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Researchers construct computational circuit boards with DNA

Professor Georg Seelig and his team utilize a new method called "DNA dominoes," using spatial organization to build nanoscale computational circuits made of synthetic DNA. The research was published in Nature Nanotechnology.

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Researchers construct computational circuit boards with DNA Banner

Professor Kannan receives NSF grant to improve groundbreaking nanopore sequencing of DNA

Assistant Professor Sreeram Kannan leads a $1.2 million collaborative NSF CIF grant. The research aims to design new algorithms for sequencing DNA using nanopore readers.

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Professor Kannan receives NSF grant to improve groundbreaking nanopore sequencing of DNA Banner

8 faculty named 2017 Amazon Catalyst Fellows

In a partnership with the University of Washington, Amazon Catalyst supports bold solutions to world problems.

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8 faculty named 2017 Amazon Catalyst Fellows Banner

UW EE leads NIST PSCR grant for next-generation broadband

The UW is one of 19 universities awarded the National Institute of Standards and Technology (NIST) Public Safety Communications Research (PSCR) grant to develop performance analysis tools for the proposed next-generation broadband LTE based FirstNet.

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UW EE leads NIST PSCR grant for next-generation broadband Banner

Alum Tong Zhang awarded the 2017 Graduate School Distinguished Dissertation Award in Mathematics, Physical Sciences and Engineering

Tong Zhang (Ph.D. ’17) received the highly-competitive award for his thesis on breakthrough full-duplex wireless communication.

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Alum Tong Zhang awarded the 2017 Graduate School Distinguished Dissertation Award in Mathematics, Physical Sciences and Engineering Banner

UW team achieves a factor of 10 performance improvement for BCI Recording Systems

UW researchers present a system that addresses BCI challenges, increasing channel recording density by ten times current state-of-the-art systems.

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UW team achieves a factor of 10 performance improvement for BCI  Recording Systems Banner

News + Awards

https://www.ee.washington.edu/spotlight/researchers-construct-computational-circuit-boards-with-dna/
https://www.ee.washington.edu/spotlight/professor-kannan-receives-nsf-grant-to-improve-groundbreaking-nanopore-sequencing-of-dna/
https://www.ee.washington.edu/spotlight/uw-ee-leads-nist-pscr-grant-for-next-generation-broadband/
UW EE leads NIST PSCR grant for next-generation broadband

UW EE leads NIST PSCR grant for next-generation broadband

The UW is one of 19 universities awarded the National Institute of Standards and Technology (NIST) Public Safety Communications Research (PSCR) grant to develop performance analysis tools for the proposed next-generation broadband LTE based FirstNet.

https://www.ee.washington.edu/spotlight/alum-tong-zhang-awarded-the-2017-graduate-school-distinguished-dissertation-award/
https://www.ee.washington.edu/spotlight/8-faculty-named-2017-amazon-catalyst-fellows/
https://www.ee.washington.edu/spotlight/researchers-advance-state-of-the-art-neural-recording-for-bci-applications/
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                    [post_content] => [caption id="attachment_11076" align="alignleft" width="599"] This figure illustrates the elementary logic gates and DNA domino representation. a. Two-input OR. b. Thresholding module. c. Two-input AND. First column: logic gate diagram. Second column: DNA domino representation and top view projection. Credit: Nature Nanotechnology[/caption]

Spatial organization as a tool for the spread of materials and information is a well-practiced concept. In Mesopotamia, it was used to coax water through a matrix of small channels to water crops. More recently, it has been used to operate semiconductor circuitry. In nature, spatial organization is used by living cells to control the transmission of molecular signals. Researchers at the University of Washington (UW) and scientists at Microsoft Research have used spatial organization to build nanoscale computational circuits made of synthetic DNA.

In a July 24th issue of Nature Nanotechnology, the researchers’ article “A spatially localized architecture for fast and modular DNA computing” discussed this method. Like an AND and OR version of the classic logics game, researchers used “DNA dominoes” as a method of propagating information. In this process, “DNA domino" molecules are positioned at regular intervals on a DNA surface. Information is transmitted when DNA dominoes interact with their immediate neighbors in a cascade.

DNA domino circuits mark an important advance in the field. For decades, researchers have puzzled over the use of DNA molecules for computation. The current components of molecular devices are made from strands of synthetic DNA, where the sequence of the strands determines how they interact. Because billions of DNA molecules rely on a slow process of random diffusion to execute a computation, this method is haphazard in speed and efficiency.

DNA dominoes offer a more robust approach. In this process, DNA dominoes are positioned close to each other on the surface, allowing them to interact quickly with their neighbors. This eliminates the need for random diffusion, leading to an order of magnitude increase in speed. This process also allows for DNA domino recycling. Since their physical location and chemical specificity determines what interactions occur, DNA dominoes can be re-used in multiple locations.

