13 research outputs found
Autonomous Navigation System for Spacecraft Using Low-Thrust Trajectories
This research describes a prototype software navigation system that would allow a spacecraft with a small amount
of continuous propulsion to navigate low-energy trajectories. First, the desired route is described in terms of basic orbit shapes, such as Lyapunov orbits. This sequence of orbit shapes is converted into an itinerary of spatial boundaries that a spacecraft executing the low-energy maneuver will cross in order.A software system then employs a guided optimization algorithm that identifies the thrust angle that will maintain the desired orbit. Using this software as a research tool, simulations have identified low-energy paths that could be used by a spacecraft with an ion drive to perform a Venus flyby within four or five years of its launch from Earth. This approach makes it possible to identify complex low-energy trajectories that rely on the gravitational effects of different two-body systems (for instance, Earthâmoon and Earthâsun) and to study the utility of continuous propulsion in flying such trajectories from Earth
The First Three Rungs of the Cosmological Distance Ladder
It is straightforward to determine the size of the Earth and the distance to
the Moon without making use of a telescope. The methods have been known since
the 3rd century BC. However, few amateur or professional astronomers have
worked this out from data they themselves have taken. Here we use a gnomon to
determine the latitude and longitude of South Bend, Indiana, and College
Station, Texas, and determine a value of the radius of the Earth of 6290 km,
only 1.4 percent smaller than the true value. We use the method of Aristarchus
and the size of the Earth's shadow during the lunar eclipse of 2011 June 15 to
derive an estimate of the distance to the Moon (62.3 R_Earth), some 3.3 percent
greater than the true mean value. We use measurements of the angular motion of
the Moon against the background stars over the course of two nights, using a
simple cross staff device, to estimate the Moon's distance at perigee and
apogee. Finally, we use simultaneous CCD observations of asteroid 1996 HW1
obtained with small telescopes in Socorro, New Mexico, and Ojai, California, to
derive a value of the Astronomical Unit of (1.59 +/- 0.19) X 10^8 km, about 6
percent too large. The data and methods presented here can easily become part
of a beginning astronomy lab class.Comment: 34 pages, 11 figures, accepted for publication in American Journal of
Physic
An in-silico & in-vitro tournament for protein engineering
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Polyextremophile engineering: a review of organisms that push the limits of life
Nature exhibits an enormous diversity of organisms that thrive in extreme environments. From snow algae that reproduce at sub-zero temperatures to radiotrophic fungi that thrive in nuclear radiation at Chernobyl, extreme organisms raise many questions about the limits of life. Is there any environment where life could not âfind a wayâ? Although many individual extremophilic organisms have been identified and studied, there remain outstanding questions about the limits of life and the extent to which extreme properties can be enhanced, combined or transferred to new organisms. In this review, we compile the current knowledge on the bioengineering of extremophile microbes. We summarize what is known about the basic mechanisms of extreme adaptations, compile synthetic biologyâs efforts to engineer extremophile organisms beyond what is found in nature, and highlight which adaptations can be combined. The basic science of extremophiles can be applied to engineered organisms tailored to specific biomanufacturing needs, such as growth in high temperatures or in the presence of unusual solvents
Engineering exclusively-quadruplet codon translation in vivo
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, February, 2021Cataloged from the official PDF version of thesis. "February 2021."Includes bibliographical references (pages 95-106).Living organisms universally encode amino acids with three-base codons specifying the twenty canonical amino acids. A genetic code entirely based on four-base codons would answer many questions about the origin of life and have profound implications for expanding the genetic code to include novel amino acids. However, the task of assembling enough quadruplet-tRNAs (qtRNAs) to implement an all-quadruplet code remains a major hurdle. Here, we create qtRNAs that decode canonical amino acids by modifying E. coli tRNAs that continue to rely upon endogenous aminoacyl-tRNA synthetases (AARSs) for charging. We find that AARSs generally tolerate quadruplet anticodons, resulting in efficient, selectively charged qtRNAs for eight of the twenty canonical amino acids, as well as candidate qtRNAs for the remaining 12 amino acids. We develop a directed evolution technique based on Phage Assisted Continuous Evolution and use it to improve the translation efficiency of qtRNAs. In order to address the large number of necessary evolutions, we execute these evolutions using a high-throughput evolution platform we developed. We find that directed evolution of qtRNAs can substantially improve quadruplet codon translation efficiency, often by 10x or more, without compromising amino acid selectivity. We use the evolved qtRNAs to implement an 10-amino acid all quadruplet codon code and processive quadruplet codon translation of a small peptide within a standard bacterial chassis, without the need for genome recoding.by Erika Alden DeBenedictis.Ph. D.Ph.D. Massachusetts Institute of Technology, Department of Biological Engineerin
Support academic access to automated cloud labs to improve reproducibility.
Cloud labs, where experiments are executed remotely in robotic facilities, can improve the reproducibility, accessibility, and scalability of experimental biology. Funding and training programs will enable academics to overcome barriers to adopting such technology
Measuring the tolerance of the genetic code to altered codon size
Translation using four-base codons occurs in both natural and synthetic systems. What constraints contributed to the universal adoption of a triplet codon, rather than quadruplet codon, genetic code? Here, we investigate the tolerance of the Escherichia coli genetic code to tRNA mutations that increase codon size. We found that tRNAs from all 20 canonical isoacceptor classes can be converted to functional quadruplet tRNAs (qtRNAs). Many of these selectively incorporate a single amino acid in response to a specified four-base codon, as confirmed with mass spectrometry. However, efficient quadruplet codon translation often requires multiple tRNA mutations. Moreover, while tRNAs were largely amenable to quadruplet conversion, only nine of the twenty aminoacyl tRNA synthetases tolerate quadruplet anticodons. These may constitute a functional and mutually orthogonal set, but one that sharply limits the chemical alphabet available to a nascent all-quadruplet code. Our results suggest that the triplet codon code was selected because it is simpler and sufficient, not because a quadruplet codon code is unachievable. These data provide a blueprint for synthetic biologists to deliberately engineer an all-quadruplet expanded genetic code.</jats:p
Enabling highâthroughput biology with flexible openâsource automation
Abstract Our understanding of complex living systems is limited by our capacity to perform experiments in high throughput. While robotic systems have automated many traditional handâpipetting protocols, software limitations have precluded more advanced maneuvers required to manipulate, maintain, and monitor hundreds of experiments in parallel. Here, we present Pyhamilton, an openâsource Python platform that can execute complex pipetting patterns required for custom highâthroughput experiments such as the simulation of metapopulation dynamics. With an integrated plate reader, we maintain nearly 500 remotely monitored bacterial cultures in logâphase growth for days without user intervention by taking regular density measurements to adjust the robotic method in realâtime. Using these capabilities, we systematically optimize bioreactor protein production by monitoring the fluorescent protein expression and growth rates of a hundred different continuous culture conditions in triplicate to comprehensively sample the carbon, nitrogen, and phosphorus fitness landscape. Our results demonstrate that flexible software can empower existing hardware to enable new types and scales of experiments, empowering areas from biomanufacturing to fundamental biology