Persuasive Engineering: Socially Influencing Systems for Behavior Change

Author: Agnis Stibe
Co-authors:
Affiliation: MIT Media Lab
Abstract:
We all are social beings by our nature for ages. Today, the physical world shrinks as information and communication technologies bring us closer together by enabling new ways for socializing. At the same time, these technologies may not only serve as media channels but they can be designed with intent to influence our thoughts and actions.
Research in psychology suggests that human beings can be proactive and engaged depending largely on the social environments in which they develop and function. Human self-development, adaptation, and change are embedded in social systems. In such systems, according to the social cognitive theory, personal factors, behavioral patterns, and environmental events all operate as interacting determinants that mutually influence each other. In other words, there is an endless dynamic interaction between the person, the behavior, and the environment in which a given behavior is performed.
This triadic reciprocal determinism unfolds multiple pathways for studying behavioral change, including environmental and personal change. In everyday interactions, user behavior alters environmental conditions and, in turn, is changed by the same conditions that it creates. In addition, social cognitive theory highlights the need to explore aspects of social persuasion maintained by ambient environments.
Information systems can facilitate social influence when augmented with relevant persuasive design principles. People can experience social influence not only from others around them, but likewise through information systems that are equipped with persuasive design principles. An information system becomes socially influencing when it is enriched with social influence design principles to facilitate changes in behaviors and attitudes of its users.
Research results reveal interplay between the design principles and indicate that they have the capacity to improve the persuasiveness of information systems and predict the behavioral intentions of users to engage with such systems in the future. These outcomes provide richer understanding of how to effectively harness social influence for enhanced user engagement through socio-technical environments and for the future development of persuasive information systems.

ThreadScan: Automatic and Scalable Memory Reclamation

Author: Alexander Matveev
Co-authors: William M. Leiserson, Dan Alistarh, Nir Shavit
Affiliation: CSAIL
Abstract:
Concurrent memory reclamation is the problem of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, there is no satisfactory solution to this problem: existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU, are either prohibitively expensive or require significant programming expertise, to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated.

In this work we propose a radically new approach to concurrent memory reclamation: instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our new framework, called ThreadScan, leverages the operating system signaling, paging and thread control, to automatically detect which memory locations are being accessed by concurrent threads.

Initial empirical evidence of using the ThreadScan approach shows that it scales surprisingly well, and requires negligible programming effort beyond the standard use of Malloc and Free.

Magnetic-less field emitter array pump for miniaturized atomic spectroscopy sensors

Author: Anirban Basu
Co-authors: Max Perez, Luis Velásquez-García
Affiliation: Microsystems Technology Laboratories
Abstract:
We report the design, fabrication, and characterization of a novel electronic pump architecture for generation and maintenance of high vacuum in small cavities that is compatible with alkali-vapor cells. The electron impact ionization pump uses a nanostructured high-current low-voltage silicon field emitter array (FEA) as electron source. The FEA does not degrade when operated in Rubidium vapor. By electron impact-ionization of gas molecules, followed by gettering of the ions so formed, pump down to 3.0×10^-7 Torr was observed in a proof-of-concept 200 cm^3 vacuum chamber. An ion current of 0.5 nA and an electron current of 6 µA was observed in this pressure range. The ion current to electron current ratio was found to be proportional to the chamber pressure. Further miniaturization of the pump will enable better performance and overall volume reduction of chip scale atomic spectroscopy sensors that operate with laser-cooled alkali atoms such as Rubidium.

Inkjet printing of organometal halide perovskite films for solar photovoltaics

Author: Anna Osherov
Co-authors: Samuel Stranks, Giovanni Azzellino, Joel Jean, Melany Sponseller and Vladimir Bulovic
Affiliation: RLE
Abstract:
Inkjet printing of organometal halide perovskites (e.g., CH3NH3PbI3) is a promising approach for low-cost and scalable manufacturing of future thin-film solar cells. Hybrid organic-inorganic perovskites exhibit efficient carrier transport and low internal losses, leading to high open-circuit voltages and solar power conversion efficiencies. To achieve large-scale deployment, however, emerging thin-film photovoltaic technologies must achieve high efficiencies using high-throughput manufacturing techniques. Inkjet printing offers several advantages over conventional lab-scale solution deposition methods (e.g., spin-coating or dip-coating), such as compatibility with roll-to-roll processing, ease of patterning, substrate temperature control, and increased material utilization.

In this work we inkjet printing thin CH3NH3PbX3 perovskite films with controlled morphology and microstructure on a variety of substrates. We further report the effect of key printing parameters, such as substrate temperature, pulse frequency, and pulse amplitude, on film thickness, morphology, and homogeneity.

Extraction of potassium by electrolysis from molten K-feldspar at high temperature and in-situ re-oxidation for fertilizer applications

Author: Carole Gadois
Co-authors: Antoine Allanore
Affiliation: DMSE
Abstract:
Potassium is an element of interest especially in the fertilizer industry, where potassium is an essential macronutrient for the growth of plants. Potassium-bearing aluminisilicates, such as K-feldspar, can be considered as a valuable source of potassium, with average K2O content of 10-14 wt%. Commonly found all over the planet, the use of K-feldspar as a substitute source of potash fertilizer has been envisaged more than a century ago. However, the potassium release from K-feldspar (KFS) is a slow process which widely overcomes the timescales for the farmers.
Therefore, methods to extract the potassium from KFS have been developed over the last centuries, either via aqueous processes or high temperature processes. So far, none of those methods have been successfully implemented in the industry. The extraction of potassium via electrolysis of KFS has been believed to be impossible, due to the glass-like properties of the molten KFS, its high viscosity and its low electrical conductivity. Despite those disadvantages, the recent experiments showed that the extraction of potassium from molten KFS was feasible. This electrochemical method implies the generation of metallic potassium at the cathode accompanied with the formation of carbon monoxide at the anode.
The method presents the major interest to only require heat and current, without additional chemical. Besides, the remaining glass containing alumina and silica is a non-hazardous waste which can possibly have other applications, for glass industry as an example.

New tools to investigate the roles of protein N-glycosylation in bacterial virulence: development of inhibitors for microbial carbohydrate acetyl transferases

Author: Cristina Zamora
Co-authors: Joris De Schutter
Affiliation: Biology
Abstract:
Infectious diseases are a major cause of mortality worldwide and the emergence of resistance to almost every antibacterial therapeutic further exacerbates the escalating health crisis. Most current antibiotics were discovered by in vitro identification of bacteriocidal agents which target essential bacterial functions. This imposes selective pressure on the pathogens for survival and results in rapid resistance evolution. We propose to target microbial virulence factors, such as cell adhesion functionality, thus mitigating damage inflicted by pathogens and promoting their clearance by the host immune system. A potential advantage of this approach is reduced selection pressure and concomitant decreased resistance emergence.
The study of microbial pathogens has demonstrated the prevalence of highly modified saccharides as constituents of bacterial N- and O-linked glycoproteins, which interact with the infected host and are intimately associated with the virulence of many medically significant Gram-negative bacteria, including Neisseria meningitidis, Neisseria gonorrhoea, and Campylobacter jejuni. Therefore, inhibitors of bacterial protein N-glycosylation may suppress pathogenic virulence. As the targeted pathways are not essential for survival, this tactic will likely evade the rapid resistance emergence which plaguing antibiotics and potentially introduce new therapeutic approaches to address infectious diseases.
We screened an extensive fragment library against C. jejuni PglD, a carbohydrate acetyl transferase involved in the early steps of N-glycan assembly, and identified promising hits, which were further developed into potent small molecule inhibitors (IC50 < 200 nM). We are currently optimizing our compounds into effective inhibitors of bacterial of N-glycosylation, applying them as tools to investigate virulence mechanisms and pathogenicity.
Synthesis, SAR, biophysical characterization and biological activity will be presented.

Developement and synthesis of hydrosyenite, a new potassium fertilizer

Author: Davide Ciceri
Co-authors: Carole Gadois and Antoine Allanore
Affiliation: Materials Science and Engineering
Abstract:
Potassium fertilizers (potash) are currently produced from soluble salts, which are mined far from the tropics, mainly in Canada and Russia. Cost for transportation increases significantly the price of potash. Furthermore, soluble salts are quickly leached in the highly weathered soils of tropical countries. To fully develop agriculture in the Global South, local production of less soluble potash would be an optimal solution. In this view, K-bearing materials such as ultrapotassic syenite rocks can be a feasible option since they contain up to ~13 wt % of K2O (in the form of feldspar) and are distributed globally. However, their rate of K+ release is too slow to provide agronomic benefit. There is need to create affordable materials that release K+ ions at a moderate rate, lower than soluble salts, but faster than framework silicates such as feldspars. We have developed a hydrothermal process that enhances the availability of K+ from ultrapotassic syenites. Here, we characterize the processed material, called hydrosyenite. The moderate rate of release of K+ and relatively low cost of the process make hydrosyenite a new potash fertilizers for tropical soils.