The scaffolding for DNA dominoes was assembled through a process called “DNA origami.” The relatively new process enables unprecedented control over complex molecular structures through the joining of long and short DNA strands. In this process, short strands of DNA (staples) are hinged to a single long strand of DNA (the scaffold).

[caption id="attachment_2313" align="alignright" width="200"] Georg Seelig[/caption]

“To build a nanoscale computational circuit, we have to incorporate our individual DNA dominoes into the origami using a special type of extended staple,” PI on the project and UW electrical engineering and computer science and engineering Professor Georg Seelig said. “We do this during the folding process, precisely positioning the DNA molecules on the origami to form a DNA domino.”

The DNA dominoes were assembled into signal transmission lines and elementary Boolean logic gates. By linking the elementary gates together, the researchers were able to create more complex circuits.

This domino approach lays the groundwork for future applications in molecular engineering, offering new opportunities in biosensing, in vitro diagnostics, biomanufacturing and smart therapeutics.

Additional authors on the work include Gourab Chatterjee, a postdoctoral researcher in the UW Department of Bioengineering, Neil Dalchau and Andrew Phillips, researchers at Microsoft Research and Richard Muscat, a former postdoctoral researcher in the UW Department of Electrical Engineering.

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Information for this article was gathered from a recent Microsoft Research article on the same topic and the paper presented in Nature Nanotechnology. 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The research aims to design new algorithms for sequencing DNA using nanopore readers. Fast and inexpensive DNA sequencing technology is beginning to impact society through applications ranging from personalized medicine to the understanding of ecological systems. However, existing DNA sequencing methods are limited in the length of DNA that can be analyzed. These systems can read only short strands of DNA, limiting the ability of algorithms to resolve and analyze regions of the genome which have repeating motifs. Nanopore sequencing is a new and emerging technology, where DNA is transmigrated through a pore, and the induced electrical current variations are measured to infer the DNA sequence. In addition to having the ability to sequence long stretches of DNA, nanopore sequencers are also relatively inexpensive and offer high mobility for testing and rapid processing of samples. An algorithm, called base-caller, is used to infer the DNA sequence from the observed current waveform. Current base-calling methods suffer from high measurement noise. Kannan and his team of collaborators seek to address this problem. In a recent paper, they have quantified the amount of information that can be extracted by the process of nanopore sequencing, establishing interesting parallels to a classical problem studied in communication theory. A telecommunication system is mathematically characterized by the probabilistic mapping between the transmitted signal and the received signal. Analogously, the mapping between the DNA sequence and the observed current waveform can be thought of as a communication channel whose information rates can be characterized using information-theoretic methods. This project develops a holistic approach for the nanopore sequencing problem, using tools from information theory and bio-informatics to build more representative mathematical models and better algorithms for inferring the DNA sequence, as well as to explore potential applications in DNA forensics, phasing and assembly. Kannan is the PI on the four-year grant. Co-PIs include UW Department of Physics Professor Jens Gundlach and UCLA electrical engineering Professor Suhas Diggavi. [post_title] => Professor Kannan receives NSF grant to improve groundbreaking nanopore sequencing of DNA [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => professor-kannan-receives-nsf-grant-to-improve-groundbreaking-nanopore-sequencing-of-dna [to_ping] => [pinged] => [post_modified] => 2017-07-21 15:44:09 [post_modified_gmt] => 2017-07-21 22:44:09 [post_content_filtered] => [post_parent] => 0 [guid] => http://www.ee.washington.edu/?post_type=spotlight&p=11071 [menu_order] => 2 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [2] => WP_Post Object ( [ID] => 11018 [post_author] => 12 [post_date] => 2017-07-14 10:51:28 [post_date_gmt] => 2017-07-14 17:51:28 [post_content] => [caption id="attachment_11019" align="alignleft" width="385"] Professors Sumit Roy and Tom Henderson[/caption] The University of Washington (UW) is one of 19 universities awarded the National Institute of Standards and Technology (NIST) Public Safety Communications Research (PSCR) grant to develop performance analysis tools for the proposed next-generation broadband LTE based FirstNet (for emergency/first responders). The grant is part of the First Responders Network Authority (FirstNet) appropriations. Congress has allocated FirstNet 20 MHz of spectrum in 700 MHz band and up to $7 billion in funding for the construction of a nationwide network (awarded to AT&T in a public-private partnership model), achieving a major recommendation post 9/11 for a single interoperable platform with the requisite capacity for new features. These features integrate new data, voice and location-based services. “UW EE is in a unique position to offer support to these efforts due to the department’s key long-standing role in developing the network simulator ns-3,” UW electrical engineering (UW EE) Professor and PI on the grant Sumit Roy said. [caption id="attachment_1281" align="alignright" width="189"] Professor Jim Ritcey[/caption] The proposed analytical studies will initially focus on benchmarking currently used by P-25 digital Land Mobile Radio (LMR) systems intended for primarily voice communications. UW EE researchers will identify a set of emergency scenarios and create corresponding traffic (demand) models for analyzing the next-generation of LTE-based public safety network architecture. This research presents an opportunity for UW EE to partner with the City of Seattle CIO’s office to analyze the city’s emergency response units current operations and prospects for broadband LTE adoption. “A key component of our proposal is the engagement with the local First Responder community,” Roy said. “Currently, there is a lack of more fine-grained demand models for both a daily routine basis as well as when emergencies at various scales and types occur, such as fire, significant traffic, other incidents or a natural disaster; it would help answer key questions, like availability and performance of public safety (PS) networks in such `stressed’ scenarios. As a cornerstone of our proposed effort, our work would greatly benefit from the availability of local data (from City or County Police/Fire/EMT) to refine and tune our models. In turn, we could then conduct techno-economic studies that highlight cost-benefit considerations for broadband LTE adoption for PS and assist the City and State with inputs or recommendations during the next stage of policymaking in this regard.” Co-PIs on the two-year grant, entitled “Modeling, Simulation and Performance Evaluation for Future Public Safety Communications Networks,” include UW EE Professor Jim Ritcey and Affiliate Professor Tom Henderson. [post_title] => UW EE leads NIST PSCR grant for next-generation broadband [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => uw-ee-leads-nist-pscr-grant-for-next-generation-broadband [to_ping] => [pinged] => [post_modified] => 2017-07-14 14:28:11 [post_modified_gmt] => 2017-07-14 21:28:11 [post_content_filtered] => [post_parent] => 0 [guid] => http://www.ee.washington.edu/?post_type=spotlight&p=11018 [menu_order] => 3 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [3] => WP_Post Object ( [ID] => 11010 [post_author] => 12 [post_date] => 2017-07-13 10:00:48 [post_date_gmt] => 2017-07-13 17:00:48 [post_content] => [caption id="attachment_11014" align="alignleft" width="452"] Tong Zhang[/caption] Tong Zhang (Ph.D. ’17) received the highly competitive University of Washington (UW) 2017 Graduate School Distinguished Dissertation Award in Mathematics, Physical Sciences and Engineering for his UW electrical engineering doctoral thesis. The thesis, entitled “Integrated Wideband Self-interference Cancellation Techniques for FDD and Full-duplex Wireless Communication,” was the top dissertation in the Mathematics, Physical Sciences and Engineering category. As a graduate student, Zhang worked with Professor Chris Rudell in the Future Analog System Technologies (FAST) Lab. Throughout his successful academic career, Zhang has received several significant honors, including the prestigious 2016 IEEE Solid-State Circuit Society Pre-Doctoral Award and the UW EE department’s Yang Research Award. Recently, Zhang was the lead author on breakthrough full duplex communication research, which illustrates the impact of his dissertation research. This is the first time in the UW EE department’s history that a Ph.D. student has received the top dissertation award. [post_title] => Alum Tong Zhang awarded the 2017 Graduate School Distinguished Dissertation Award in Mathematics, Physical Sciences and Engineering [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => alum-tong-zhang-awarded-the-2017-graduate-school-distinguished-dissertation-award [to_ping] => [pinged] => [post_modified] => 2017-07-20 10:28:31 [post_modified_gmt] => 2017-07-20 17:28:31 [post_content_filtered] => [post_parent] => 0 [guid] => http://www.ee.washington.edu/?post_type=spotlight&p=11010 [menu_order] => 4 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [4] => WP_Post Object ( [ID] => 11006 [post_author] => 12 [post_date] => 2017-07-19 16:14:01 [post_date_gmt] => 2017-07-19 23:14:01 [post_content] => UW EE Professors Les Atlas, Karl Böhringer, Howard Chizeck, Blake Hannaford, Eric Klavins, Arka Majumdar, Shwetak Patel and Joshua Smith were awarded the 2017 Amazon Catalyst Fellowship.  In a partnership with the University of Washington, Amazon Catalyst supports bold solutions to world problems. The program provides funding, mentorship and community to the innovative projects. Congratulations to all newly-minted Amazon Catalyst Fellows! The Projects: simsong.org PI: Les Atlas Active self-cleaning technology for solar panels PI: Karl Böhringer Haptic Passwords PI: Howard Chizeck IRA, the robot surgical assistant PI: Blake Hannaford UW BIOFAB: A cloud laboratory for genetic engineering PI: Eric Klavins Smart Eyewear PI: Arka Majumdar OsteoApp PI: Shwetak Patel Enabling district shared parking via energy harvesting wireless sensing technology PI: Joshua Smith [post_title] => 8 faculty named 2017 Amazon Catalyst Fellows [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => 8-faculty-named-2017-amazon-catalyst-fellows [to_ping] => [pinged] => [post_modified] => 2017-07-21 13:33:19 [post_modified_gmt] => 2017-07-21 20:33:19 [post_content_filtered] => [post_parent] => 0 [guid] => http://www.ee.washington.edu/?post_type=spotlight&p=11006 [menu_order] => 6 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [5] => WP_Post Object ( [ID] => 10990 [post_author] => 12 [post_date] => 2017-07-07 14:06:13 [post_date_gmt] => 2017-07-07 21:06:13 [post_content] => [caption id="attachment_10991" align="alignleft" width="458"] From left: Dr. Anthony Smith and Professor Visvesh Sathe[/caption] Brain computer interfaces (BCIs) offer a direct communication pathway between the brain and external technologies. BCIs are of significant research interest for their potential role in repairing human cognitive or sensory-motor functions for conditions like stroke and paralysis. Although BCIs present great opportunities for brain to device connectivity, there are several challenges in application: next-generation BCIs require a large number of neural recording and stimulation electrodes for broad and dense coverage. Existing recording electronics techniques are unable to scale to these large counts without a prohibitive increase in silicon-die area. Further, BCIs generate large stimulation artifacts, obscuring important signals shortly after stimulation. In an article, entitled “A Scalable, Highly-Multiplexed Delta-Encoded Digital Feedback ECoG Recording Amplifier with Common and Differential-Mode Artifact Suppression,” UW researchers present a system that addresses these challenges, increasing channel recording density by ten times current state-of-the-art systems. “The focus of the effort was on developing architectural techniques that could be leveraged to allow us to design high-density recording electronics,” UW electrical engineering Assistant Professor and PI on the project Visvesh Sathe said. “The system allows for highly multiplexed recording channels, exploiting the inherent structure in neural signals to achieve high precision recording using simple, robust circuits. The system also suppresses, for the first time, both common-mode and differential-mode artifacts.” The system is useful for a variety of bio-potential signal acquisition applications, offering support to researchers when signals from the human body have to be read. This process expands to numerous medical applications, including nervous system diseases like Alzheimer’s and Parkinson’s. "This work is a first step toward a realistic Bidirectional Brain Computer Interface on a single chip,” senior author on the paper Anthony Smith (Ph.D. ’17) said. “The next step will be integrating this system with the CMOS-compatible stimulation platform that has also been developed at UW and adding on-chip computation to enable closed-loop operation." Additional authors on the paper include UW electrical engineering graduate student John Uehlin, UW physiology and biophysics Research Associate Steve Perlmutter and UW electrical engineering Associate Professor Chris Rudell. The work is funded by the Center for Sensorimotor Neural Engineering (CSNE), a UW-based center established through the National Science Foundation Engineering Research Centers (NSF ERC) program. [post_title] => UW team achieves a factor of 10 performance improvement for BCI Recording Systems [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => researchers-advance-state-of-the-art-neural-recording-for-bci-applications [to_ping] => [pinged] => [post_modified] => 2017-07-18 14:02:00 [post_modified_gmt] => 2017-07-18 21:02:00 [post_content_filtered] => [post_parent] => 0 [guid] => http://www.ee.washington.edu/?post_type=spotlight&p=10990 [menu_order] => 7 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) ) [_numposts:protected] => 6 [_rendered:protected] => 1 [_classes:protected] => Array ( [0] => view-block [1] => block--spotlight-robust-news ) [_finalHTML:protected] =>
https://www.ee.washington.edu/spotlight/researchers-construct-computational-circuit-boards-with-dna/
https://www.ee.washington.edu/spotlight/professor-kannan-receives-nsf-grant-to-improve-groundbreaking-nanopore-sequencing-of-dna/
https://www.ee.washington.edu/spotlight/uw-ee-leads-nist-pscr-grant-for-next-generation-broadband/
UW EE leads NIST PSCR grant for next-generation broadband

