter, we propose novel schemes to update the flow priorities safely in SDN-based real-time systems. To this end, we first analyze such problems through two types of cases. Then, we develop schemes that determine a safe procedure for priority adjustment and synchronize the priority settings of all switches. By network emulations, we demonstrate that the above problem occurs in 149 out of 300 flow sets, but our schemes can effectively prevent all of them. [ABSTRACT FROM AUTHOR]

The spread of COVID-19 issues high demand on measuring body temperature, which necessitates thermometers. To alleviate a burden to equip/carry thermometers, this paper develops a framework “Ther- Mobile” that measures body temperature using a commercial-off-the-shelf smartphone that most people carry everywhere. Considering that most (if not all) smartphones have a temperature sensor on its battery, we utilize heat transfer from a body part that makes contact with the smartphone, to the smartphone battery. To this end, we collect a time series of the smartphone battery temperature for different pairs of the initial temperature of the smartphone battery and the temperature of a body part, and then classify them. To enable the data collection and classification to infer the temperature of the body part, we address important practical issues, including how to gather data for different target temperatures of a body part (although human body temperature is not controllable), and how to minimize a burden for individual users to gather all necessary data. Our experiments demonstrate that “Ther- Mobile” achieves 90.0% accuracy of measuring body temperature with 1.0°C granularity, enabling a commercial-off-the-shelf smartphone to substitute for a thermometer without any additional hardware. [ABSTRACT FROM AUTHOR]

In this article, an adaptive real-time communication system is proposed that leverages the software-defined networking (SDN) paradigm to provide end-to-end deadline guarantees. SDN is an emerging networking paradigm that allows control of the network through directly programmable software controllers, offering the flexibility to manage and optimize network resources dynamically. By utilizing these SDN features, a novel networking system, called RT-SDN, is presented that can effectively support real-time communication through cooperative routing and scheduling. To this end, we present a highly efficient routing algorithm that can adaptively reconfigure the routes of existing flows to find bandwidth-guaranteed routes for all flows. We then introduce a new priority assignment scheme that can achieve better deadline guarantees (i.e., better schedulability). In addition, RT-SDN allows routing and scheduling to operate together by employing a feedback loop between them. We implemented a prototype of RT-SDN as an SDN controller and deployed it on a testbed network of 30 BeagleBone devices. Our experiment results show that RT-SDN can be deployed in real-world commodity networks to provide end-to-end deadline guarantees, and the proposed schemes collectively improve the schedulability to a significant degree. [ABSTRACT FROM AUTHOR]

Lateral size effects of ferroelastic domain structures in epitaxial PbTiO3 thin films were investigated systematically with a viewpoint of misfit strain relaxation mechanism. The epitaxial PbTiO3 thin films were patterned into discrete islands and the effects of lateral dimension were analyzed by reciprocal space mapping using synchrotron x-ray diffraction as well as finite element simulation. As the lateral two-dimensional planar size decreases in the PbTiO3 patterns on MgO(001), some of the a domains turned into c domains due to the relaxed tensile strain. In the PbTiO3 patterns on Pt(001)/MgO(001), on the other hand, the formation of 90° domains is enhanced by the reduction in compressive misfit strain. As the pattern size decreases further to 100 nm, the untilted a domains arise due to the almost completely relaxed misfit strains. Equilibrium domain structures in the epitaxial thin films and discrete islands are also analyzed by the finite element simulation and found to be consistent with the experimental observation. These results manifest that the domain structure and evolution of the epitaxial thin films could be engineered by the control of misfit strain and its relaxation. [ABSTRACT FROM AUTHOR]

Equilibrium domain structures commonly observed in epitaxial Pb-based ferroelectric thin films are analyzed by the finite element method (FEM) using a commercial package, ABAQUS (Hibbit, Karlsson & Sorensen, Inc., 1080 Main Street, Pawtucket, RI 02860-4847). Structures of periodic 90° domains in epitaxial PbTiO[sub 3] thin films on cubic single crystalline substrates are analyzed as a function of decreasing temperature in order to simulate cooling process after the film deposition at elevated temperature (T[sub G]). The degree of c-axis orientation (α) is determined as a function of temperature below the Curie temperature and compared to the experimental results. It is then possible to calculate the magnitude of misfit strain during film growth and its relaxation due to dislocation generation. The effect of PZT composition on c-domain abundance is also simulated. FEM simulation is performed with the assumption that the major driving force for such domain formation is thermoelastic strains arising from the film-substrate interaction and the cubic-tetragonal phase transformation. The FEM analysis also suggests that initial misfit stress at T[sub G] is not fully relaxed and the unrelaxed misfit stress is inversely related to final c-domain abundance. [ABSTRACT FROM AUTHOR]