Designing Organic Materials for Humidity-Resistant Benzene Sensing

Author: Elizabeth S. Sterner
Co-authors: Federico Bertani, Jisun Im, Timothy M. Swager
Affiliation: Chemistry
Abstract:
Benzene, toluene and xylene are industrial pollutants hazardous to both human and environmental health with OSHA permissible exposure limits ranging from 1-200 ppm. While devices with sufficient sensitivity to detect such low concentrations have been produced in the lab, their translation to real-world deployment has been challenging due to issues with reduced device performance in air or when exposed to humidity. We have developed materials based on resorcinol-derived cavitands and synthetic (styrene, acrylate or acrylamide) polymers prepared by radical polymerization designed for use as preconcentrator layers in SWCNT chemiresistor sensors. These sensors respond to benzene adsorption by displaying a decrease in device current when under a constant voltage. These materials display sensitivity to the 100 ppm level, even when operating in air at 2-9 % relative humidity. It was observed that high benzene adsorption, as measured by quartz crystal microbalance, does not directly translate to effective chemiresistor response. Therefore, further characterization of the preconcentrating layers and refinement of the chemiresistor transduction mechanism are underway.

Low temperarure Synthesis of carbon nanotubes on Glass substrate and Carbon Fiber weaves

Author: Erica F Antunes
Co-authors: Richard Li, Andrew H Liotta, Akira Kudo, Brian L Wardle
Affiliation: AERO/ASTRO
Abstract:
Recent papers has showed the development of growth techniques or new catalysts for producing carbon nanotubes (CNTS) in low temperature [1-2]. The low temperature (400-500oC) is a key to obtain CNT on critical substrates, which can melt or promote high diffusion of metallic nanocatalyst, in high temperature, such as glass or carbon fiber. Glass and carbon fibers are largely used in laminate composites in aeronautic industry. The insertion of CNT in carbon fiber/epoxy composites can become them a multifunctional material, since CNTs improve their mechanical, electrical and thermal properties[3-4]
In this work, the CNT growth has been investigated by chemical vapor deposition using acetylene and carbon dioxide [5], as carbon source, at 480oC. A reducing step, using a mixture of hydrogen and argon, is performed before insertion of carbon source in a 1” tubular furnace.
The catalysts used were aqueous solutions containing PSMA, potassium carbonate and sodium hydroxide, followed (or not) by iron nitrate solution in isopropanol [6-7]. The catalyst applying and drying process on de-sized TohoTenax carbon fiber weaves, and on glass from microscope slides were studied to produce homogenous catalyst layers, using vacuum oven, ambient condition, and several rack designs.
Our experiments has been evaluated by scanning electron microscopy, Raman spectroscopy and X-Ray diffraction.

[1] J. V. Anguita, D. C. Cox, M. Ahmad, Y. Y. Tan, J. Allam, S. R. P. Silva. Advanced Functional Materials (2013) 5502–5509
[2] R. Cartwrighta, S. Esconjaureguia, , D. Hardeman, S. Bhardwaj, R. Weatherup, Y. Guo, L. D’Arsié, B. Bayer, P. Kidambi, S. Hofmann, E. Wright, J. Clarke, D. Oakes, C. Cepek, J. Robertson. Carbon 81 (2015) 639–649
[3] S. S Wicks, W Wang, M. R Williams, B. L.Wardle,. Composites Science and Technology 100 (2014)128-135
[4] N. Yamamoto, R. G. de Villoria, B. L. Wardle.Composites Science and Technology 72 (2012)2009–2015

[5] A. Magrez, J. W. Seo; R. Smajda, B. Korbely; J. C. Andresen, M. Mionić, S. Casimirius, L. Forró. ACS Nano 4(2010)3702-3708
[6] S. A. Steiner III. Carbon nanotube growth on challenging substrates : applications for carbon-fiber composites. PhD Thesis. Massachusetts Institute of Technology. Dept. of Aeronautics and Astronautics.. Advisor: Brian L. Wardle. (2011)
[7] R. Li. Hierarchical carbon fiber composites with radially aligned carbon nanotubes: preservation of in-plane tensile properties. Master Thesis. Massachusetts Institute of Technology. Department of Aeronautics and Astronautics. Advisor: B. L. Wardle (2013)

The curious case of TorsinA-LAP1: A heterohexameric AAA+ ATPase with only three active sites

Author: F Esra Demircioglu
Co-authors: Brian A Sosa, James Z Chen, Jessica Ingram, Hidde L Ploegh, Thomas U Schwartz
Affiliation: Biology
Abstract:
Lamin-associated polypeptide 1 (LAP1) resides at the nuclear envelope and interacts with Torsins, poorly understood ER-localized AAA+ ATPases, through a conserved, perinuclear domain. We determined the crystal structure of the perinuclear domain of human LAP1. LAP1 possesses an atypical AAA+ fold. While LAP1 lacks canonical nucleotide binding motifs, its strictly conserved arginine 563 is positioned exactly where the arginine finger of canonical AAA+ ATPases is found. Based on modeling and electronmicroscopic analysis we propose that LAP1 targets Torsin to the nuclear envelope by forming an alternating, heterohexameric (LAP1-Torsin)3 ring, in which LAP1 acts as the Torsin activator. The experimental data shows that mutation of arginine 563 in LAP1 reduces its ability to stimulate TorsinA ATPase hydrolysis. This knowledge may help understand the etiology of DYT1 primary dystonia, a movement disorder caused by a single glutamate deletion in TorsinA.

Microbial foraging in complex microenvironment

Author: Francesco Carrara
Co-authors: Douglas Brumley; Andrew Hein; Simon Levin; Roman Stocker
Affiliation: CEE
Abstract:
Heterotrophic bacteria are the primary consumers of dissolved organic matter in the ocean, which they often encounter as a complex, dynamic landscape made of patches, pulses, filaments and plumes. A fundamental, quantitative understanding of the consequences on microbial foraging of heterogeneity in the nutrient at small spatial scales and its fluctuations at small temporal scales is paramount to infer macroscopic nutrient flows. Here we present a new laboratory approach to address this question, and investigate the foraging behavior of the marine bacterium Vibrio ordalii. We engineered a small PDMS chamber in which bacteria could actively swim while being tracked by video microscopy. Nutrients were “caged” by photoremovable protecting groups: they were uniformly present in the bacterial suspension but not available for consumption until their sudden ‘release’, which occurred at user-defined points in time and space using an LED source, so as to generate resource landscapes with prescribed spatial and temporal variability. Our novel experimental microfluidic approach, mimicking nutrient landscapes that marine bacteria might face under natural environmental conditions, allows the systematic study of the foraging behavior of species that are essential in the cycling of nutrients at the macroscopic scale in the ocean. These data will be valuable in developing modeling approaches to understand the optimal foraging strategies of bacteria in the ocean and beyond.

Consumption of oil by bacteria in the ocean — one drop at a time

Author: Gabriel Juarez
Co-authors: Roman Stocker
Affiliation: CEE
Abstract:
Bacteria play a crucial role in the degradation of crude oil in the ocean. Despite the immense societal and ecological importance of this process, little is known about the biophysical mechanisms that govern microscale interactions between individual bacteria and single oil droplets, which ultimately determine the efficiency of biodegradation. Through experiments using microfluidics and time-lapse microscopy, we study the effect of droplet diameter on the physical interactions between oil degrading marine bacteria and isolated crude oil droplets. For large droplets, bacteria attach, grow, and divide at the interface leading to the self-assembly of a jammed monolayer of cells that encapsulates the entire oil drop. The continued growth at the interface causes the oil drop to buckle and the interface to undergo large deformations. For small droplets, we find that attachment, growth, and colonization become strongly limited for drops smaller than a critical diameter. A theoretical model of attachment supports this finding, suggesting that rendering oil droplets too small by the excessive addition of dispersants, as often done in oil spills, might be a counterproductive strategy. Our results provide a new framework for understanding how the interplay between physical, chemical, and biological processes at interfaces shape the degradation dynamics of crude oil by bacteria in the ocean.

Corona Phase Molecular Recognition of Fibrinogen

Author: Gili Bisker
Co-authors:
Affiliation:
Abstract:
Corona Phase Molecular Recognition (CoPhMoRe) is a method whereby a heteropolymer is adsorbed onto a nanoparticle surface, templating it for the recognition of a specific target analyte. Recently demonstrated for small molecules, CoPhMoRe has not yet been shown to work for macromolecules such as proteins. In this work a CoPhMoRe screen of single walled carbon nanotubes (SWNT) wrapped in a library of phospholipid-poly ethylene glycol derivatives and oligonucleotides against a panel of human blood proteins reveals a phase highly selective to fibrinogen. This corona phase has one of the highest relative coverage of the nanotube surface, of more the 87%, and upon the interaction with fibrinogen, a 54% decreases in fluorescent emission intensity is observed. The three nodules of fibrinogen are shown to bind sequentially in a three step mechanism, with equilibrium constants that increase with the SWNT diameter, ranging from 3.5 nM for the (6,5) chirality to 31.4 nM for the (11,3) chirality. Protein CoPhMoRe is a promising method for recognizing specific bio-macromolecules, proteins, and peptides, for biological applications.

