Binary Research Group

Dr. Chen received his Ph.D. from the University of Maryland, USA in 1998. The BINARY lab (Biology, Information science and Nanotechnology Applications and Research laboratorY) was founded in Spring 2003. The mission is to provide a cross-disciplinary research environment for exploring new nanoscale device & circuit designs and nanotechnology for bio-medical applications. Our primary research focuses include:

  1. Developing a pulsed-wave technology platform to stimulate cell growth (with the applications in cell therapy, tissue engineering, mental health and antibody productions), and microorganism growth (with the applications in increasing renewable biofuel /algal oil, antibiotics, omega-3, and wine/beverage productions);
  2. Building functional nanomaterials for water filtration (removing microorganisms, organic chemicals and heavy metals), gene transformation of agricultural products, targeted cancer imaging and treatment, gene/peptide/microRNA delivery (especially across the blood-brain-barrier);
  3. Designing portable impedance-based point-of-care devices for detecting metabolic biomarkers, monitoring environmental toxins, sensing plant infections at an earlier stage, and screening pathogens for food safety.

The University of Alberta is home to cutting edge facilities such as the National Institute for Nanotechnology, as well as having the interdisciplinary expertise to be an epicentre for new waves of innovation in Biomedical Engineering. The University of Alberta was ranked 46th in the world for the impact of its engineering publications.

  
News

 
"Low-Power Noise-Immune Nanoscale Circuit Design Using Coding-based Partial MRF Method" was accepted by IEEE Journal of Solid State Circuits    (15/05/2018)

"Low-Power Noise-Immune Nanoscale Circuit Design Using Coding-based Partial MRF Method" was accepted by IEEE Journal of Solid State Circuits Abstract:  Reliability is one of the major concerns for ultra-low power circuit designs. Markov Random Field (MRF) techniques have been applied to logic circuits to resist random noise when operating under ultra-low supply voltage or sub-threshold voltage. Although conventional MRF networks can be easily mapped onto simple logic circuits, it becomes difficult when the circuits are large and complex. In this paper, we present a general coding-based partial MRF (CPMRF) method for multi-logic operations in one basic unit, which is referred to as a CPMRF pair. A CPMRF pair saves circuit area by sharing a common MRF network. It also inherits noise immunity from the MRF theory while obtaining noise immunity complement from the coding structure as a combination of robust “1” and “0”. The resulting architectures become more cost-effective than the conventional one. To validate the performance of our proof-of-concept design, we fabricated a carry-lookahead adder implemented by the proposed CPMRF pairs using IBM 130nm CMOS technology. Measurement results indicate that the CPMRF CLA can achieve high noise-tolerance with 20% improvement while occupying 37.7% less area and reducing power consumption 93% compared with the Master-and-slave MRF CLA design.

Biosensor Workshop 2018    (02/05/2018)

Biosensor: Future and Scopes We are pleased to invite you to the Workshop of the "Biosensors: Future and Scopes" in University of Alberta, Edmonton, Alberta Aims: Healthcare Agri-food Environmental Security sectors Nanotechnology Water purification Innovation in Biomedical Engineering Market development Event Date: Thursday, 3rd May 2018 Registration if FREE Venue: East Solarium, ETLC, Faculty of Engineering, University of Alberta Food will be served To confirm RSVP at: aanwar@ualberta.ca

"Design of A Novel Wearable LIPUS Treatment Device for Mental Health Treatment" was accepted for publication in IEEE EMBC'2018    (28/04/2018)

"Design of A Novel Wearable LIPUS Treatment Device for Mental Health Treatment" by Shiang Qi, Yufeng Li, Wei Zhang and Jie Chen was accepted for publication in 40th Annual International Conference on the IEEE Engineering in Medicine and Biology Society, Hawaii, July 2018 Abstract—Low-intensity pulsed ultrasound (LIPUS) has been proven to be an effective treatment modality to improve bone fractures, soft tissue regeneration and neuromodulation. Recently, it has been shown for treating mental health diseases. In this paper, a novel wearable LIPUS treatment device, including a wearable headband and a LIPUS generator, is designed. The circuit in the LIPUS generator is specially built to generate LIPUS for stimulating the brain via temples. Considering comfortableness and safety, we designed a flexible cap to cover ultrasound transducer. The custom-made replaceable transducer cap can be refilled by different ultrasound coupling agents. We demonstrated how polyurethane rubber caps filled with different ultrasound coupling agents affect the ultrasound transmission intensity. Milli-Q water is identified to be the best ultrasound coupling agent for the polyurethane rubber cap with about 39.76% LIPUS intensity transmission. 

