Using the Features of Brownian Motion to Characterize the Nuclear Pore Complex, Molecular Robots, and Antimony-Doped Tin Oxide.

Brownian motion is the apparently random motion of small particles in a solution that results from the bombardment of molecules within the solution. The theoretical understanding of this motion was developed by Einstein in the early 1900s. Since then, features of Brownian motion, such as the fact that Brownian motion can be modeled using a random walk, or the fact that ensemble mean squared displacement (MSD) can be used to determine a diffusion coefficient and type of diffusive behavior, have been utilized to characterize a vast array of systems that are both naturally occurring and synthetic. In this thesis, I characterize three different types of systems using features of Brownian motion: naturally occurring nuclear pore complexes, synthetic molecular robots that are based on naturally occurring bipedal molecular walkers, and synthetic conductive nanoporous antimony-doped tin oxide (ATO). For the nuclear pore complex, the diffusion of particles through each region of the complex was modeled using a random walk in order to help determine the relative diffusion coefficients of the three regions. For the molecular robots, the movement of the robots was modeled using a more advanced random-walk simulation that utilizes the Gillespie algorithm; the movement of the robots was evaluated based on the MSDs, and the results were used to characterize the directional bias in the walking mechanism of the robots. For the ATO, fluorescent particles were monitored as they underwent Brownian motion while diffusing through the nanopores; MSDs were used to determine that these particles are embedded in the nanopores and that the diffusion coefficient depended in an unexpected way on the potential applied across the material.PhDPhysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/99910/1/michelot_1.pd

Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology

Nucleic acid nanotechnology exploits the programmable molecular recognition properties of natural and synthetic nucleic acids to assemble structures with nanometer‐scale precision. In 2006, DNA origami transformed the field by providing a versatile platform for self‐assembly of arbitrary shapes from one long DNA strand held in place by hundreds of short, site‐specific (spatially addressable) DNA ‘staples’. This revolutionary approach has led to the creation of a multitude of two‐dimensional and three‐dimensional scaffolds that form the basis for functional nanodevices. Not limited to nucleic acids, these nanodevices can incorporate other structural and functional materials, such as proteins and nanoparticles, making them broadly useful for current and future applications in emerging fields such as nanomedicine, nanoelectronics, and alternative energy. WIREs Nanomed Nanobiotechnol 2012, 4:139–152. doi: 10.1002/wnan.170 For further resources related to this article, please visit the WIREs website .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90282/1/170_ftp.pd

Molecular robots guided by prescriptive landscapes

Traditional robots rely for their function on computing, to store internal representations of their goals and environment and to coordinate sensing and any actuation of components required in response. Moving robotics to the single-molecule level is possible in principle, but requires facing the limited ability of individual molecules to store complex information and programs. One strategy to overcome this problem is to use systems that can obtain complex behaviour from the interaction of simple robots with their environment. A first step in this direction was the development of DNA walkers, which have developed from being non-autonomous, to being capable of directed but brief motion on one-dimensional tracks. Here we demonstrate that previously developed random walkers—so-called molecular spiders that comprise a streptavidin molecule as an inert ‘body’ and three deoxyribozymes as catalytic ‘legs’—show elementary robotic behaviour when interacting with a precisely defined environment. Single-molecule microscopy observations confirm that such walkers achieve directional movement by sensing and modifying tracks of substrate molecules laid out on a two-dimensional DNA origami landscape. When using appropriately designed DNA origami, the molecular spiders autonomously carry out sequences of actions such as ‘start’, ‘follow’, ‘turn’ and ‘stop’. We anticipate that this strategy will result in more complex robotic behaviour at the molecular level if additional control mechanisms are incorporated. One example might be interactions between multiple molecular robots leading to collective behaviour; another might be the ability to read and transform secondary cues on the DNA origami landscape as a means of implementing Turing-universal algorithmic behaviour

The Future of Our Seas: Marine scientists and creative professionals collaborate for science communication

To increase awareness of the current challenges facing the marine environment, the Future of Our Seas (FOOS) project brought together the expertise of scientists, public engagement experts and creatives to train and support a group of marine scientists in effective science communication and innovative public engagement. This case study aims to inspire scientists and artists to use the FOOS approach in training, activity design and development support (hereafter called the ‘FOOS programme’) to collaboratively deliver novel and creative engagement activities. The authors reflect on the experiences of the marine scientists: (1) attending the FOOS communication and engagement training; (2) creating and delivering public engagement activities; (3) understanding our audience; and (4) collaborating with artists. The authors also share what the artists and audiences learned from participating in the FOOS public engagement activities. These different perspectives provide new insights for the field with respect to designing collaborative training which maximizes the impact of the training on participants, creative collaborators and the public. Long-term benefits of taking part in the FOOS programme, such as initiating future collaborative engagement activities and positively impacting the scientists’ research processes, are also highlighted

Anatomy of STEM Teaching in American Universities: A Snapshot from a Large-Scale Observation Study

National and local initiatives focused on the transformation of STEM teaching in higher education have multiplied over the last decade. These initiatives often focus on measuring change in instructional practices, but it is difficult to monitor such change without a national picture of STEM educational practices, especially as characterized by common observational instruments. We characterized a snapshot of this landscape by conducting the first large scale observation-based study. We found that lecturing was prominent throughout the undergraduate STEM curriculum, even in classrooms with infrastructure designed to support active learning, indicating that further work is required to reform STEM education. Additionally, we established that STEM faculty’s instructional practices can vary substantially within a course, invalidating the commonly-used teaching evaluations based on a one-time observation

Développement et validation d'un outil d'évaluation des perceptions corporelles en Afrique

Communications orales et affichées de la 1836ème Journée de la Société d'Anthropologie de Paris parues dans Bulletins et Mémoires de la Société d'Anthropologie de Paris , 23 S1-S4

Anatomy of STEM Teaching in American Universities: A Snapshot from a Large-Scale Observation Study

National and local initiatives focused on the transformation of STEM teaching in higher education have multiplied over the last decade. These initiatives often focus on measuring change in instructional practices, but it is difficult to monitor such change without a national picture of STEM educational practices, especially as characterized by common observational instruments. We characterized a snapshot of this landscape by conducting the first large scale observation-based study. We found that lecturing was prominent throughout the undergraduate STEM curriculum, even in classrooms with infrastructure designed to support active learning, indicating that further work is required to reform STEM education. Additionally, we established that STEM faculty’s instructional practices can vary substantially within a course, invalidating the commonly-used teaching evaluations based on a one-time observation

Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs.

Identifying effective antivirals for treating Ebola virus disease (EVD) and minimizing transmission of such disease is critical. A variety of cell-based assays have been developed for evaluating compounds for activity against Ebola virus. However, very few reports discuss the variable assay conditions that can affect the results obtained from these drug screens. Here, we describe variable conditions tested during the development of our cell-based drug screen assays designed to identify compounds with anti-Ebola virus activity using established cell lines and human primary cells. The effect of multiple assay readouts and variable assay conditions, including virus input, time of infection, and the cell passage number, were compared, and the impact on the effective concentration for 50% and/ or 90% inhibition (EC50, EC90) was evaluated using the FDA-approved compound, toremifene citrate. In these studies, we show that altering cell-based assay conditions can have an impact on apparent drug potency as measured by the EC50. These results further support the importance of developing standard operating procedures for generating reliable and reproducible in vitro data sets for potential antivirals