Impact of Interfacial Engineering in Water Purification Via Vapor Deposited Polymers

Author: Hossein Sojoudi
Co-authors: Amelia Servi, Simon Choong, Gregory Rutledge, Gareth H. McKinley, and Karen K. Gleason
Affiliation: Chemical Engineering
Abstract:
We study the impact of interfacial engineering via vapor deposited polymers in the performance of water filtration membranes. In the first part of this work, we developed a new membrane using initiated chemical vapor deposition (iCVD) of poly(divinyl benzene) (pDVB) on commercial phase-inversion nylon membranes. We obtained up to 22 L/m2/hr permeate flux and maintained greater than 99.99% salt rejection lasted over 30 hours of testing in a lab-scale DCMD system. In the second part of this work, we investigated the impact of various vapor deposited polymers on the wettability and eventual water flux of electrospun mat membranes. A thin layer of hydroxyethyl methacrylate (HEMA) and perfluoro decylacrylate (PFDA) were deposited on the membranes and resulted in ~ 80 ° decrease and ~ 20 ° increase in the water contact angle when compared to bare electrospun mat membranes, respectively. We found that the surface chemistry affects the wetting of the electrospun mat membranes and the water flux at low operating pressures.

Surface Modification for Reducing Ice Adhesion Using CVD Polymers

Author: Hossein Sojoudi
Co-authors: Gareth H. McKinley and Karen K. Gleason
Affiliation: Mechanical Engineering
Abstract:
Thin films of bilayer divinyl benzene (DVB)/poly(perfluorodecylacrylate) (p-PFDA) were synthesized via substrate-independent and all-dry-initiated chemical vapor deposition (iCVD) technique. Coated surfaces exhibited high advancing water contact angle (WCA) and low WCA hysteresis. Mechanical properties of the films were enhanced through proposed bilayer structure and the adhesions of the films to the substrates were improved via in-situ grafting mechanism. Strength of ice adhesion to the substrates was evaluated through a custom-built laboratory-scale adhesion apparatus. The strength of ice adhesion was reduced when the surfaces were coated with CVD polymers. These surfaces are very desirable for flow assurance strategies aimed at reducing the occurrence of blockages in oil and gas pipelines.

“Exploring city attractiveness

Author: Iva Bojic
Co-authors:
Affiliation:
Abstract:
Scientific studies of laws and regularities in human behavior nowadays increasingly rely on the wealth of widely spread digital information produced by various aspects of human social activity. Utilizing a multidisciplinary approach, a novel concept of combining three different datasets (i.e., credit card transactions and geotagged photographs and tweets) was introduced with the goal of explaining city attractiveness for cities around the globe. City attractiveness can be defined as the absolute number of photographs, tweets or transactions made in the city by either its residents or its tourists. The focus of this comparative study is on the ways how residents and tourists explore urban spaces – specifically how they are attracted to different cities across countries, as well as to different locations in the city. The study of geotagged photographs, which was conducted on global and local levels, compares the spatial behavior of residents and tourists in ten most photographed cities all around the world. On the global scale the ten most photographed cities were analyzed by measuring how attractive each city is for people visiting it from other cities within the same country or from abroad. For the purpose of the analysis a user mobility network was constructed as a measure of the strength of the links between each pair of cities as a level of attachment of people living in one city (i.e., origin) to the other city (i.e., destination). On the local level the spatial distribution of user activity was studied by identified the hotspots inside each city and by analyzing activity at the most photographed locations in the city. Finally, by developing a multiagent model, the results showing that city attractiveness superlinearly scales with its size were explained.

“The Perception of Reverberation is Constrained by Environmental Statistics

Author: James A. Traer
Co-authors: Josh H. McDermott
Affiliation: Department of Brain and Cognitive Sciences, MIT
Abstract:
Human sound recognition is remarkably robust to the distortion introduced by reverberation in everyday environments. We explored the hypothesis that this robustness is rooted in the ability to decompose the acoustic input into the contributions of the sound source and the reverberation, the latter of which can be described by a linear filter. As the separation of source and filter (given only their convolution) is inherently ill-posed, any such capacity should depend on prior assumptions about the nature of filter and/or source. We attempted to measure the distribution of environmental impulse responses (IRs) and to test whether it constrains perception.  Our results suggest that naturally occurring IRs have stereotyped properties that have been internalized by the auditory system over the course of development or evolution. Human listeners have some ability to separately estimate the source and filter in reverberant conditions, and are strongly constrained by whether the filter conforms to the naturally occurring distribution.

Alkbh7 promotes programmed cell death following alkylation damage

Author: Jennifer J. Jordan
Co-authors: Carrie M. Margulies, Roderick T. Bronson, Arne Klungland, and Leona D. Samson
Affiliation: Biological Engineering
Abstract:
Historically, necrosis has been believed to be a passive, default cell death pathway. However, recent evidence suggests that in addition to programmed apoptosis, cells can trigger a programmed, highly regulated necrotic pathway that leads to cell death in response to specific stimuli including inflammation and damage due to ischemia-reperfusion. The Samson lab recently showed that the human AlkB dioxygenase homolog, ALKBH7 plays an essential role in programmed necrosis in response to alkylating and oxidizing agent induced DNA damage. Although ALKBH7 does not possess the DNA demethylation repair activity characteristic of ALKBH2 and ALKBH3 proteins, loss of the mitochondrial targeted ALKBH7 protein renders cells unable to carry out necrosis induced by DNA damaging agents. Following exposure, ALKBH7 deficient cells acquire similar levels of DNA damage and undergo similar DNA damage response signaling, which includes activation of the ATM/ATR kinases, hyperactivation of poly-ADP-ribose polymerase (PARP), NAD+ depletion, and loss of ATP. However, unlike their wild type counterparts, ALKBH7 deficient cells recover cellular bioenergetic levels and survive albeit with an increased level of damage. While it has been shown that deletion of Alkbh7 in mice leads to obesity and metabolic disorders due to aberrant fatty acid metabolism, the role of Alkbh7 in response to alkylation-induced damage in vivo has not been investigated. Here, we are the first to show evidence that Alkbh7 contributes to alkylation-induced cellular death in vivo, in a tissue and sex specific manner. Alkbh7 deficient animals exhibit protection against alkylation-mediated tissue damage in the retinal photoreceptor cells and cerebellar granule neurons, two cell types that undergo cell death that is dependent on the hyperactivation of Parp1. Interestingly, the protection against the alkylation-induced cerebellar degeneration is only observed in male mice, where the female mice display enhanced alkylation sensitivity. Our results support the notion that the Alkbh7 protein plays a role mediating the cell death and survival in vivo as a result of alkylation exposure. Furthermore, the results suggest that Alkbh7 can be used as a tool to understand necrotic pathways such as within ischemia-reperfusion models and as a target in chemotherapeutic approaches where cells are resistant to apoptotic-induced death. Finally, the sexually dimorphic response to alkylation-induced damage suggests a potential for gender stratification in therapeutic approaches utilizing alkylating agents.

“Unified Capacity Limit of Non-Coherent Wideband Fading Channels

Author: Jinfeng Du
Co-authors:
Affiliation:
Abstract:
Peaky and non-peaky signaling schemes have long been considered species apart in non-coherent wideband fading channels, as the first approaches asymptotically the linear-in-power capacity of a wideband AWGN channel with the same SNR, whereas the second reaches a nearly power-limited peak rate at some finite \emph{critical bandwidth} and then falls to zero as bandwidth grows to infinity.  In this paper it is shown that this  distinction is in fact an artifact of the limited attention paid in the past  to the product between the bandwidth and the fraction of time it is in use. This fundamental quantity, that is termed  bandwidth occupancy, measures average bandwidth usage over time. As it turns out, a peaky signal that transmits in an infinite bandwidth but only for an infinitesimal fraction of the time may only have a small  bandwidth occupancy, and so does a non-peaky scheme that limits itself to the critical bandwidth even though more spectrum is available, so as to not degrade rate. The two types of signaling  in the literature are harmonized to show  that, for any type of signals,  there is a fundamental limit—a  critical bandwidth occupancy. All signaling schemes with the same bandwidth occupancy approach the linear-in-power capacity of wideband AWGN channels with the same asymptotic behavior as the bandwidth occupancy approaches its critical value. For a bandwidth occupancy above the critical value, rate decreases to zero as the occupancy goes to infinity. This unified analysis not only recovers previous results on capacity bounds for (non-)peaky signaling schemes, but also reveals the fundamental tradeoff between accuracy and convergence when characterizing the maximal achievable rate.