UW EE leads NIST PSCR grant for next-generation broadband

The UW is one of 19 universities awarded the National Institute of Standards and Technology (NIST) Public Safety Communications Research (PSCR) grant to develop performance analysis tools for the proposed next-generation broadband LTE based FirstNet.

https://www.ee.washington.edu/spotlight/alum-tong-zhang-awarded-the-2017-graduate-school-distinguished-dissertation-award/
https://www.ee.washington.edu/spotlight/8-faculty-named-2017-amazon-catalyst-fellows/
https://www.ee.washington.edu/spotlight/researchers-advance-state-of-the-art-neural-recording-for-bci-applications/
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Two-input OR. b. Thresholding module. c. Two-input AND. First column: logic gate diagram. Second column: DNA domino representation and top view projection. Credit: Nature Nanotechnology[/caption] Spatial organization as a tool for the spread of materials and information is a well-practiced concept. In Mesopotamia, it was used to coax water through a matrix of small channels to water crops. More recently, it has been used to operate semiconductor circuitry. In nature, spatial organization is used by living cells to control the transmission of molecular signals. Researchers at the University of Washington (UW) and scientists at Microsoft Research have used spatial organization to build nanoscale computational circuits made of synthetic DNA. In a July 24th issue of Nature Nanotechnology, the researchers’ article “A spatially localized architecture for fast and modular DNA computing” discussed this method. Like an AND and OR version of the classic logics game, researchers used “DNA dominoes” as a method of propagating information. In this process, “DNA domino" molecules are positioned at regular intervals on a DNA surface. Information is transmitted when DNA dominoes interact with their immediate neighbors in a cascade. DNA domino circuits mark an important advance in the field. For decades, researchers have puzzled over the use of DNA molecules for computation. The current components of molecular devices are made from strands of synthetic DNA, where the sequence of the strands determines how they interact. Because billions of DNA molecules rely on a slow process of random diffusion to execute a computation, this method is haphazard in speed and efficiency. DNA dominoes offer a more robust approach. In this process, DNA dominoes are positioned close to each other on the surface, allowing them to interact quickly with their neighbors. This eliminates the need for random diffusion, leading to an order of magnitude increase in speed. This process also allows for DNA domino recycling. Since their physical location and chemical specificity determines what interactions occur, DNA dominoes can be re-used in multiple locations. The scaffolding for DNA dominoes was assembled through a process called “DNA origami.” The relatively new process enables unprecedented control over complex molecular structures through the joining of long and short DNA strands. In this process, short strands of DNA (staples) are hinged to a single long strand of DNA (the scaffold). [caption id="attachment_2313" align="alignright" width="200"] Georg Seelig[/caption] “To build a nanoscale computational circuit, we have to incorporate our individual DNA dominoes into the origami using a special type of extended staple,” PI on the project and UW electrical engineering and computer science and engineering Professor Georg Seelig said. “We do this during the folding process, precisely positioning the DNA molecules on the origami to form a DNA domino.” The DNA dominoes were assembled into signal transmission lines and elementary Boolean logic gates. By linking the elementary gates together, the researchers were able to create more complex circuits. This domino approach lays the groundwork for future applications in molecular engineering, offering new opportunities in biosensing, in vitro diagnostics, biomanufacturing and smart therapeutics. Additional authors on the work include Gourab Chatterjee, a postdoctoral researcher in the UW Department of Bioengineering, Neil Dalchau and Andrew Phillips, researchers at Microsoft Research and Richard Muscat, a former postdoctoral researcher in the UW Department of Electrical Engineering.

