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Observing Solar Limb Darkening in the Classroom
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| Pengarang | : | - |
| Nama Majalah/Jurnal | : | The Physics Teacher |
| Volume / Edisi | : | 59 (No. 4) |
| Halaman | : | 292-293 |
| Abstrak | : | The falling temperature of the photosphere with height is responsible for the effect known as limb darkening. The Sun is not equally bright all over the disc. When we observe the Sun towards the limbs, it appears to get darker. Light from the photosphere travels through an absorptive medium. Therefore, one can see only so far into the photosphere. This is the optical depth (Fig. 1). The line of sight at the center sees deeper into the Sun to an optical depth of about 2/3 into the photosphere. In other words, photons that escape from a smaller radius of the photosphere have originated in a hotter region; therefore, they will have a higher intensity. Photons that originate from a larger radius come from a cooler part of the photosphere; therefore, this results in lower intensity. This effect is known as solar limb darkening. In addition, the solar photosphere displays various phenomena that can easily be observed in images obtained with small telescopes, such as sunspots, faculae, and granulation. Limb darkening results from the fact that we are looking into hot gas when we look at the Sun and, as a consequence of this, the brightness of the Sun decreases as one looks from the center of the disc (where we see deeper inside the Sun) towards the limb (where we will not see as deeply into the solar atmosphere because we are looking at a slant through the photospheric material). |
Bayesian and Algebraic Strategies to Design in Synthetic Biology
| Pengarang | : | - |
| Nama Majalah/Jurnal | : | Proceedings of the IEEE |
| Volume / Edisi | : | 110 (No. 5) |
| Halaman | : | 675-687 |
| Abstrak | : | Innovation in synthetic biology often still depends on large-scale experimental trial and error, domain expertise, and ingenuity. The application of rational design engineering methods promises to make this more efficient, faster, cheaper, and safer. However, this requires mathematical models of cellular systems. For these models, we then have to determine if they can meet our intended target behavior. Here, we develop two complementary approaches that allow us to determine whether a given molecular circuit, represented by a mathematical model, is capable of fulfilling our design objectives. We discuss algebraic methods that are capable of identifying general principles guaranteeing desired behavior; we provide an overview of Bayesian design approaches that allow us to choose a model that has the highest probability of fulfilling our design objectives from a set of models. We discuss their uses in the context of biochemical adaptation and, then, consider how robustness can and should affect our design approach. |
Motivating Premedical Students to Get Interested in Physics
| Pengarang | : | |
| Nama Majalah/Jurnal | : | The Physics Teacher |
| Volume / Edisi | : | 59 (No. 4) |
| Halaman | : | 288-290 |
| Abstrak | : | Physics teachers around the world are trying to create classroom environments that would allow life science students to be more intrinsically motivated in their work. These efforts include, among others, matching classroom activities to students’ interests as well as structurally variable activities to match different student abilities. While physics instruction at the Université libre de Bruxelles also strives to make classes more relevant for life science students, two stimulation approaches will be presented here in detail. These include the in-class motivation using historical examples of physicians’ role in physics development and the small group work outside of class on physics problems that have engaging, motivating, and challenging biomedical headings. |
Advances in the Computational Design of Small-Molecule-Controlled Protein-Based Circuits for Synthetic Biology
| Pengarang | : | Simon Kretschmer |
| Nama Majalah/Jurnal | : | Proceedings of the IEEE |
| Volume / Edisi | : | 110 (No. 5) |
| Halaman | : | 659-674 |
| Abstrak | : | Synthetic biology approaches living systems with an engineering perspective and promises to deliver solutions to global challenges in healthcare and sustainability. A critical component is the design of biomolecular circuits with programmable input–output behaviors. Such circuits typically rely on a sensor module that recognizes molecular inputs, which is coupled to a functional output via protein-level circuits or regulating the expression of a target gene. While gene expression outputs can be customized relatively easily by exchanging the target genes, sensing new inputs is a major limitation. There is a limited repertoire of sensors found in nature, and there are often difficulties with interfacing them with engineered circuits. Computational protein design could be a key enabling technology to address these challenges, as it allows for the engineering of modular and tunable sensors that can be tailored to the circuit’s application. In this article, we review recent computational approaches to design protein-based sensors for small-molecule inputs with particular focus on those based on the widely used Rosetta software suite. Furthermore, we review mechanisms that have been harnessed to couple ligand inputs to functional outputs. Based on recent literature, we illustrate how the combination of protein design and synthetic biology enables new sensors for diverse applications ranging from biomedicine to metabolic engineering. We conclude with a perspective on how strategies to address frontiers in protein design and cellular circuit design may enable the next generation of sense-response networks, which may increasingly be assembled from de novo components to display diverse and engineerable input-output behaviors. |
Cybergenetics: Theory and Applications of Genetic Control Systems
| Pengarang | : | - |
| Nama Majalah/Jurnal | : | Proceedings of the IEEE |
| Volume / Edisi | : | 110 (No. 5) |
| Halaman | : | 631-658 |