Oceanic influence on air-sea CO2 fluxes

Author: Jonathan Lauderdale
Co-authors: Stephanie Dutkiewicz, Jeffery Scott, Richard Williams and Michael Follows
Affiliation: Department of Earth, Atmospheric and Planetary Science
Abstract:
Oceanic and atmospheric carbon reservoirs are tightly linked by air-sea exchange of carbon dioxide. Regional and seasonal variations in the CO2 flux reflect the balance of drivers such as surface heat (solubility) forcing, dilution by freshwater fluxes, biological sources and sinks associated with photosynthesis and respiration, and upwelling of biologically regenerated dissolved inorganic carbon. Here, we present a comprehensive, consistent diagnostic framework that quantifies the relative contributions of these processes to the total air-sea CO2 flux. We demonstrate the value of the framework by diagnosing a physical circulation-biogeochemistry model (MITgcm) where the “true” CO2 fluxes are known allowing interpretation of the relative contributions of the physical and biological drivers in setting the regional patterns of air-sea fluxes.

Identifying the molecular determinants of N-linked glycosylation in Campylobacter jejuni

Author: Julie Silverman
Co-authors:
Affiliation:
Abstract:
Asparagine (N)-linked glycosylation is a posttranslational modification found in eukaryotes and prokaryotes. This protein modification is capable of altering protein function through changes in folding, antigenicity and cell signaling. In eukaryotes, N-linked glycosylation is a tightly regulated process that modifies a diverse, but specific, set of proteins that enter the endoplasmic reticulum (ER) lumen through the general secretory pathway (Sec) and that contain a glycosylation consensus sequence (N-X-S/T). In addition to the consensus sequence, a major determinant of substrate specificity is the folded state of the protein. Protein substrates are modified in an unfolded conformation either co-translationally, as they pass through the ER membrane, or posttranslationally, prior to folding. While the details of eukaryotic N-linked glycosylation are well described, less is known about the temporal and spatial aspects of this process in bacteria. Campylobacter jejuni, a Gram-negative foodborne pathogen, harbors an N-linked glycosylation system that has been implicated in its pathogenesis. Although activity assays with the oligosaccharyltransferase, PglB, have demonstrated a preference for substrates with consensus sequences in flexible loop regions, several glycoproteins are known to harbor consensus sequences within structured regions of the protein, suggesting that the folded state of these substrates may be important for efficient glycosylation in vivo. This work aims to determine the structural context in which proteins are modified in bacteria using the C. jejuni N-linked glycosylation pathway as a model system. These studies will broaden our understanding of the molecular mechanisms underlying N-linked glycosylation in bacteria.

Multivariate analysis of intestinal epithelial cell and immune cell crosstalk in normal and inflammatory conditions

Author: Kelly WL Chen
Co-authors: Jason Velazquez, Hikaru Miyasaki, Emily C. Suter, Linda G. Griffith, Rebecca L. Carrier, Douglas A. Lauffenburger
Affiliation: Biological Engineering
Abstract:
The human gut is the largest immune organ in the body. Intestinal homeostasis is tightly regulated by the coordinated actions of a multitude of cell types, including enterocytes, goblet cells and immune cells. However, a quantitative understanding of how these cellular constituents communicate and contribute to overall tissue function is lacking.

To this end, we developed an immune-competent human intestinal model, which incorporates representative cellular components of the mucosal environment (enterocytes, goblet cells and immune cells). To investigate the complex crosstalk in this multi-cellular intestinal model, the secreted signals (cytokines, chemokines, growth factors and matrix metalloproteases) were measured using multiplex assays under normal and perturbed conditions (e.g., LPS, drugs). Multivariate modeling techniques were used to quantitatively relate soluble signals to cell type-specific phenotypes and functions (e.g., barrier function, mucus production, enterocyte differentiation and cell death), thereby enabling the identification of key soluble mediators that contribute to divergent cell responses (normal versus diseased). The predictive models generated from this study can guide hypothesis generation regarding cytokine-mediated multicellular interactions and their implications for tissue-level phenotypes/functions.

Our experimental approach, which integrates physiological relevant in vitro culture platforms and computational strategies, has broad applicability in both fundamental understanding of mucosal immunology and drug development.

La0.8Sr0.2MnO3−δ Decorated with Ba0.5Sr0.5Co0.8Fe0.2O3−δ: A Bifunctional Surface for Oxygen Electrocatalysis with Enhanced Stability and Activity

Author: Marcel Risch
Co-authors: Kelsey A. Stoerzinger, Shingo Maruyama, Wesley T. Hong, Ichiro Takeuchi, and Yang Shao-Horn
Affiliation: RLE
Abstract:
Developing highly active and stable catalysts based on earth-abundant elements for oxygen electrocatalysis is critical to enable efficient energy storage and conversion. In this work, we took advantage of the high intrinsic oxygen reduction reaction (ORR) activity of La0.8Sr0.2MnO3−δ (LSMO) and the high intrinsic oxygen evolution reaction (OER) activity of Ba0.5Sr0.5Co0.8Fe0.2O3−δ (BSCF) to develop a novel bifunctional catalyst. We used pulsed laser deposition to fabricate well-defined surfaces composed of BSCF on thin-film LSMO grown on (001)-oriented Nb-doped SrTiO3. These surfaces exhibit bifunctionality for oxygen electrocatalysis with enhanced activities and stability for both the ORR and OER that rival the state-of-the-art single- and multicomponent catalysts in the literature.

Intracellular delivery by cell squeezing is affected by perturbation of actin cytoskeleton and lipid rafts

Author: Martin Stewart
Co-authors: Armon Sharei, Xiaoyun Ding, Robert Langer, Klavs Jensen
Affiliation: Koch
Abstract:
Cell squeezing is a new intracellular delivery modality based on rapid mechanical deformation of cells passaging through precisely fabricated constrictions in a microfluidic device. Delivery of molecules is achieved by diffusion through membrane disruptions, however, little is known about how the properties of the cell surface affect the membrane disruption and recovery behavior. Using specific inhibitors in conjunction with flow cytometry to assess delivery efficiency, we uncover roles for actin and lipid rafts in the cell response. While perturbation of rafts decreased cell robustness and recovery, inhibitors of actin dynamics exhibited variable effects, with some even improving membrane recovery. We anticipate continued studies on these underlying mechanisms should yield insight into the mechanical response to rapid cell deformations and lead to improved efficiency in delivery applications.

MAS NMR Assignments of Abeta1-42 Amyloid Fibrils

Author: Michael T. Colvin
Co-authors: Robert Silvers, Yongchao Su, Sara Linse, and Robert G. Griffin
Affiliation: Chemistry
Abstract:
The presence of amyloid plaques composed of amyloid beta (Aβ) fibrils is a hallmark of Alzheimer’s disease (AD). Aβ is typically found in two predominant alloforms, consisting of 40 and 42 amino acids, denoted Aß and Aß1-42, respectively. While there have been numerous reports on the structural characterization of fibrils of Aß, very little is known about the structure of Aß1-42 amyloid fibrils, which are considered the more toxic alloform involved in AD. We have prepared isotopically 13C/15N labeled M0Aß1-42 fibrils in vitro from recombinant protein, and examined their 13C-13C and 13C-15N magic angle spinning (MAS) NMR spectra. In contrast to several other studies of Aß we observe spectra with excellent resolution and a single set of chemical shifts, suggesting the presence of a single fibril morphology. We report the initial structural characterization of M0Aß1-42 fibrils utilizing 13C and 15N shift assignments of 38 of the 43 residues, including the backbone and sidechains, obtained through a series of cross polarization based 2D and 3D 13C-13C, 13C-15N MAS NMR experiments for rigid residues along with J-based 2D TOBSY experiments for dynamic residues. Calculation of φ and ψ dihedral angles from the chemical shift assignments indicate that 4 β-strands are present in the fibril’s secondary structure.

A Hyperstable Minimalist Protein for Molecular Recognition

Author: Michael W. Traxlmayr
Co-authors: Jonathan D. Kiefer, Raja R. Srinivas, Elisabeth Lobner, Naveen Mehta, Bruce Tidor, K. Dane Wittrup
Affiliation: Department of Chemical Engineering, Department of Biological Engineering
Abstract:
Antibodies are the most rapidly growing class of therapeutic proteins. Their most important properties are their high affinity and specificity for a given target molecule. In recent years there has been increasing interest in alternative binder scaffolds, which combine high affinity and specificity with other desired properties, such as high stability and solubility, as well as low propensity for aggregation and small size. One promising candidate is the DNA-binding protein Sso7d from the hyperthermophilic archaeon Sulfolobus solfataricus. This protein is highly stable (Tm value of 98°C), small (7 kDa) and it does not contain any cysteines. In recent studies the potential of Sso7d for the construction of binders against various target molecules has been demonstrated. However, since Sso7d is a DNA-binding protein, it contains a high number of positive charges, with 22% of all amino acids being lysines. Here, we show that the positively charged residues cause unspecific binding to mammalian cells. Importantly, we also demonstrate that this stickiness can be completely eliminated by charge-neutralization of the protein. In fact, a direct correlation between the net formal charge of various Sso7d-mutants and unspecific binding to mammalian cells was observed. Based on the reduced-charge mutant of Sso7d we constructed libraries and selected for binding to human epidermal growth factor receptor (EGFR) and mouse serum albumin (MSA). Binders from the naïve libraries without any affinity maturation showed affinities up to 20 nM for EGFR and 225 nM for MSA. Affinity maturation further improved affinities to the single digit nanomolar range. Furthermore, competition experiments on EGFR-positive human cells demonstrated that the selected EGFR-binders target multiple different EGFR-epitopes. Finally, analysis of EGFR-binders by size exclusion chromatography showed that the majority of the EGFR binders are monomeric and do not show any aggregation. Thus, in this study we optimized the scaffold Sso7d by reducing the net formal charge, resulting in a highly stable, but non-sticky protein that can be engineered for high affinity and specificity.