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Information for this article was gathered from a recent Microsoft Research article on the same topic and the paper presented in Nature Nanotechnology. [post_title] => Researchers construct computational circuit boards with DNA [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => researchers-construct-computational-circuit-boards-with-dna [to_ping] => [pinged] => [post_modified] => 2017-07-24 16:37:45 [post_modified_gmt] => 2017-07-24 23:37:45 [post_content_filtered] => [post_parent] => 0 [guid] => http://www.ee.washington.edu/?post_type=spotlight&p=11075 [menu_order] => 1 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [1] => WP_Post Object ( [ID] => 11071 [post_author] => 12 [post_date] => 2017-07-21 15:42:20 [post_date_gmt] => 2017-07-21 22:42:20 [post_content] => [caption id="attachment_10222" align="alignleft" width="484"] Professor Sreeram Kannan[/caption] UW electrical engineering Assistant Professor Sreeram Kannan leads a $1.2 million collaborative National Science Foundation (NSF) Communications and Information Foundations (CIF) Grant. The research aims to design new algorithms for sequencing DNA using nanopore readers. Fast and inexpensive DNA sequencing technology is beginning to impact society through applications ranging from personalized medicine to the understanding of ecological systems. However, existing DNA sequencing methods are limited in the length of DNA that can be analyzed. These systems can read only short strands of DNA, limiting the ability of algorithms to resolve and analyze regions of the genome which have repeating motifs. Nanopore sequencing is a new and emerging technology, where DNA is transmigrated through a pore, and the induced electrical current variations are measured to infer the DNA sequence. In addition to having the ability to sequence long stretches of DNA, nanopore sequencers are also relatively inexpensive and offer high mobility for testing and rapid processing of samples. An algorithm, called base-caller, is used to infer the DNA sequence from the observed current waveform. Current base-calling methods suffer from high measurement noise. Kannan and his team of collaborators seek to address this problem. In a recent paper, they have quantified the amount of information that can be extracted by the process of nanopore sequencing, establishing interesting parallels to a classical problem studied in communication theory. A telecommunication system is mathematically characterized by the probabilistic mapping between the transmitted signal and the received signal. Analogously, the mapping between the DNA sequence and the observed current waveform can be thought of as a communication channel whose information rates can be characterized using information-theoretic methods. This project develops a holistic approach for the nanopore sequencing problem, using tools from information theory and bio-informatics to build more representative mathematical models and better algorithms for inferring the DNA sequence, as well as to explore potential applications in DNA forensics, phasing and assembly. Kannan is the PI on the four-year grant. Co-PIs include UW Department of Physics Professor Jens Gundlach and UCLA electrical engineering Professor Suhas Diggavi. [post_title] => Professor Kannan receives NSF grant to improve groundbreaking nanopore sequencing of DNA [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => professor-kannan-receives-nsf-grant-to-improve-groundbreaking-nanopore-sequencing-of-dna [to_ping] => [pinged] => [post_modified] => 2017-07-21 15:44:09 [post_modified_gmt] => 2017-07-21 22:44:09 [post_content_filtered] => [post_parent] => 0 [guid] => http://www.ee.washington.edu/?post_type=spotlight&p=11071 [menu_order] => 2 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [2] => WP_Post Object ( [ID] => 11018 [post_author] => 12 [post_date] => 2017-07-14 10:51:28 [post_date_gmt] => 2017-07-14 17:51:28 [post_content] => [caption id="attachment_11019" align="alignleft" width="385"] Professors Sumit Roy and Tom Henderson[/caption] The University of Washington (UW) is one of 19 universities awarded the National Institute of Standards and Technology (NIST) Public Safety Communications Research (PSCR) grant to develop performance analysis tools for the proposed next-generation broadband LTE based FirstNet (for emergency/first responders). The grant is part of the First Responders Network Authority (FirstNet) appropriations. Congress has allocated FirstNet 20 MHz of spectrum in 700 MHz band and up to $7 billion in funding for the construction of a nationwide network (awarded to AT&T in a public-private partnership model), achieving a major recommendation post 9/11 for a single interoperable platform with the requisite capacity for new features. These features integrate new data, voice and location-based services. “UW EE is in a unique position to offer support to these efforts due to the department’s key long-standing role in developing the network simulator ns-3,” UW electrical engineering (UW EE) Professor and PI on the grant Sumit Roy said. [caption id="attachment_1281" align="alignright" width="189"] Professor Jim Ritcey[/caption] The proposed analytical studies will initially focus on benchmarking currently used by P-25 digital Land Mobile Radio (LMR) systems intended for primarily voice communications. UW EE researchers will identify a set of emergency scenarios and create corresponding traffic (demand) models for analyzing the next-generation of LTE-based public safety network architecture. This research presents an opportunity for UW EE to partner with the City of Seattle CIO’s office to analyze the city’s emergency response units current operations and prospects for broadband LTE adoption. “A key component of our proposal is the engagement with the local First Responder community,” Roy said. “Currently, there is a lack of more fine-grained demand models for both a daily routine basis as well as when emergencies at various scales and types occur, such