Traffic redundancy elimination (RE) is an attractive approach to improve the throughput in bandwidth-limited networks. While previous studies show that the RE is useful for improving the throughput in such networks, we observed that the RE would not be an effective solution in wireless networks. We found the TCP congestion control cannot take advantage of the RE, without knowing how the underlying RE system manipulates each TCP packet. In this letter, we present a novel technique called REboost to enable the TCP layer to be aware of the underlying RE system and improve the throughput. Our evaluation with a prototype shows that REboost significantly improves the throughput compared with the previous RE systems. [ABSTRACT FROM PUBLISHER]

Zero-laxity (ZL) and contention-free (CF) policies have received considerable attention owing to their simplicity and applicability to real-time systems equipped with symmetry multiprocessors. Recently, the ZL policy for mixed-criticality (MC) systems has been proposed and studied, but the applicability to and performance of the CF policy for MC systems have not been investigated yet. In this paper, we propose the CF policy (as a scheduling policy) for MC symmetry multiprocessor systems, referred to as the MC systems tailored CF policy (MC-CF), and a schedulability analysis in support thereof. We define the notion of contention-free slots for two different criticalities (of MC systems) of tasks, propose a technique to limit the amount to be utilized for each task by defining an upper bound, and subsequently explain the way in which the contention-free slots are systematically utilized to improve the schedulability of MC symmetry multiprocessor systems. Following this, we develop a deadline analysis (DA) for MC-CF. Using our experimental results under various environmental settings, we demonstrate that MC-CF can significantly improve the schedulability of fixed-priority scheduling. [ABSTRACT FROM AUTHOR]

The ferroelastic twin-domain structures and piezoelectric properties were investigated in epitaxial Pb(Zr0.35,Ti0.65)O3 thin films with various c-domain volume fractions by metal organic chemical vapor deposition on (100)cSrRuO3/(100)SrTiO3 substrates. The domain structures could be characterized into three regions: a-domain dominant, c-domain dominant, and their mixed domain regions. The mixed domain structure is quite unusual but formed a bilayer with two regions of different a/c domain proportions: the bottom layer is the a1-a2 domain structure and top layer is the a-c domain structure. The films of the mixed region have attained largest piezoelectric coefficients, d33, presumably due to enhanced a-to-c domain switching. [ABSTRACT FROM AUTHOR]

In order to test a critical lateral dimension in two-dimensional (2D) planar ferroelectrics, epitaxial PbTiO3 thin films are patterned into discrete islands lithographically with different lateral sizes. As the pattern size decreases, the substrate clamping effect is significantly reduced and thus the misfit strain in the films could he relaxed further. Evolution of 90° domain structures as a function of lateral dimensions was characterized extensively by reciprocal space mapping using synchrotron x ray. As the lateral 2D planar size decreases in the PbTiO3 patterns on MgO(001), some of the a domains turned into c domains due to the relaxed tensile strain. In the PbTiO3 patterns on Pt(001 ) /MgO(001), on the other hand, the formation of 90° domains is enhanced by the reduction in compressive misfit strain. Equilibrium domain structures in the PbTiO3 thin film islands are also analyzed by the finite element simulation and found to be consistent with the experimental observation. [ABSTRACT FROM AUTHOR]

Studies of both systematic experiments and detailed simulations for examining the effects of N[sub 2][SUP ARRANGE="STAGGER"]+] implant on channel dopants are described. Step-by-step monitor wafer experiments have clearly confirmed the nitrogen-induced transient enhanced diffusion (TED) of dopants. Process simulations within the “+1” N[sub 2][SUP ARRANGE="STAGGER"]+] profile approach have demonstrated the need to scale down the +1 model parameter for matching the measured depth profiles. The underlying mechanism for the reduced +1 model parameter is that nitrogen which diffuses toward the Si surface becomes a sink for the interstitials. These combined studies also show that nitrogen-induced TED of dopants increases with N[sub 2][SUP ARRANGE="STAGGER"]+] dose. © 2002 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Previous studies have demonstrated the feasibility of producing fatty-acid-derived hydrocarbons in Escherichia coli. However, product titers and yields remain low. In this work, we demonstrate new methods for improving fatty acid production by modifying central carbon metabolism and storing fatty acids in triacylglycerol. Based on suggestions from a computational model, we deleted seven genes involved in aerobic respiration, mixed-acid fermentation, and glyoxylate bypass (in the order of cyoA, nuoA, ndh, adhE, dld, pta, and iclR) to modify the central carbon metabolic/regulatory networks. These gene deletions led to increased total fatty acids, which were the highest in the mutants containing five or six gene knockouts. Additionally, when two key enzymes in the fatty acid biosynthesis pathway were over-expressed, we observed further increase in strain △cyoA△adhE△nuoA△ndh△pta△dld, leading to 202 mg/g dry cell weight of total fatty acids, ~250% of that in the wild-type strain. Meanwhile, we successfully introduced a triacylglycerol biosynthesis pathway into E. coli through heterologous expression of wax ester synthase/acyl-coenzyme:diacylglycerol acyltransferase (WS/DGAT) enzymes. The added pathway improved both the amount and fuel quality of the fatty acids. These new metabolic engineering strategies are providing promising directions for future investigation. [ABSTRACT FROM AUTHOR]