Identification of genes that affect the replication stress response in Bacillus subtilis

Author: Milena Lazova
Co-authors: Chris Johnson, Alan Grossman
Affiliation: MIT Department of Biology
Abstract:
Major task of all organisms is to maintain their genomic content and ensure faithful replication and segregation of the their genomes. Thus cells have evolved mechanisms to monitor and respond to defects in DNA replication process or to perturbations of the genomic integrity. We use a high-throughput screen: transposon mutagenesis followed by massive parallel sequencing (Tn-seq) to determine the genes involved in response to defects in DNA replication or DNA damage in the bacterium Bacillus subtilis. Genes in which the transposon insertions frequency increases upon replication stress have a function in survival mechanisms, whereas genes in which the transposon insertion frequency decreases upon replication stress increase the sensitivity of the bacteria to DNA or replication damaging agents.

“Emergence of Intestinal Organoids from Human Pluripotent Stem Cells

Author: Natasha Arora
Co-authors: Natasha Arora1, Jasmin Alsous2, James Wells3, Stas Shvartsman2, Linda Griffith1, Roger Kamm1
Affiliation: 1 Massachusetts Institute of Technology, 2 Princeton University, 3Cincinnati Children’s Hospital Medical Center
Abstract:
Organoids are cell aggregates that arise in vitro with three-dimensional structure, which more closely mimics the in vivo tissue than two-dimensional models.  Given the proper environment and growth factors, pluripotent stem cells (PSCs) will differentiate into organoids of many tissues including pituitary, retina, brain, and intestine. When a monolayer of PSCs is directly differentiated towards a hindgut fate, cell aggregates or spheroids reminiscent of the intestine bud off of the monolayer.  Spheroids receiving the proper external stimuli mature into intestinal organoids.  We are studying the emergence of spheroids and how external stimuli affect maturation into intestinal organoids.  The spheroids are heterogeneous in many parameters including cell number and diameter of the lumen.  We are analyzing the types of cells present in the spheroids and how the cells form into spheroids from the monolayer of hindgut.  This analysis will provide insights into the formation of intestinal organoids, which have the potential to be used for disease models and to replace the two-dimensional models that are currently used in drug discovery and development.

Bubble dynamics and the boiling crisis on textured surfaces

Author: Navdeep Singh Dhillon
Co-authors: Jacopo Buongiorno, Kripa K. Varanasi
Affiliation: Mechanical Engineering
Abstract:
We present experimental results and a physical model to demonstrate the effect of surface texture on bubble dynamics and the phenomenon of boiling crisis. Boiling is a phenomenon of fundamental importance in many scientific and engineering applications and the most widely used high-performance heat transfer process. However, boiling crisis limits the maximum amount of heat flux that can be dissipated from the boiling surface. Although it is well known that surface roughness or micro-texture can increase this critical heat flux (CHF), the physics underlying this process is not well understood. In this study, we use high speed optical and infrared (IR) imaging to explore the mechanism of single bubble growth and departure on textured surfaces fabricated using photolithography techniques. Interestingly, we observe a clear correlation between the salient micro-texture parameters and bubble properties such as the departure diameter and frequency. Based on important experimental insights about the thermal and hydrodynamic aspects of the problem, we develop a mechanistic model for the boiling crisis that accurately captures the effect of surface texture on CHF enhancement.

Spatially-resolved live-cell proteomic map of human heterochromatin

Author: Ozan Aygun
Co-authors: Catherine Amaya, Namrata Udeshi, Steve Carr, Alice Y. Ting
Affiliation: Chemistry
Abstract:
Eukaryotic chromosomes are organized into distinct subdomains that are critical for genome function. Heterochromatin is a substantial nuclear structure, which constitutes highly compacted DNA predominantly from centromeres and perinuclear domains. Constitutive heterochromatin is essential for the three-dimensional organization and integrity of the genome, as well as epigenetic silencing of large chromosomal domains containing repetitive DNA sequences. Despite the spatially distinct organization of heterochromatin in the nucleus, its exact protein composition remains as a fundamental unresolved research problem. Here we demonstrate the application of a novel proteomic technology, which combines concepts in chemical biology, microscopy, mass-spectrometry (MS), and enzyme engineering to provide spatially-resolved, unbiased proteomic map of heterochromatin domains in living human cells. By using this unique interdisciplinary approach, we discovered several novel bona fide heterochromatin proteins in human cells. We will present the mechanistic characterization of one of these novel proteins in the context of human heterochromatin assembly. Our observations paved the way for developing a generic technology to characterize the proteomic composition of every single genomic locus in human cells at nanometer scale resolution. To this end, our approach will introduce technological innovations that will benefit the entire chromatin research field, and help us to tackle complex biological questions pertaining chromosome biology, which have been impossible to address by traditional approaches.

A Rapid Microfluidic Assay for Genetic Engineering

Author: Paulo A. Garcia
Co-authors: Zhifei Ge, Jeffrey L. Moran, Cullen R. Buie
Affiliation: Mechanical Engineering
Abstract:
Synthetic biology and genetic engineering hold the potential to solve many of mankind’s most pressing challenges including the needs for alternative fuels, enhancing oil recovery, and even cancer treatment. However, a major limitation of synthetic biology is the inability to incorporate genetic material into many bacteria due to the challenge of permeating the cell envelope while maintaining high cell viability. Electroporation results from exposure of cells to pulsed electric fields of sufficient strength to disrupt the plasma membrane. The local trans-membrane voltage (TMV) significantly increases during exposure of cells to external electric fields. When the local TMV exceeds a critical threshold, pores are created on the cell membrane, allowing transport of ions and macromolecules (e.g. DNA/RNA) across the membrane. There is vast empirical literature establishing protocols to increase the electrocompetency (capacity for DNA uptake by electroporation) of cells, a process that is currently time consuming and lacks real-time feedback. Despite the tremendous need, there are currently no protocols for improving bacterial electrocompetency without relying upon time-consuming empirical experimental processes. We developed a rapid microfluidic platform capable of determining electric field thresholds for bacterial electroporation. In our microfluidic platform, a converging microchannel generates a linear gradient of electric field. Fluorescence-encoded DNA plasmids or nucleic acid stains permeate cell membranes in regions where the electric field is sufficiently high. We correlate the fluorescent region of bacteria with the range of electric fields that results in electroporation. We envision this rapid microfluidic platform as a tool to enable and optimize genetic transformation of intractable or previously challenging microbial chassis. Results of this study will broaden the scope of bacteria available for applications in synthetic biology and genetic engineering.

Scale-up of oCVD: Large-area conductive polymer thin films for next-generation electronics

Author: Peter Kovacik
Co-authors: Karen Gleason
Affiliation: Chemical Engineering
Abstract:
This work demonstrates scalability of oxidative chemical vapor deposition (oCVD) as a method for fabrication of conductive and semiconductive polymer thin films. oCVD is a solvent-free method which yields high-quality conformal films applicable to any substrate. Excellent functionality of the films combined with the low deposition temperature (<200 °C) and mild vacuum requirements (>10 Pa) make this technique economically feasible and suitable for various applications, extending its versatility beyond standard vapor- and solution-based deposition techniques. For example, film conformality allows deposition on rough and fibrous materials such as paper, textiles, or wood. Transfer of functional nanoscale coatings to ‘scientifically’ unconventional materials and objects, as demonstrated in this work, is an important step towards integration of organic electronics into everyday life.

A case for leveraging 802.11p for direct phone-to-phone communication

Author: Pilsoon Choi
Co-authors: Jason Gao
Affiliation: CSAIL
Abstract:
Video/file sharing between smartphones, as well as multiplayer games have started to leverage device-to-device (D2D) communication, and there are peer-to-peer applications that benefit from the faster response times of D2D communications. However, existing D2D communication (e.g. WiFi Direct or LTE Direct) cannot support highly mobile networks with rapidly changing topologies due to insufficient range and poor reliability. We make the case for using IEEE 802.11p DSRC instead, which has been adopted for vehicle-to-vehicle (V2V) communications, providing lower latency and longer range. We have developed a 802.11p radio prototype system targeted for D2D, in which the designed CMOS+GaN RF circuit is interfaced with a baseband processor on an FPGA, connected to Android phones. We demonstrated significant potential power savings on traces of novel Intelligent Transportation Systems (ITS) and D2D applications such as RoadRunner, SingalGuru, and DIPLOMA. Application-level power control dramatically reduces power consumption by 47-56%. We see this development opening up D2D communications to a much larger class of applications, with mobile devices on pedestrians, passengers, and drivers now interconnected at low latency and high bandwidth, enabling highly interactive mobile applications.