as fire, significant traffic, other incidents or a natural disaster; it would help answer key questions, like availability and performance of public safety (PS) networks in such `stressed’ scenarios. As a cornerstone of our proposed effort, our work would greatly benefit from the availability of local data (from City or County Police/Fire/EMT) to refine and tune our models. In turn, we could then conduct techno-economic studies that highlight cost-benefit considerations for broadband LTE adoption for PS and assist the City and State with inputs or recommendations during the next stage of policymaking in this regard.” Co-PIs on the two-year grant, entitled “Modeling, Simulation and Performance Evaluation for Future Public Safety Communications Networks,” include UW EE Professor Jim Ritcey and Affiliate Professor Tom Henderson. [post_title] => UW EE leads NIST PSCR grant for next-generation broadband [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => uw-ee-leads-nist-pscr-grant-for-next-generation-broadband [to_ping] => [pinged] => [post_modified] => 2017-07-14 14:28:11 [post_modified_gmt] => 2017-07-14 21:28:11 [post_content_filtered] => [post_parent] => 0 [guid] => http://www.ee.washington.edu/?post_type=spotlight&p=11018 [menu_order] => 3 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [3] => WP_Post Object ( [ID] => 11010 [post_author] => 12 [post_date] => 2017-07-13 10:00:48 [post_date_gmt] => 2017-07-13 17:00:48 [post_content] => [caption id="attachment_11014" align="alignleft" width="452"] Tong Zhang[/caption] Tong Zhang (Ph.D. ’17) received the highly competitive University of Washington (UW) 2017 Graduate School Distinguished Dissertation Award in Mathematics, Physical Sciences and Engineering for his UW electrical engineering doctoral thesis. The thesis, entitled “Integrated Wideband Self-interference Cancellation Techniques for FDD and Full-duplex Wireless Communication,” was the top dissertation in the Mathematics, Physical Sciences and Engineering category. As a graduate student, Zhang worked with Professor Chris Rudell in the Future Analog System Technologies (FAST) Lab. Throughout his successful academic career, Zhang has received several significant honors, including the prestigious 2016 IEEE Solid-State Circuit Society Pre-Doctoral Award and the UW EE department’s Yang Research Award. Recently, Zhang was the lead author on breakthrough full duplex communication research, which illustrates the impact of his dissertation research. This is the first time in the UW EE department’s history that a Ph.D. student has received the top dissertation award. [post_title] => Alum Tong Zhang awarded the 2017 Graduate School Distinguished Dissertation Award in Mathematics, Physical Sciences and Engineering [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => alum-tong-zhang-awarded-the-2017-graduate-school-distinguished-dissertation-award [to_ping] => [pinged] => [post_modified] => 2017-07-20 10:28:31 [post_modified_gmt] => 2017-07-20 17:28:31 [post_content_filtered] => [post_parent] => 0 [guid] => http://www.ee.washington.edu/?post_type=spotlight&p=11010 [menu_order] => 4 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [4] => WP_Post Object ( [ID] => 11006 [post_author] => 12 [post_date] => 2017-07-19 16:14:01 [post_date_gmt] => 2017-07-19 23:14:01 [post_content] => UW EE Professors Les Atlas, Karl Böhringer, Howard Chizeck, Blake Hannaford, Eric Klavins, Arka Majumdar, Shwetak Patel and Joshua Smith were awarded the 2017 Amazon Catalyst Fellowship.  In a partnership with the University of Washington, Amazon Catalyst supports bold solutions to world problems. The program provides funding, mentorship and community to the innovative projects. Congratulations to all newly-minted Amazon Catalyst Fellows! The Projects: simsong.org PI: Les Atlas Active self-cleaning technology for solar panels PI: Karl Böhringer Haptic Passwords PI: Howard Chizeck IRA, the robot surgical assistant PI: Blake Hannaford UW BIOFAB: A cloud laboratory for genetic engineering PI: Eric Klavins Smart Eyewear PI: Arka Majumdar OsteoApp PI: Shwetak Patel Enabling district shared parking via energy harvesting wireless sensing technology PI: Joshua Smith [post_title] => 8 faculty named 2017 Amazon Catalyst Fellows [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => 8-faculty-named-2017-amazon-catalyst-fellows [to_ping] => [pinged] => [post_modified] => 2017-07-21 13:33:19 [post_modified_gmt] => 2017-07-21 20:33:19 [post_content_filtered] => [post_parent] => 0 [guid] => http://www.ee.washington.edu/?post_type=spotlight&p=11006 [menu_order] => 6 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [5] => WP_Post Object ( [ID] => 10990 [post_author] => 12 [post_date] => 2017-07-07 14:06:13 [post_date_gmt] => 2017-07-07 21:06:13 [post_content] => [caption id="attachment_10991" align="alignleft" width="458"] From left: Dr. Anthony Smith and Professor Visvesh Sathe[/caption] Brain computer interfaces (BCIs) offer a direct communication pathway between the brain and external technologies. BCIs are of significant research interest for their potential role in repairing human cognitive or sensory-motor functions for conditions like stroke and paralysis. Although BCIs present great opportunities for brain to device connectivity, there are several challenges in application: next-generation BCIs require a large number of neural recording and stimulation electrodes for broad and dense coverage. Existing recording electronics techniques are unable to scale to these large counts without a prohibitive increase in silicon-die area. Further, BCIs generate large stimulation artifacts, obscuring important signals shortly after stimulation. In an article, entitled “A Scalable, Highly-Multiplexed Delta-Encoded Digital Feedback ECoG Recording Amplifier with Common and Differential-Mode Artifact Suppression,” UW researchers present a system that addresses these challenges, increasing channel recording density by ten times current state-of-the-art systems. “The focus of the effort was on developing