“Polyethylenimine-coated Iron Oxide Magnetic Nanoparticles for High Efficient Gene Delivery” was accepted by Applied Nanoscience    (15/04/2018)

Anh H. Nguyen, Gaser N. Abdelrasoul, Donghai Lin, Hamid Maadi, Junfeng Tong, Grace Chen, Richard Wang, Afreen Anwar, Lian Shoute, Qiang Fang, Zhixiang Wang and Jie Chen, “ Polyethylenimine-coated Iron Oxide Magnetic Nanoparticles for High Efficient Gene Delivery”, Applied Nanoscience (Accepted on April 7, 2018) Abstract: Properties of magnetic nanoparticles (MNPs) are of notable interest in many fields of biomedical engineering, especially for gene therapy. In this paper, we report a method for synthesis and delivery of MNPs loaded with DNAs, which overcomes the drawbacks of high-cost and cytotoxicity associated with current delivery techniques (chemical- and liposome-based designs). 24-nm MNPs (Fe3O4) were synthesized, functionalized and characterized by analytical techniques to understand the surface properties for DNA binding and cellular uptake. The simple surface functionalization with polyethylenimine (PEI) through glutaraldehyde linker activation gave the complex of PEI-coated MNPs, resulting in high stability with a positive surface charge of about + 31 mV. Under the guidance of an external magnetic field, the functionalized MNPs with a loaded isothiocyanate (FITC) or green fluorescent protein (GFP) will enter the cells, which can be visualized by the fluorescence of FITC or GFP. We also examined the cytotoxicity of our synthesized MNPs by MTT assay. We showed that the IC50s of these MNPs for COS-7 and CHO cells were low and at 0.2 and 0.26 mg/mL, res [ ... ]

Video: Point-of-care device for management of water quality assurance    (03/04/2018)

Video:  Point-of-care device for management of water quality assurance (you can download the video and play) Introduction: Nowadays, we are all bring exposed to environmental hazards at almost every point. There are various contributing factors to environmental hazards and one of the current major areas is that of biological hazards. The effect of these particular hazards is enormous, leading to loss of human productivity and eventually leading to overload of the public health budget. The expenditure of the management of enviromental biohazards includes, but is not limited to the collection and transportation of samples, bioanalysis using costly instruments and reagents, as well as treatment and health services. At this point, there is a need for an integrated system which could act as a portal detection device, or PDD, for monitoring bioenvironmental threats such as bacteria or any other pathogens, and at the same time provide accurate, fast, low cost and real time results. Over the past years, we have developed a portable impedance-based biosensing system, which consists of interdigitated electrodes with surface functionalized biorecognition elements, an impedance measurement board, and developed interfacing software. This biosensor setup is easy to use, requires fewer reagents, operates with minimal human interaction and delivers results with a targeted detection time of 20 minutes. Experimental Protocol:  1) We begin the experiment by cleaning th [ ... ]

“Feedback-based Low-Power Soft-Error Tolerant Design for Dual Modular Redundancy" was accepted by IEEE Transactions on Very Large Scale Integrated Systems     (13/03/2018)