Tunable molecular transport through atomically thin graphene membranes

Author: Piran R. Kidambi
Co-authors: Piran R. Kidambi, Doojoon Jang, Luda Wang, Michael Boutilier, Sean O’Hern and Rohit Karnik
Affiliation: Mechanical Engineering
Abstract:
Atomically thin graphene membranes have generated a lot of interest in filtration and gas separation applications. Graphene offers the minimum theoretical membrane resistance along with the opportunity to tune pore sizes at the nanometer scale in contrast to solution-diffusion of molecules through the membrane material for all other membranes.
We demonstrate selective molecular transport by precisely engineering controlled, high-density, sub nanometer diameter pores in graphene membranes grown via scalable chemical vapor deposition processes. The density of such defects can be tuned to be >1012 cm-2. A combination of pressure driven and diffusive transport measurements across these membrane reproducibly shows clear evidence for size selective transport behavior.
This ability to tune the selectivity of graphene through controlled generation of sub nanometer pores addresses a significant challenge in the development of advanced nano-porous graphene membranes for nanofiltration, desalination, gas separation and several biological applications. Finally, these membranes offer opportunities to study the complex dynamics and transport phenomena at these length scales.

1. Kidambi et al. Chemistry of Materials (2014).

2. Boutilier et al. ACS Nano (2014).

3. Kidambi et al. Nano Letters (2013).

4. O’Hern et al. Nano Letters (2013).

5. O’Hern et al. ACS Nano (2012).

Assessment of energy saving potential in residential buildings: a system dynamic approach

Author: Reza Fazeli
Co-authors:
Affiliation: Sloan School of Management
Abstract:
Growing incomes, rising populations, and decreasing prices of energy consuming durable goods resulted in increases in the residential energy consumption over the past few decades globally. In addition, climate change is expected to accelerate this growth in the absence of significant adaptation actions. The overall effect on residential energy consumption depends on the region, as milder winters are projected to decrease the demand for heating fuel (e.g. natural gas, fuel oil), one assumes that warmer summers will lead to higher demand for cooling.
To investigate the dynamics of the dwelling stock we have used a system dynamics (SD) approach. SD is extensively applied in the study of dynamic systems by representing them as a set of connected stocks, flows and feedback mechanisms and simulating their temporal development. In this study, the system scope is set to the Danish residential built stock and its energy-related renovation, i.e. refurbishment that improves building energy performance. In this study, three balancing loops were identified to significantly affect the energy performance of dwellings as well as the benefit from implementing the retrofitting measures: 1- Energy Conservation: Regardless of any renovation efforts, with the increase in energy expenses, the ratio of expenses to income for households rises. As a result households tend to reduce their energy consumption and their energy expenses. 2- Efficiency gain: To cope with the increase in the energy consumption, households may change the thermostat set point to a higher (or a lower) degree. After implementing retrofitting measures, the energy consumption is expected to decrease, as well as the ratio of expenses to income per household. As a result, households could increase the intensity of energy consuming activities as a result of increasing income which directly corresponds to the rebound effect broadly discussed in the energy consumption literature. 3- Saturation: Households can also change the energy efficiency of the dwelling through retrofitting, which is considered as a longer-term response in our model. By improving the efficiency of dwelling through retrofitting, the potential for efficiency improvement slowly saturates and the tendency/ability of households for renovation incrementally declines.
Using the developed system dynamics model, we explored the effectiveness of certain policy options that can reduce the inertia of existing dwelling stock and improve the energy efficiency of the whole stock.

Low-pressure and Low-cost Drip Irrigation Systems

Author: Ruo-Qian Wang
Co-authors: Amos G Winter V
Affiliation: Mechanical Engineering
Abstract:
One of the major issues that prevent a large-scale dissemination of drip irrigation system is the requirement of high pumping pressure, which incurs a high cost of pumping and power systems. The high pressure is used to maintain the working condition of pressure-compensate emitters, which are installed at the outlets of drip irrigation system to compensate pressure loss and evenly distribute flows for each crop. A new architecture of the pressure-compensate emitter is proposed using a flexible tube enclosed in a pressurized chamber similar to the design of a medical instrument called “Starling resistor”. This design enables the external pressure of the tube to correlate with the driving pressure, such that a higher driving pressure leads to a higher external pressure and consequently collapses the tube. The desirable feature that the flow rate is independent of the upstream pressure variation (also called “flow limitation”) can be achieved with this new design at a lower driving pressure. This paper is aimed to find the optimal combination of the design parameters that govern the physics behind the collapsible tube. A laboratory experiment has been conducted using rubber tubes with a variety of lengths, wall thicknesses and inner diameters. Then, an attempt to collapse the experimental results are made and empirical formula of activation pressure and regulated flow rate are given.

Recombination Kinetics and Slow Transient Behaviour in Organic-Inorganic Perovskites

Author: Samuel D. Stranks
Co-authors: Samuel D. Stranks, Dane deQuilettes, Wei Zhang, Tomas Leijtens, Victor M. Burlakov, Anna Osherov, Matthew T. Klug, Angela M. Belcher, Alain Goriely, David S. Ginger, Vladimir Bulovic, Henry J. Snaith
Affiliation: Research Laboratory of Electronics
Abstract:
Organic-inorganic perovskites have attracted an enormous amount of recent attention and have the potential to be a “disruptive” photovoltaic technology, with certified power conversion efficiencies already exceeding 20%. Nevertheless, a detailed understanding of recombination pathways and an explanation for the observed slow transient behaviour, crucial for further device improvement, are still required.

We have recently developed a very generic yet analytically solvable model describing the recombination kinetics of photo-excited carriers in the presence of electronic sub-gap trap states in solution-processed CH3NH3PbI3 perovskite films. We can use this model to estimate the sub-gap trap density, and we show that it can be more generally applied to compare the trap densities in perovskites fabricated using a variety of methods.

We then speculate that the traps result from halide vacancies, and extend the model to include an interplay between the vacancies and halides in the interstitial sites. The numerical solutions are able to reproduce a wide range of experimental data, in particular providing an explanation for the very slow rise times (seconds to minutes) observed from photoluminescence and open-circuit voltage measurements following illumination. We show how the work relates to the effects reported in recent passivation and hysteresis studies.
Our work provides an understanding of how to further enhance the material performance for high-efficiency perovskite solar cells and light-emitting devices.

Climbing Large Area Fluid Sheet against Gravity: A Simple and Robust Technique for Sub-10 nm Single Particle Positioning Using Directed Self-Assembly

Author: Shafigh Mehraeen
Co-authors: Mohamed Asbahi, Joel K. W. Yang, Jianshu Cao, and Mei Chee Tan
Affiliation: MIT, Department of Chemistry
Abstract:
Direct positioning of nanoparticles, particularly in a large area with minimal defects, has great potential in nanostructure fabrication and device miniaturization. Despite this potential, controlling direct single particle positioning is very difficult as soon as the diameter of particles goes below 10 nm. This size limitation has challenged application of many techniques in single particle positioning, including existing lithographic capabilities and directed self-assembly technologies, to achieve miniaturization and high throughput fabrication. Even directed self-assembly of nanoparticles confronts with a fundamental challenge for large area particle positioning with minimal defects of particles below 50 nm in diameter.

Guided by systematic experimentations, and numerical simulations, we have recently developed a robust experimental technique to overcome above mentioned challenging size limitation. This technique involves creation of very thin large area fluid sheet containing sub-10 nm particles, ascending against gravity to coat a pre-patterned template. Particles are then inserted into nano-cavities by a nano-meniscus during fluid sheet descending. Enabling single particle positioning to access sub-10 nm dimension, this technique lends a lot of opportunities to enhance device fabrication in biosensing, photonics, plasmonics, coating, and printing.

“Self-Assembly, Complex Fluids, and Molecular Charge Transport in Nanoscience

Author: Shafigh Mehraeen
Co-authors:
Affiliation:
Abstract:
Being convenient and cost-effective approach for achieving nanostructures, and enabling scalability with minimal material wastage, directed self-assembly (DSA) on flat or patterned substrates has recently gained a great deal of attention in biotechnology, photonics, plasmonics, shape selection, printing, and coating. Despite its advantages, DSA is still very complex because the interplay of several driving forces dictates the assembly and ordering of its constituents. Unraveling this interplay of driving forces, through experimentation and computational modeling, we have recently developed a novel approach to directly self-assembly sub-10 nm particles on arbitrarily patterned substrates with very high yield. Our approach is quire general, and can be applied to any nanoparticle suspension. Using experimental observations and computational modeling we have also (1) unraveled the impact of doping on charge transport properties of organic semiconductors, (2) investigated the effect of morphology on charge carrier recombination loss mechanisms in organic photovoltaics, and (3) explored the influence of energetic disorder and crystalline domain size on charge transport properties of organic photovoltaic cells.

