gig em and go gators

Welcome to Jekyll!

2023-01-30T22:57:45-06:00

You’ll find this post in your _posts directory. Go ahead and edit it and re-build the site to see your changes. You can rebuild the site in many different ways, but the most common way is to run jekyll serve, which launches a web server and auto-regenerates your site when a file is updated.

Jekyll requires blog post files to be named according to the following format:

YEAR-MONTH-DAY-title.MARKUP

Where YEAR is a four-digit number, MONTH and DAY are both two-digit numbers, and MARKUP is the file extension representing the format used in the file. After that, include the necessary front matter. Take a look at the source for this post to get an idea about how it works.

Jekyll also offers powerful support for code snippets:

def print_hi(name)
  puts "Hi, #{name}"
end
print_hi('Tom')
#=> prints 'Hi, Tom' to STDOUT.

Check out the Jekyll docs for more info on how to get the most out of Jekyll. File all bugs/feature requests at Jekyll’s GitHub repo. If you have questions, you can ask them on Jekyll Talk.

Surface Functionalized Anodic Aluminum Oxide Membrane for Opto-Nanofluidic SARS-CoV-2 Genomic Target Detection

2021-09-01T00:00:00-05:00

Abstract

An ultra-thin and highly sensitive SARS-CoV-2 detection platform was demonstrated using a nano-porous anodic aluminum oxide (AAO) membrane. The membrane surface was functionalized to enable efficient trapping and identification of SARS-CoV-2 genomic targets through DNA-DNA and DNA-RNA hybridization. To immobilize the probe oligonucleotides on the AAO membrane, the pore surface was first coated with the linking reagents, 3-aminopropyltrimethoxysilane (APTMS) and glutaraldehyde (GA), by a compact vacuum infiltration module. After that, complementary target oligos with fluorescent modifier was pulled and infiltrated into the nano-fluidic channels formed by the AAO pores. The fluorescent signal applying the AAO membrane sensors was two orders stronger than a flat glass template. In addition, the dependence between the nano-pore size and the fluorescent intensity was evaluated. The optimized pore diameter d is 200 nm, which can accommodate the assembled oligonucleotide and aminosilane layers without blocking the AAO nano-fluidic channels. Our DNA functionalized membrane sensor is an accurate and high throughput platform supporting rapid virus tests, which is critical for population-wide diagnostic applications.

Keywords

AAO, biosensor, COVID-19, DNA, nanoporous

Citation

M. Makela, Z. Lin, P. T. Lin, “Surface Functionalized Anodic Aluminum Oxide Membrane for Opto-Nanofluidic SARS-CoV-2 Genomic Target Detection,” IEEE Sensors Journal, accepted.

Maths Example with Mathjax

2021-06-16T17:57:49-05:00

Below is an example of maths using mathjax.

Any page needing maths should start with the frontmatter:

usemathjax: true

\[\begin{align*} y = y(x,t) &= A e^{i\theta} \\ &= A (\cos \theta + i \sin \theta) \\ &= A (\cos(kx - \omega t) + i \sin(kx - \omega t)) \\ &= A\cos(kx - \omega t) + i A\sin(kx - \omega t) \\ &= A\cos \Big(\frac{2\pi}{\lambda}x - \frac{2\pi v}{\lambda} t \Big) + i A\sin \Big(\frac{2\pi}{\lambda}x - \frac{2\pi v}{\lambda} t \Big) \\ &= A\cos \frac{2\pi}{\lambda} (x - v t) + i A\sin \frac{2\pi}{\lambda} (x - v t) \end{align*}\]

Inline maths can be written with the \\( and \\) characters, producing inline maths such as \(\delta(t) \xrightarrow{\mathscr{F}} 1\).

The above is accomplished with thanks to Alan Duan and Zichen Vincent Zhang.

On Negativity

2021-03-11T00:00:00-06:00

The thought of sitting down to write coherently on this has been with me for a while now - a year or two maybe - but it’s really a topic that I’ve carried close for much of my ~20 years of aware life. Inspired by the relationships I’ve worn out, the people that continue to stick with me, and especially those willing to give me uncomfortable feedback sometimes… I’m sorry, thank you, I hear you, I’m working on it. My relationship with my own negativity (and inversely, gratitude!) is constantly growing and changing and I hope this collection of thoughts will too.