architectural techniques that could be leveraged to allow us to design high-density recording electronics,” UW electrical engineering Assistant Professor and PI on the project Visvesh Sathe said. “The system allows for highly multiplexed recording channels, exploiting the inherent structure in neural signals to achieve high precision recording using simple, robust circuits. The system also suppresses, for the first time, both common-mode and differential-mode artifacts.” The system is useful for a variety of bio-potential signal acquisition applications, offering support to researchers when signals from the human body have to be read. This process expands to numerous medical applications, including nervous system diseases like Alzheimer’s and Parkinson’s. "This work is a first step toward a realistic Bidirectional Brain Computer Interface on a single chip,” senior author on the paper Anthony Smith (Ph.D. ’17) said. “The next step will be integrating this system with the CMOS-compatible stimulation platform that has also been developed at UW and adding on-chip computation to enable closed-loop operation." Additional authors on the paper include UW electrical engineering graduate student John Uehlin, UW physiology and biophysics Research Associate Steve Perlmutter and UW electrical engineering Associate Professor Chris Rudell. The work is funded by the Center for Sensorimotor Neural Engineering (CSNE), a UW-based center established through the National Science Foundation Engineering Research Centers (NSF ERC) program. [post_title] => UW team achieves a factor of 10 performance improvement for BCI Recording Systems [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => researchers-advance-state-of-the-art-neural-recording-for-bci-applications [to_ping] => [pinged] => [post_modified] => 2017-07-18 14:02:00 [post_modified_gmt] => 2017-07-18 21:02:00 [post_content_filtered] => [post_parent] => 0 [guid] => http://www.ee.washington.edu/?post_type=spotlight&p=10990 [menu_order] => 7 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) ) [post_count] => 6 [current_post] => -1 [in_the_loop] => [post] => WP_Post Object ( [ID] => 11075 [post_author] => 12 [post_date] => 2017-07-24 16:22:39 [post_date_gmt] => 2017-07-24 23:22:39 [post_content] => [caption id="attachment_11076" align="alignleft" width="599"] This figure illustrates the elementary logic gates and DNA domino representation. a. Two-input OR. b. Thresholding module. c. Two-input AND. First column: logic gate diagram. Second column: DNA domino representation and top view projection. Credit: Nature Nanotechnology[/caption] Spatial organization as a tool for the spread of materials and information is a well-practiced concept. In Mesopotamia, it was used to coax water through a matrix of small channels to water crops. More recently, it has been used to operate semiconductor circuitry. In nature, spatial organization is used by living cells to control the transmission of molecular signals. Researchers at the University of Washington (UW) and scientists at Microsoft Research have used spatial organization to build nanoscale computational circuits made of synthetic DNA. In a July 24th issue of Nature Nanotechnology, the researchers’ article “A spatially localized architecture for fast and modular DNA computing” discussed this method. Like an AND and OR version of the classic logics game, researchers used “DNA dominoes” as a method of propagating information. In this process, “DNA domino" molecules are positioned at regular intervals on a DNA surface. Information is transmitted when DNA dominoes interact with their immediate neighbors in a cascade. DNA domino circuits mark an important advance in the field. For decades, researchers have puzzled over the use of DNA molecules for computation. The current components of molecular devices are made from strands of synthetic DNA, where the sequence of the strands determines how they interact. Because billions of DNA molecules rely on a slow process of random diffusion to execute a computation, this method is haphazard in speed and efficiency. DNA dominoes offer a more robust approach. In this process, DNA dominoes are positioned close to each other on the surface, allowing them to interact quickly with their neighbors. This eliminates the need for random diffusion, leading to an order of magnitude increase in speed. This process also allows for DNA domino recycling. Since their physical location and chemical specificity determines what interactions occur, DNA dominoes can be re-used in multiple locations. The scaffolding for DNA dominoes was assembled through a process called “DNA origami.” The relatively new process enables unprecedented control over complex molecular structures through the joining of long and short DNA strands. In this process, short strands of DNA (staples) are hinged to a single long strand of DNA (the scaffold). [caption id="attachment_2313" align="alignright" width="200"] Georg Seelig[/caption] “To build a nanoscale computational circuit, we have to incorporate our individual DNA dominoes into the origami using a special type of extended staple,” PI on the project and UW electrical engineering and computer science and engineering Professor Georg Seelig said. “We do this during the folding process, precisely positioning the DNA molecules on the origami to form a DNA domino.” The DNA dominoes were assembled into signal transmission lines and elementary Boolean logic gates. By linking the elementary gates together, the researchers were able to create more complex circuits. This domino approach lays the groundwork for future applications in molecular engineering, offering new opportunities in biosensing, in vitro diagnostics, biomanufacturing and smart therapeutics. Additional authors on the work include Gourab Chatterjee, a postdoctoral researcher in the UW Department of Bioengineering, Neil Dalchau and Andrew Phillips, researchers at Microsoft Research and Richard Muscat, a former postdoctoral researcher in the UW Department of Electrical Engineering.