Characterization and Quantification of DNA Phosphorothioate Modifications in the Mouse Gut Microbiome

Author: Stefanie Kellner
Co-authors: Alex Sheh , Michael S Demott, James Fox and Peter Dedon
Affiliation: Department of Biological Engineering
Abstract:
Modifications of nucleobases in RNA and DNA have been identified in all trees of life, with well recognized functions in restriction-modification and control of gene expression. Only recently, however, was phosphorothioation (PT) discovered as the first naturally-occurring backbone modification of DNA. PT was originally developed as a synthetic modification that protects DNA and RNA against nuclease degradation for the development of nucleic acid-based therapeutics. Only a few years ago – in 2007 – this modification was found to occur naturally in bacterial DNA, with insertion by horizontally-transferred, five-gene dnd cluster (dndA-E) [1]. PT modifications appear to function in both restriction-modification, coupled with dndF-H restriction genes, as well as non-RM functions in bacteria lacking dndF-H [2,3]. However, little is known about how PT-containing bacteria are involved in human health and disease. Here we assessed the presence of PT-containing bacteria in the gut microbiome.To this end, we analyzed DNA extracted from stool samples from healthy mice for the presence of PT modifications. This analysis is based on a sensitive LC-MS/MS method for the identification of all 16 possible PT-bridged dinucleotides remaining from a limit digestion with nuclease P1. The dinucleotides are resolved by reversed-phase HPLC and then identified and quantified by quadrupole time-of-flight and tandem quandrupole mass spectrometry. This LC-MS/MS method permits simultaneous identification and quantification of all 16 PT dinucleotide permutations in a single 18-minute run, with limits of detection for PT-containing dinucleotides in the single-digit fmol range. Accurate quantification is achieved by addition of isotope-labeled PT-modified dinucleotides, GpsA and GpsT, isolated from E.coli B7A cultured with 13C- glucose (SIL-IS). Using this technique we found several different PTs in the microbiome of healthy mice, including CpsC, GpsA, TpsC at 75, 39 and 3 PT per 106 nt. These levels suggest that PT-containing bacterial DNA represents about 1% of fecal DNA given the presence of PT in bacterial DNA ranging from 1 PT per 103 to 104 nt. Further studies will identify PT-containing bacteria in the gut and possible shifts in bacterial populations during pathological conditions such as inflammatory bowel disease.

A versatile inducible gene regulation system for functional genetics in malaria parasites

Author: Suresh Maddur Ganesan
Co-authors: Alejandra Fala, Stephen J. Goldfless, A. Sebastian Nasamu and Jacquin C. Niles
Affiliation: BE
Abstract:
Malaria is a parasitic disease that is widespread in tropical and subtropical regions, and a major cause of human morbidity and mortality. The most severe form of malaria is caused by the parasite, Plasmodium falciparum. Only limited antimalarial drugs are available to treat the disease, but the drug resistance is rampant. Hence, identification of new antimalarial drugs is high priority. However, the functional genomics of malaria parasites poses a greater challenge due to lack of reliable gene regulatory tool to explore the biology of this parasite. To address this need, our laboratory has previously developed a novel small molecule-regulated protein-RNA interaction (TetR-aptamer system) that facilitates robust and inducible regulation of target gene translation in eukaryotic organisms including Plasmodium. Here, we present the application of protein engineering approaches to integrate our synthetic control system with native Plasmodium translational regulatory mechanisms. Results from our study showed substantial increase in regulatory dynamic ranges (up to 200-fold) compared to a 5-10 fold range of the original system. Further, this engineered system has expanded the means by which we can manipulate Plasmodium genes. As a proof-of-concept, we have generated P. falciparum strain that conditionally knocks down P-type cation-ATPase (PfATP4). PfATP4 is considered to be an important antimalarial drug target in the field. However, the importance of this protein has not been genetically validated so far. This study provides first, direct evidence for the essentiality of this gene in asexual stages of the parasite. With a view to identifying new drug targets, we are currently using our gene regulatory system to study multiple Plasmodium genes.

Lyapunov Functions Family Approach for Transient Stability Assessment of Power Grids

Author: Thanh Long Vu
Co-authors: Konstantin Turitsyn
Affiliation: ME
Abstract:
The electrical power grid is currently undergoing an architectural
revolution with the increasing penetration of renewable and
distributed energy sources and the presence of millions of active
endpoints. As a sequence, the existing planning and operation
computational techniques largely developed several decades ago
will have to be reassessed and adopted to the new physical models
in order to ensure secure and stable operation of the modern power
grids. This research proposes a novel approach, namely Lyapunov
Function Family approach, for assessment of transient stability of
large-scale power grids. This approach outperforms the existing
methods in screening more contingency scenarios in the real time
and totally avoids time-domain simulations currently widely
utilized in practice. In addition, this approach is applicable to
solve the longstanding problem of stability certification for
power networks with losses.

Development of an ex vivo culture system for intestinal organoids using peptide-functionalized PEG-based hydrogels

Author: Victor Hernandez-Gordillo
Co-authors: GiHun Choi, Rebecca Carrier, Linda Griffith
Affiliation: Biological Engineering
Abstract:
Intestinal organoids or “mini guts’ are three-dimensional (3D) multilobulated structures composed of budding crypts, epithelial cells and well-defined lumens. Organoids have gained interest as a tool to study intestinal biology and as a platform for drug screening because they resemble aspects of the intestinal complexity found in vivo (1). Organoids are commonly cultured in ill-defined Matrigel-based hydrogels; thus, special care should be taken to eliminate any possible bias due to Matrigel’s lot-to-lot variability or the presence of residual growth factors that can affect the biological outcome. Therefore, the development of a well-defined matrix that can support the culture of organoids is of vital importance. PEG-based hydrogels are good candidates as synthetic matrices because they can be tailored to different applications by varying the stiffness, degradability and cell adhesion properties. Here we report our efforts to develop PEG-based hydrogels functionalized with a fibronectin-derived peptide (Synk-RGDS) or a collagen-derived peptide (GFOGER) for intestinal organoid culture. Preliminary results suggest that direct encapsulation of single cells obtained from mouse organoids in these PEG-based hydrogels results in formation of organoids similar to those that form in Matrigel. The PEG-GFOGER hydrogel showed higher number of organoids when compared to PEG-SYNK-RGDS hydrogel. A two steps encapsulation procedure with varying stiffness and cell adhesion properties in a gradient hydrogel resulted in a completely different morphology. Mouse cells developed multicellular growth structures that resemble the villi of the intestine. Further analysis will be needed to confirm the identity of these structures. In summary, we were able to identify defined, synthetic PEG-hydrogel culture conditions that allow single mouse cells to develop into three-dimensional structures that resemble mouse organoids.

1.- Sato T, Vries RG, Snippert HJ, van de Wetering M, Barker N, Stange DE, et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature. 2009;459:262-5.

Author: Vincent Chan
Co-authors: Devin Neal, Sebastien Uzel, Hyeonyu Kim, Rashid Bashir, and H. Harry Asada
Affiliation: Mechanical Engineering
Abstract:
Cardiac tissue engineering aims to recreate functional tissue constructs similar to the structure and function of the native myocardium. To date, in vitro tissue constructs lack the architectural complexity of a vascular network and the precise motor unit control of muscle fibers. Here, we present a method to construct engineered multi-strip cardiac muscle that simulates the bundle-like architecture of the native myocardium. Densely packed primary myocytes and cardiac fibroblasts were co-cultured with optogenetic, non-excitable cells. The resulting 3D syncytium triggered contraction upon localized blue light illumination to selectively activate and pace the multi-strip cardiac muscles, similar to the activity of pacemaker cells. Acting on a single load, we demonstrated graded force production through light-modulated multi-strip recruitment. These results demonstrate an in vitro platform of optogenetic, multi-strip cardiac muscles that can be used in a wide variety of applications, such as drug discovery, tissue engineering, and bio-hybrid robotic systems.