Photonic Chips for Miniaturized Raman and Mid-Infrared Spectrometers

2021-03-04T00:00:00-06:00

On-Chip Detection of SARS-CoV-2 DNA Targets Using Optofluidic Nano-Slot Waveguides

2021-03-01T00:00:00-06:00

Link here.

Abstract

Chip-scale SARS-CoV-2 testing was demonstrated using silicon nitride (Si3N4) nanoslot fluidic waveguides to detect a tagged oligonucleotide with a coronavirus DNA sequence. The slot waveguides were fabricated using complementary metal–oxide–semiconductor (CMOS) fabrication processes, including multiscale lithography and selective reactive ion etching (RIE), forming femtoliter fluidic channels. Finite difference method (FDM) simulation was used to calculate the optical field distribution of the waveguide mode when the waveguide sensor was excited by transverse electric (TE) and transverse magnetic (TM) polarized light. For the TE polarization, a strong optical field was created in the slot region and its field intensity was 14× stronger than the evanescent sensing field from the TM polarization. The nanoscale confinement of the optical sensing field significantly enhanced the light–analyte interaction and improved the optical sensitivity. The sensitivity enhancement was experimentally demonstrated by measuring the polarization-dependent fluorescence emission from the tagged oligonucleotide. The photonic chips consisting of femtoliter Si3N4 waveguides provide a low-cost and high throughput platform for real-time virus identification, which is critical for point-of-care (PoC) diagnostic applications.

Keywords

Genetics, Fluorescence, Chemical structure, Light, Waveguides

Citation

M. Makela, P. T. Lin, “On-Chip Detection of SARS-CoV-2 DNA Targets Using Optofluidic Nano-Slot Waveguides,” Analytical Chemistry, March 1, 2021.

Map Test with Mapbox

2021-01-25T00:00:00-06:00

Static Map

Auto-generated Mapbox map image from coordiantes in post front matter.

Light/dark mode map styling
~~Interactive map (vs. static)~~
Map layer polyline

Bringing Order to Chaos, 2021

2021-01-01T00:00:00-06:00

Beyond the obvious reasons, this year is a interesting one for me as it’s pretty much the first time since early high school that I am not in classes for credit/grades most of the year. Offically done with the coursework required for my degree - with only research and writing left, I’m interested to see how this list changes. Already there’s far less demand on scheduling and I’ve been able to be a lot more relaxed using my calendar. Still stand by time-blocking type methods and I group my tasks by topic and type of work, but find myself a lot less tethered to a tight schedule in order to function efficently like I have been for the last deacade or so. Odd but kind of nice? We’ll see how long it lasts.

Physical Things (I have sold my soul to Apple):

2020 13” MacBook Pro (2.3GHz Intel i7 processor, 16GB RAM, 512GB storage)
- HyperDrive 7-in-2 USB-C hub, because I miss all the ports on my old MacBook
24” monitor, one in the home office and one at work
iPhone 8 Plus in an OtterBox case
Apple Watch Series 4
Kindle Paperwhite
Beats Solo 3 and Powerbeats Pro wireless headphones

Incorperal Things:

Things 3
Bear
Obsidian
Apple/iOS Calendar
Apple/iOS Mail
Zotero
Parallels
Alfred
Spotify

Graduate and Professional Student Government Senator

2020-09-01T00:00:00-05:00

Welcome to Jekyll!

2020-08-28T21:29:20-05:00

Jekyll requires blog post files to be named according to the following format:

YEAR-MONTH-DAY-title.MARKUP

Jekyll also offers powerful support for code snippets:

def print_hi(name)
  puts "Hi, #{name}"
end
print_hi('Tom')
#=> prints 'Hi, Tom' to STDOUT.

Check out the Jekyll docs for more info on how to get the most out of Jekyll. File all bugs/feature requests at Jekyll’s GitHub repo. If you have questions, you can ask them on Jekyll Talk.