Yan Li, Yufeng Li, Han Jie, Jianhao Hu, Fan Yang, Xuan Zeng, Bruce Cockburn and Jie Chen, “Feedback-based Low-Power Soft-Error Tolerant Design for Dual Modular Redundancy”, IEEE Transactions on Very Large Scale Integrated Systems (accepted March 13, 2018)
Abstract: Triple modular redundancy (TMR), which consists of three identical modules and a voting circuit, is a common architecture for soft-error tolerance. However, the original TMR suffers from two major drawbacks: the large area overhead and the vulnerability of the voter. In order to overcome these drawbacks, we propose a new complementary dual modular redundancy (CDMR) scheme for mitigating the effect of soft errors. Inspired by Markov random field (MRF) theory, a two-stage voting system is implemented in CDMR, including a first-stage optimalMRFstructureand a second-stage high-performance merging unit. The CDMR scheme can reduce the voting circuit area by 20% while saving the area of one redundant module, achieving at least 26% error rate reduction at an ultra-low supply voltage of 0.25 V with 8.33% faster timing compared to previousvoter designs. Keywords- Triple modular redundancy, Soft-error tolerance, Markov random field.

Invited talk in the session of “Multi-technologies-platforms: Advanced Sensors and Actuators for Life Science Applications”    (26/02/2018)

“Detecting Gold Nanoparticles Covalently Bound to Interdigitated Gold Electrode Substrates for Applications in Biosensing”, (invited talk in the session of “Multi-technologies-platforms: Advanced Sensors and Actuators for Life Science Applications”), 40th International Conference on the IEEE Engineering in Medicine and Biology Society, Honolulu, Hawaii, USA, July 17-21, 2018

Dr. Chen was elected as the Chair of Therapeutic Systems and Technologies Technical Committee, IEEE Engineering in Medicine and Biology Society (EMBS)     (13/02/2018)

Dr. Chen was elected as the Chair of Therapeutic Systems and Technologies Technical Committee, IEEE Engineering in Medicine and Biology Society (EMBS)

"Low Power Area-efficient DCT Implementation Based on Markov Random Field-stochastic Logic” was accepted by IEEE Symposium on Circuits and Systems 2018    (29/01/2018)

Yufeng Li, Yan Li, Deqiang Cheng and Jie Chen, “Low Power Area-efficient DCT Implementation Based on Markov Random Field-stochastic Logic”, IEEE Symposium on Circuits and Systems, Florence, Italy, May 27-30, 2018  Abstract:  Markov Random Field has been adopted to achieve high noise immunity for computing systems indeepsub-micron condition. However, complete MRF designs consume large area overhead, limiting its direct hardware implementation for one-dimensional discrete cosine transform. As a low-cost number representation, stochastic logic can efficiently simplify computing circuits. By combining the two techniques, we present an MRF-based gate group design in order to achieve area and power saving with high noise immunity for stochastic adders used in discrete cosine transform. To validate the performance of our design, we implement an 8-point one-dimensional discrete cosine transform system applied the proposed design in 65 nm CMOS technology. Simulation results show that the proposed design can achieve 7% higher noise-immunity with 31% area-saving for stochastic adders and 52% power-saving, compared with the previous area-saving Master-and-slave design. Theproposed design benefits outdoor sensors and biological portable devices dealing with image compression. 

Dr. Chen is spending his sabbatical at Yale University starting January 2018    (09/01/2018)

Dr. Chen is spending his sabbatical at Yale University starting Jan. 2018.

Chinese National Xinhua News Agency interviewed Dr. Jie Chen about his microfluidic-controlled point-of-care biosensor design    (29/12/2017)

Chinese National Xinhua News Agency interviewed Dr. Jie Chen about his microfluidic-controlled point-of-care biosensor design video file or you can download the video and play. 癌症 Cancer 早期诊断是一种专门针对癌症早期患者的诊疗方法 Early diagnosis aims to discover 目的在于早发现,早治疗 cancers at an early stage. 从而减轻患者的各项负担 Early intervention minimizes the patient burden and subsequent treatment expenses. Conversation: 很多的癌症 There are many types of cancers, 比如说直肠癌肺癌 for example, colorectal cancer, lung cancer, 还有就是胃癌 as well as stomach cancer. 这些通常(开始)检测 People often do not seek medical help 都是等病人都开始有症状(之后) until severe symptoms start to interfere with their daily lives 肺癌的话 Lung cancer, for instance, 当病人不断咳嗽 patients won’t go for medical exams 甚至咳嗽出血的时候病人才回去检测 until they start to cough blood 但是他通常检测的时候 However, when symptoms like this show up, 已经是三期到四期 patients are often diagnosed at third, even fourth stage lung cancer 通常都是到晚期的 At later-stages, 有些甚至已经开始扩散了 cancers are more likely to metastasize to different organs. 所以对这种来讲 If a cancer is diagnosed late, 就是非常的难以治愈 it becomes very difficult to treat. 所以我们目前来做 [ ... ]