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Information for this article was gathered from a recent Microsoft Research article on the same topic and the paper presented in Nature Nanotechnology. [post_title] => Researchers construct computational circuit boards with DNA [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => researchers-construct-computational-circuit-boards-with-dna [to_ping] => [pinged] => [post_modified] => 2017-07-24 16:37:45 [post_modified_gmt] => 2017-07-24 23:37:45 [post_content_filtered] => [post_parent] => 0 [guid] => http://www.ee.washington.edu/?post_type=spotlight&p=11075 [menu_order] => 1 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [comment_count] => 0 [current_comment] => -1 [found_posts] => 551 [max_num_pages] => 92 [max_num_comment_pages] => 0 [is_single] => [is_preview] => [is_page] => [is_archive] => 1 [is_date] => [is_year] => [is_month] => [is_day] => [is_time] => [is_author] => [is_category] => [is_tag] => [is_tax] => [is_search] => [is_feed] => [is_comment_feed] => [is_trackback] => [is_home] => [is_404] => [is_embed] => [is_paged] => [is_admin] => [is_attachment] => [is_singular] => [is_robots] => [is_posts_page] => [is_post_type_archive] => 1 [query_vars_hash:WP_Query:private] => 0f87fe429e20a1f4e53778b54d8d4588 [query_vars_changed:WP_Query:private] => 1 [thumbnails_cached] => [stopwords:WP_Query:private] => [compat_fields:WP_Query:private] => Array ( [0] => query_vars_hash [1] => query_vars_changed ) [compat_methods:WP_Query:private] => Array ( [0] => init_query_flags [1] => parse_tax_query ) ) )
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