Cell-free transcription and translation systems promise to accelerate and simplify the engineering of synthetic proteins, biological circuits or metabolic pathways. Microfluidic droplet platforms can generate millions of reactions in parallel. This allows cell-free reactions to be miniaturized down to picoliter volumes. Nevertheless, the true potential of microfluidics have not been reached for cell-free bioengineering. Better approaches are needed for reaching sufficient in-drop expression levels while efficiently creating DNA diversity among droplets. This work develops a...

With the growth of online media, surveillance and mobile cameras, the amount and size of video databases are increasing at an incredible pace. For example, YouTube reported that over 400 hours of video are uploaded every minute to their servers. Arguably, people are the most important and interesting subjects of such videos. The computer vision community has embraced this observation to validate the crucial role that human action recognition plays in building smarter surveillance systems,...

In several fields, such as biology, chemistry, combustion and environmental science, laser absorption spectroscopy represents an invaluable tool for the detection and identification of a variety of molecular species in the gas phase. For this detection to be quantitative, it is of paramount importance to rely on accurate spectroscopic parameters for the involved absorption lines in terms of line strength, line center frequency, pressure broadening, and pressure shift coefficients. The mid-infrared region offers the most...

The GenRot program takes a typical Gaussian .gjf file (connectivity written after XYZ) as input, and generates new XYZ data based on inputs from the user. After opening the file in the program, the user clicks on 4 atoms to define a dihedral angle and determines the degree of rotation they wish for that angle. This is repeated until all the dihedral angles that the user wants to rotate have been defined. The program will...

Neural networks was shown to be very susceptible to small and imperceptible perturbations on its input. In this thesis, we study perturbations on two-layer piecewise linear networks. Such studies are essential in training neural networks that are robust to noisy input. One type of perturbations we consider is `1 norm bounded perturbations. Training Deep Neural Networks (DNNs) that are robust to norm bounded perturbations, or adversarial attacks, remains an elusive problem. While verification based methods...

NMDA receptors are the most studied receptors in the field of neuroscience and are known to play an important role in development and plasticity. These receptors exhibit different kinetics depending on their subunit composition. NR2A and NR2B are the predominating NMDAR subunits in the brain. These receptors localize to synapses where they interact with other proteins including CaMKIIα, an abundant kinase which plays an important role in synaptic plasticity. Although CaMKIIα is known to bind...

Tropical coral reefs provide important ecosystem goods and services that are supported by one or more ecosystem functions (e.g., recruitment, primary production, calcification, and nutrient recycling). Scleractinian corals drive most of these functions, but a combination of global and local anthropogenic stressors has caused persistent shifts from coral- to algae-dominated benthic reef communities globally. Such phase shifts likely have major consequences for ecosystem functions; yet, related knowledge is scarce in general, but particularly at the...

Data Centers (DCs) have become an intrinsic element of emerging technologies such as big data, artificial intelligence, cloud services; all of which entails interconnected and sophisticated computing and storage resources. Recent studies of conventional data center networks (DCNs) revealed two key challenges: a biased distribution of inter-rack traffic and unidentified flow classes: delay sensitive mice flows (MFs) and throughput-hungry elephant flows (EFs). Unfortunately, existing DCN topologies support only uniform distribution of capacities, provide limited bandwidth...

The possibility to manipulate electromagnetic radiation, as well as mechanical and acoustic waves has been an engaging topic since the beginning of the 20th century. Nowadays, thanks to the progress in technologies and the evolution of fabrication processes, realizing artificial materials that are able to interact with the environment in a desired fashion has become reality. The interest in micro/nanostructured metamaterials involves different field of research, ranging from optics to biology, through optoelectronics and photonics....

Baroclinic tides play a significant role in driving deep-ocean mixing, which not only influences the transport of nutrients and other biological tracers, but also affects the large scale circulations. This thesis combines advanced numerical modeling techniques and available observations to investigate the characteristics of baroclinic tides in the Red Sea, and understand their formation and fate, and their influence on the circulation and ecosystem. Based on a validated 3D, non-hydrostatic and high-resolution MIT General Circulation...

RNA interference (RNAi) is an important pathway that regulates gene expression in several organisms. The role of RNAi in post-transcriptional gene silencing in the cytoplasm is well characterized. In contrast, the role of RNAi components in the nucleus remains to be elucidated. Previous reports have indicated that RNAi components (Dicer and Argonaute proteins) and small RNAs act in the nucleus to regulate various pathways including heterochromatin formation, transposable elements repression, RNA Pol II processivity and...

In this research, I explore the changes in the functional diversity of herbivorous fishes in zones of coral reefs with different benthic composition: a zone dominated by corals, a zone dominated by algae and a transition zone in between the previous two. I choose to use functional traits which explain the feeding mechanics of this group of fish, as well their feeding rates and their previously established functional groups to understand how different assemblages of...

For millions of years, the nutrient exchange symbiosis between corals and their endosymbiotic algae has formed the foundation of the ecological success of coral reefs. Yet, in recent decades anthropogenic climate change is increasingly destabilizing this symbiosis, and thus the reefs that rely on it. High-temperature anomalies have caused mass mortality of corals due to repeated coral bleaching, the expulsion or digestion of symbionts by the host during stress. Hence, in-depth knowledge of the cellular...

Irrigated lands generate crop yields that are more than double those of rain-fed lands. Unfortunately, these systems are often heavily reliant on water supplies, which are diminishing globally. Alternative use of impaired quality waters for irrigation can reduce soil quality through secondary salinization, affecting plant health and yields. With salinization of agricultural lands increasing around the world, further understanding the impacts of this on crop production are required. The aim of this research is to...

The global consumption of fossil fuels continues to increase due to the rapid growth of energy demand, as a consequence of expanding population and human activities. Fast climate change is another inescapable issue caused by humans that need to be addressed. The development of solar energy conversion technologies is widely considered as one of the most promising solutions to sustainably maintain a modern lifestyle of the society and create a carbon-neutral social development operation mode....