IEEE EMBC 2018    (21/12/2017)

Our proposed session "Multi-technologies-platforms: Advanced Sensors and Actuators for Life Science Application" was accepted by the 40th Annual International Conference of IEEE Engineering in Medicine and Biolog Society, held in Honolulu, HI, USA  July 17-21, 2018

Increasing Vaccine Production Using Pulsed Ultrasound Waves    (18/11/2017)

"Increasing Vaccine Production Using Pulsed Ultrasound Waves" by Jida Xing, Shrishti Singh, Yupeng Zhao, Yan Duan, Huining Guo, Chenxia Hu, Allan Ma, Rajan George, James Z. Xing, Ankarao Kalluri, Isaac Macwan, Prabir Patra, and Jie Chen was accepted by PLOS ONE Abstract:  Vaccination is a safe and effective approach to prevent deadly diseases. To increase vaccine production, we propose that a mechanical stimulation can enhance protein production. In order to prove this hypothesis, Sf9 insect cells were used to evaluate the increase in the expression of a fusion protein from hepatitis B virus (HBV S1/S2).  We discovered that the ultrasound stimulation at a frequency of 1.5 MHz, intensity of 60 mW/cm2, for a duration of 10 minutes per day increased HBV S1/S2 by 27%. We further derived a model for transport through a cell membrane under the effect of ultrasound waves, tested the key assumptions of the model through a molecular dynamics simulation package, NAMD (Nanoscale Molecular Dynamics program) and utilized CHARMM force field in a steered molecular dynamics environment. The results show that ultrasound waves can increase cell permeability, which, in turn, can enhance nutrient / waste exchange thus leading to enhanced vaccine production. This finding is very meaningful in either shortening vaccine production time, or increasing the yield of proteins for use as vaccines. 

High-Efficiency Charge Pumps for Low-Power On-chip Applications    (03/11/2017)

Xiaoxue Jiang, Xiaojian Yu, Kambiz Moez, Duncan G. Elliott and Jie Chen, “High-Efficiency Charge Pumps for Low-Power On-chip Applications”, (invite paper). It was selected from 1000+ submitted proceeding papers to IEEE Symposium on Circuits and Systems, May 28-31, 2017, Baltimore, USA as one of the top-ranked articles. It was included in the special issue of IEEE Trans. on Circuits and System – TCAS-I. Abstract—This paper proposes charge pumps with improved power efficiency suitable for low-power on-chip applications. Undesired charge transfer, which has a direction opposite to that of the intended current flow, presents a significant source of power loss in charge pumps. The proposed charge pump circuit utilizes charge transfer switches with a complementary branch scheme to significantly reduce undesired charge transfer, thereby improving power efficiency and increasing output voltage effectively. An optimized gate control strategy is applied to further decrease the power loss caused by undesired charge transfer. Simulations of 8-stage charge pumps in a 0.13 um standard CMOS technology show that for an input supply voltage of 1.2 V, the proposed charge pump circuit reaches a power efficiency of 58.72% with an output voltage of 7.45 V when delivering 5 mA load current, and is able to maintain a power efficiency of around 50% and an output voltage of over 5 V as the load current increases  [ ... ]

According to the QS worldwide University ranking 2017-2018, the University of Alberta is ranked 90 (number 4 in Canada).    (21/10/2017)

According to the QS worldwide University ranking 2017-2018, the University of Alberta is ranked 90 (number 4 in Canada).