| Abstrak | : | There is no design template more important than DNA. Within the sequences of this exquisite substance lie the design plans for each of us and for every living organism. Shaped over billions of years by the creative machinations of evolution, this design template encodes the most complex dynamical systems known to us. Yet, it is only in our lifetimes that we are able to directly edit this template and engineer our own designs. The story that I tell in this article is about our early attempts to design and commission our own control systems in living cells. Guided by what we have learned from controlling man-made systems, we are beginning to develop the theory and methodologies needed to build control systems at the molecular level, an endeavor that is as challenging as it is rewarding. If carried out responsibly, this new ability to reshape the DNA template can have a tremendous benefit for our health and well-being, and will drive major advances in basic science, industrial biotechnology, and medical therapy. In this article, I will take the readers of the proceedings on a journey through the new and promising world of rationally designed genetic control systems. Using a minimum of jargon, I will introduce them to the biological concepts needed to develop an understanding and appreciation of the main design concepts emerging in this nascent area of research. My goal is to convey my own sense of excitement about the possibilities, but it is also to impart a feeling of the opportunities that lay ahead for members of the IEEE to contribute with their own creative ideas to the shaping of this most versatile of design templates, the DNA. |
Color-Coded Algebra
| Pengarang | : | Bradley K. McCoy |
| Nama Majalah/Jurnal | : | The Physics Teacher |
| Volume / Edisi | : | 59 (No. 4) |
| Halaman | : | 286-287 |
| Abstrak | : | In a typical first physics class, homework consists of problems in which numerical values for physical quantities are given and the desired answer is a number with appropriate units. In contrast, most calculations in upper-division undergraduate physics are entirely symbolic. Despite the need to learn symbolic manipulation, students are often resistant to performing symbolic calculations in their introductory classes. As instructors, we face a choice between encouraging students to use symbolic calculations, including helping them learn the necessary skills to do so, or allowing students to default to numerical calculations, which does not adequately prepare them for their future courses. In this paper, I will describe a color-coded algebra scheme, which helps lower the barriers to symbolic calculations for students. |
Understanding a Paradox in Special Relativity
| Pengarang | : | - |
| Nama Majalah/Jurnal | : | The Physics Teacher |
| Volume / Edisi | : | 59 (No. 4) |
| Halaman | : | 284-285 |
| Abstrak | : | Einstein’s special theory of relativity includes many non-intuitive and apparently paradoxical conclusions about space and time. One of these is time dilation, the fact that a clock moving relative to an observer runs slower than an identical clock at rest in the observer’s reference frame. This is clearly exhibited in the extended mean lifetime of elementary particles moving at high speed, compared to their mean lifetime when at rest, and must be taken into account when processing signals from atomic clocks carried by satellites in the global positioning system (GPS). My intent in this note is not to derive this or other relativistic effects; such derivations may be found in many textbooks. Rather, I would like to share two figures I prepared while teaching elementary physics quite a few years ago, to help understand the apparent paradox that two observers, in relative motion, both measure the other’s clock to run slower than their own. It is my hope that instructors can reproduce these two figures and find them useful in discussions to illustrate these basic concepts. The sketches are only approximately drawn to scale. |
Synthetic Gene Circuits: Design, Implement, and Apply
| Pengarang | : | - |
| Nama Majalah/Jurnal | : | Proceedings of the IEEE |
| Volume / Edisi | : | 110 (No. 5) |
| Halaman | : | 613-630 |
| Abstrak | : | Synthetic biologists engineered the first genetic toggle switch and clock at the turn of the 21st century. Since the development of these first gene circuits, methods for circuit design and construction have improved dramatically, narrowing the gap between concept and proof-of-principle implementation. Engineered genetic constructs have started to leave the lab for the real world where they are being used in applications, including medicine, biosensing, and industrial chemical production. The field of synthetic gene circuits has also grown from focusing on single, isolated circuits to designing complex systems that operate across multiple populations in carefully engineered consortia. In addition, design methods have progressively moved toward including detailed models of the interactions between the host genome and the synthetic gene circuits that it contains in order to better predict circuit dynamics. This article will review some of the most recent advances in gene circuit design and implementation, with a focus on synthetic gene circuits being applied to address real-world problems. |
An Analysis of Shadows Made from Sunlight Reflected by a Curved Surface
| Pengarang | : | Umbu Rauta |
| Nama Majalah/Jurnal | : | The Physics Teacher |
| Volume / Edisi | : | 59 (No. 4) |
| Halaman | : | 282-283 |
| Abstrak | : | Shadows produced by sunlight reflected from convex surfaces can be very well defined. This article provides an explanation for this phenomenon as well as a demonstration/lab activity for students to investigate properties of shadows made from sunlight reflected by a curved surface. |
Learning Outside the Brain: Integrating Cognitive Science and Systems Biology
| Pengarang | : | - |
| Nama Majalah/Jurnal | : | Proceedings of the IEEE |
| Volume / Edisi | : | 110 (No. 5) |
| Halaman | : | 590-612 |
| Abstrak | : | Learning is commonplace in organisms such as ourselves and even in organisms as far distant as the bee and the octopus. Such learning is implemented by brains, or neuronal networks, and has been extensively studied within ethology, psychology, cognitive science, and neuroscience. Whether learning also takes place in nonneuronal settings has remained a matter of sustained controversy, too often dominated by ideological views. In this survey, I will explain how learning can be rigorously interpreted as a form of information processing and then explore the evidence for whether learning also takes place in organismal contexts outside the brain, such as physiology, development, and individual cells. I will try to explain why it is important to build bridges in this way between cognitive science and systems biology, why concepts and methods from various branches of engineering may be helpful in this task, and what the eventual impact may be on how we think about the organism. |