“De novo Approaches for High Field Dynamic Nuclear Polarization from Small Molecules to Complex Biological Solids

Author: Vladimir K. Michaelis
Co-authors: Vladimir K. Michaelis and Robert G. Griffin
Affiliation: Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
Abstract:
Hyperpolarization has become a valuable approach for studying challenging chemical structures using magnetic resonance in various areas including biological, materials, and medical fields. Dynamic nuclear polarization (DNP) is one such approach, offering significant reduction in acquisition time; offering an ability to study previously hindered structural problems. The gain in sensitivity is offered by the large thermal electron spin polarization of a paramagnetic compound such as a radical. This electron polarization is transferred to nearby nuclei, most often 1 H’s, when irradiating the sample with microwave. Nitroxide based radicals are widely used and provide efficient polarization transfer to high-gamma nuclei via the cross effect DNP mechanism. This method is attractive for studying various chemical systems with abundant 1 H’s, allowing for efficient 1 H-DNP followed by X{ 1 H} cross polarization. Many chemical systems however may not fall into this category, or cannot be modified by an external solvent often used to introduce the radical. In particular, inert inorganic species such as coordination polymers, crystalline solids, and geological samples cannot easily be “wetted” and therefore current DNP approaches may be limited. We have been developing various approaches to offer an ability to induce hyperpolarization in an assortment of chemical systems ranging from inorganic coordination complexes and materials to drug molecules and complex amyloid proteins responsible for many diseases. A discussion of these approaches at magnetic fields from 5 to 16.4 T will be illustrated, including the basis of how one can obtain DNP on an assortment of structural problems.

Prediction of Rogue Ocean Waves

Author: William Cousins
Co-authors: Themistoklis P. Sapsis
Affiliation: Mechanical Engineering
Abstract:
Huge, unexpected “rogue” ocean waves have caused considerable damage to ships and coastal structures. We develop a new tool for predicting these rogue waves a couple minutes before they occur. This scheme could allow those in the path of an upcoming rogue wave to take action to mitigate the wave’s damaging effects.

Sun and smog: the meteorological drivers of air quality extremes

Author: William Porter
Co-authors: Colette Heald
Affiliation: Civil and Environmental Engineering
Abstract:
High levels of ozone (O3) and fine particulate matter (PM2.5) have well-documented negative impacts on human health and society, making them two of the most commonly regulated pollutants worldwide. Mean levels of these pollutants are primarily determined by both local climatology and emission rates, but day-to-day pollutant variability is driven mostly by meteorological fluctuations rather than variability in the emissions themselves. Changes in local climatology, therefore, are likely driving changes in local air quality, both in terms of mean pollutant levels as well as the frequencies and magnitudes of extreme events. While the impact of changing meteorology on O3 and PM2.5 has been explored previously, much of the existing literature has focused on averages and linear regressions, statistical techniques that largely ignore extreme behavior and tail dependence. Since current air-quality standards often include limits on high quantiles of pollutant level observations (e.g. annual 4th highest daily maximum 8-hour concentration of O3 and 98th percentile of PM2.5 in the United States), statistical analyses that do not focus on tail dependence will be unable to fully evaluate impacts on exceedance frequencies. Using methodologies based on quantile regression (QR), we analyze relationships between meteorology and extreme pollution episodes in the United States, both in the observed data record and in modeled output generated by the Community Earth System Model (CESM). Through this analysis, we propose a statistical framework for the identification of the meteorological drivers of these air-quality extremes, the evaluation of modeled extremes, and the improvement of future extreme projections based on observed sensitivities and assumed climatological changes.

Highly Aligned Polymer Composite for Thermal Management Application

Author: Yanfei Xu
Co-authors: Jianjian Wang, James Loomis, Hadi Ghasemi, Xiaopeng Huang, Xiaobo Li, Cheng-Te Lin, and Gang Chen
Affiliation: Department of Mechanical Engineering
Abstract:
While polymers has had a remarkable impact on modern life, low thermal conductivity values associated with bulk polymers (typically 0.1 – 0.4 W m–1K–1) have hindered widespread development of these materials in heat transfer applications. One such solution, molecular chain alignment by mechanical drawing, has been demonstrated to greatly improve thermal properties. Another direction commonly used to improve thermal conductivity in polymers is through the addition of filler materials – such as metals and ceramics, to create polymer-based composites.

Here, we present a ultra high molecular weight polyethylene (UHMWPE)/graphite film with low filler loadings (<15 wt% graphite) that is achieved via mechanical drawing-induced molecular chain alignment and filler orientation. Using a combination of UHMWPE and highly thermally conductive 2D carbon fillers, our fabrication method consists of custom extrusion, drying, and drawing platforms. This stretching results in macroscopic UHMWPE deformation and orientation of 2D filler network along the film in-plane direction to achieve higher alignment structure. The high-aspect-ratio structure of the filler material combined with draw-induced orientation of the polymer chain matrix makes for an ideal composite structure, as continuous percolation network and aligned filler particulate interfaces reduces phonon scattering sites. Structural characterization (XRD, SEM, and AFM) of these films suggests highly aligned polymer chains and crystallinity. We believe that further development of 2D graphite-based polymer composites will extend the promising potential of these versatile materials in a range of heat transfer applications.

This work was supported by the U.S. Department of Energy/Office of Energy Efficiency and Renewable Energy/Office of Advanced Manufacturing Program (DOE/EERE/AMO) under award number DE-EE0005756.

Systemic delivery of Liposome-anchored anti-CD137 and IL2-Fc prevents lethal toxicity and elicits potent antitumor immunity

Author: Yuan Zhang
Co-authors: Darrell Irvine
Affiliation: Koch Institute
Abstract:
Many immunostimulatory cytokines, such as anti CD-137 and interleukin (IL)-2, generate effective antitumor immune responses in preclinical studies, but demonstrate serious toxicity profiles after in vivo administration, which hampers their clinical application. We synthesized cytokines anchored liposomes which served as a scaffold to deliver sufficient quantities of immunostimulatory cytokines to primary and metastatic tumors following systemic administration with minimal systemic inflammatory toxicity. Anti CD-137 and an engineered IL2-Fc fusion protein were anchored to the surface of PEGylated liposomes (Lipo-CD137/IL2-Fc). Lipo-CD137/IL2-Fc was intravenously (IV) injected to subcutaneous B16F10 melanoma tumor-bearing mice. PEGylated liposomes conjugated with isotype IgG antibody were used as control liposomes. The soluble mixture of anti CD-137 and IL2-Fc (soluble CD137/IL2-Fc) was also administered as a comparison to Lipo-CD137/IL2-Fc in terms of antitumor response and in vivo toxicity. The particle sizes of cytokine anchored liposomes were ~ 80 nm, with surface zeta potentials of ~ -35 mV. In the aggressive, poorly immunogenic B16F10 melanoma model, though soluble CD137/IL2-Fc dramatically retarded tumor growth, it also elicited severe toxicity (body weight loss and cytokine storm), which was 100% lethal in the soluble CD137/IL2-Fc group by day 5 post injection. In striking contrast, lipo-CD137/IL2-Fc treatment showed significant tumor growth inhibition with little in vivo toxicity. Lipo-CD137/IL2-Fc induced increased CTL infiltration in tumors and triggered higher level of IFN-γ secretion in tumor, peripheral blood and lymphoid organs. CD137/IL2-Fc anchored liposomes quickly cleared out of body after bolus IV administration. Soluble CD137/IL2-Fc showed prolonged blood circulation profile, which persistently activate the circulating T lymphocytes, leading to severe in vivo toxicity and decreased survival. This is also evidenced by the fact that soluble IL2-Fc displayed much higher uptake in T lymphocytes comparing to liposomal IL2-Fc in peripheral blood and lymphoid organs. Inflammatory cytokine results also indicated that the toxicity induced by soluble CD137/IL2-Fc treatment is mainly from IL2-Fc. Lipo-CD137/IL2-Fc showed significant tumor accumulation due to enhanced permeability and retention (EPR) effect in tumor microenvironment. This study demonstrated cytokine-anchored liposomes significantly reduced in vivo toxicity while remaining antitumor efficacy compared to their soluble form at equivalent cytokine doses after systemic administration. Reduced in vivo toxicity was due to the biodistribution and pharmacokinetic profiles offered by the liposome scaffold.

Low-pressure and Low-cost Drip Irrigation Systems

Author: Ruo-Qian Wang
Co-authors: Amos G Winter V
Affiliation: Mechanical Engineering
Abstract:
One of the major issues that prevent a large-scale dissemination of drip irrigation system is the requirement of high pumping pressure, which incurs a high cost of pumping and power systems. The high pressure is used to maintain the working condition of pressure-compensate emitters, which are installed at the outlets of drip irrigation system to compensate pressure loss and evenly distribute flows for each crop. A new architecture of the pressure-compensate emitter is proposed using a flexible tube enclosed in a pressurized chamber similar to the design of a medical instrument called “Starling resistor”. This design enables the external pressure of the tube to correlate with the driving pressure, such that a higher driving pressure leads to a higher external pressure and consequently collapses the tube. The desirable feature that the flow rate is independent of the upstream pressure variation (also called “flow limitation”) can be achieved with this new design at a lower driving pressure. This paper is aimed to find the optimal combination of the design parameters that govern the physics behind the collapsible tube. A laboratory experiment has been conducted using rubber tubes with a variety of lengths, wall thicknesses and inner diameters. Then, an attempt to collapse the experimental results are made and empirical formula of activation pressure and regulated flow rate are given.