"Using Impedance Measurements to Characterize Surface Modified with Gold Nanoparticles" was published    (13/10/2017)

Our article "Using Impedance Measurements to Characterize Surface Modified with Gold Nanoparticles" was published in "Sensors"  Abstract:   With the increased practice of preventative healthcare to help reduce costs worldwide, sensor technology improvement is vital to patient care. Point-of-care (POC) diagnostics can reduce time and lower labor in testing, and can effectively avoid transporting costs because of portable designs. Label-free detection allows for greater versatility in the detection of biological molecules. Here, we describe the use of an impedance-based POC biosensor that can detect changes in the surface modification of a micro-fabricated chip using impedance spectroscopy. Gold nanoparticles (GNPs) have been employed to evaluate the sensing ability of our new chip using impedance measurements. Furthermore, we used impedance measurements to monitor surface functionalization progress on the sensor’s interdigitated electrodes (IDEs). Electrodes made from aluminum and gold were employed and the results were analyzed to compare the impact of electrode material. GNPs coated with mercaptoundecanoic acid were also used as a model of biomolecules to greatly enhance chemical affinity to the silicon substrate. The portable sensor can be used as an alternative technology to ELISA (enzyme-linked immunosorbent assays) and polymerase chain reaction (PCR)-based techniques. This system has advantages over PCR and ELISA both in the amount of time [ ... ]

Article "Efficient Memory Partitioning for Parallel Data Access in FPGA via Data Reuse", has been published on IEEE Xplore.    (21/09/2017)

Abstract—Parallelizing the memory accesses in a loop nest is a critical challenge to enable loop pipelining. An effective way to tackle this issue in high-level synthesis for FPGA is to map these accesses to multiple on-chip memory banks using memory partitioning technique. In this paper, we propose an efficient memory partitioning algorithm with low overhead and low time complexity for parallel data access via data reuse. We find that for most of the applications in image and video processing, a large amount of data can be reused among different iterations of a loop nest. Motivated by this observation, we propose to cache these reusable data by on-chip registers. The on-chip registers used to cache the re-fetched data can be organized as register chains. The non-reusable data are then partitioned into several memory banks by a memory partition algorithm. We revise the existing padding method to cover cases occurring frequently in our method that some components of partition vector are zeros. Experimental results have demonstrated that compared with the state-of-the-art algorithms, the proposed method is efficient in terms of execution time, resource overhead and power consumption for most of the access patterns extracted from applications in image and video processing. As for the testing patterns, the execution time is typically less than one millisecond. And the number of required memory banks is reduced by 59.7% on average, which brings in an average reduction [ ... ]

Undergrad researchers change the world    (07/09/2017)

Undergrad researchers change the world (PDF) Building a better biosensor (PDF)
http://www.engineering.ualberta.ca/NewsEvents/Engineering%20News/2017/July/NSERC%20Student%20Researchers%202.aspx Copyright belongs to University of Alberta Faculty of Engineering.

"Impact of Low-intensity Pulsed Ultrasound on Transcript and Metabolite Abundance in Saccharomyces cerevisae" was accepted by Journal of Proteome Research    (04/08/2017)

"Impact of Low-intensity Pulsed Ultrasound on Transcript and Metabolite Abundance in Saccharomyces cerevisae" was accepted by Journal of Proteome Research Abstract: The interactions of ultrasound with biological materials are exploited for diagnostic, interventional, and therapeutic applications in humans and can improve productivity in industrial-scale generation of organic molecules such as biofuels, vaccines, and antibodies. Accordingly, there is great interest in better understanding the biological eff ects of ultrasound. We studied the impact of low-intensity pulsed ultrasound (LIPUS) on RNA expression and metabolism of S. cerevisiae . Although the transcript expression signature of LIPUS-treated cells does not diff er signifi cantly from that of untreated cells after 5 days, metabolomic profi ling by chemical-isotopic-labeling− liquid-chromatography− mass-spectrometry suggests that LIPUS has an impact on the pathways of pyrimidine, proline, alanine, aspartate, glutamate, and arginine metabolism. Therefore, LIPUS triggers metabolic eff ects beyond reprogramming of the core pathways of carbon metabolism. Further characterization of metabolism will likely be important for elucidation of the biological eff ects of LIPUS.

Happy Canada Day (150 birthday of Canada)    (01/07/2017)

Today is July 1, 2017. It is 150 birthday of Canada. Happy Canada Day!

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Dr. Jie Chen