Laptop backup week 10? (for safety reasons)

8th-Semester-Spring-2025/biology/week-8/pre-lab-project-8/pre-lab-project-8.md

@@ -0,0 +1,3 @@
+A key concept from the video "The Action Potential" is how an impulse travels down an axon within a neuron. Initially, the voltage across the membrane is about -70mV. The impulse begins when potassium ions begin to leave the axon, and sodium ions enter. Then, once the potential approaches -55mV, sodium voltage gated channel open up, allowing sodium ions to rush into the axon, causing depolarization. As the voltage reaches 30mV, the sodium channels close and potassium voltage gated channels open. The potassium voltage-gated channels allow potassium ions to rush out of the cell, initiating repolarization. Importantly, for the signal to travel along the axon, the depolarization of one section initiates the depolarization of the next section in one direction.
+
+Once the sodium ions enter the cell and the potassium ions leave, how does the system reset to its initial state?

8th-Semester-Spring-2025/biology/week-8/thesis/Sharpe_TermProjectPart1.md

@@ -0,0 +1,11 @@
+---
+title: BIOL01113 Term Project Part 1
+author: Aidan Sharpe
+date: March 17th, 2025
+geometry: margin=1in
+---
+# Question
+Why are the pancreas, liver, and gallbladder called accessory organs of the digestive system?
+
+# Thesis Statement
+The pancreas, liver, and gallbladder are considered accessory organs because they do not directly process food and merely assist with digestion.

8th-Semester-Spring-2025/biology/week-8/vocab/Sharpe_VocabularyAssignment8.md

@@ -0,0 +1,36 @@
+---
+title: BIOL01113 Vocabulary Assignment 8
+author: Aidan Sharpe
+date: March 17th, 2025
+geometry: margin=1in
+---
+
+# Ingestion
+The act of taking in food.
+
+# Mechanical Digestion
+Breaking down food with mechanical force (chewing).
+
+# Chemical Digestion
+Breaking down food with chemicals.
+
+# Absorption
+The movement of a substance into a cell or through a membrane.
+
+# Esophagus
+The tube that transports food from the mouth to the stomach.
+
+# Stomach
+A sac-like organ that mixes food and gastric juices to perform chemical digestion.
+
+# Small Intestines
+The longer of the two intestines, responsible for absorbing most nutrients.
+
+# Colon
+The long tube structure of the large intestine, responsible for absorbing water.
+
+# Accessory Organs
+The accessory organs to the digestive system are pancreas, gallbladder, and liver, which are responsible for producing enzymes and chemicals to aid in metabolism.
+
+# Microbiome
+The collection of microbes living in the digestive tract that aid in the digestion process.

8th-Semester-Spring-2025/clinic-consultant/labs/lab-3/lab3q3.py

@@ -6,20 +6,32 @@ import matplotlib.pyplot as plt
 def u(n):
     return np.heaviside(n, 1)
 
-
+# Transfer function for an ideal lowpass filter
 def ideal_lowpass(omega, omega_c):
     return np.where(np.abs(omega) <= omega_c, 1, 0)
 
 
 def main():
-    omega_c = 0.4*np.pi
+    f_c = 0.4                                           # Cutoff frequency
-    omega = np.arange(0, np.pi, 0.05*np.pi)
+    omega_c = np.pi*f_c                                 # Angular cutoff frequency
+    omega = np.arange(0, np.pi, 0.05*np.pi)             # Frequency range
 
-    h_lpf = ideal_lowpass(omega, omega_c)
+    n = np.arange(-50, 51)                              # Sample range (100 samples centered at 0)
 
-    plt.plot(omega, h_lpf)
+    x = f_c*np.sinc(f_c*n)                              # Impulse resonse of ideal LPF
+    plt.stem(n,x)
     plt.show()
 
+    h_lpf = ideal_lowpass(omega, omega_c)               # Plot X(e^jw)
+    plt.plot(omega, h_lpf)
+    plt.xlabel("Frequency")
+    plt.ylabel("DTFT of Ideal Lowpass Filter")
+
+
+    for k in (10, 20, 30):                              # K values for truncated DTFT
+        w,h = sp.signal.freqz(x[50-k:50+k], 1, omega)   # Calculate truncated DTFT
+        plt.plot(omega, np.abs(h))                      # Plot magnitude of truncated DTFT
+    plt.show()
 
 if __name__ == "__main__":
     main()

8th-Semester-Spring-2025/clinic-consultant/labs/lab-3/lab3q5.m

@@ -1,12 +1,17 @@
+% First 100 samples
 for n=0:99
     y1(n+1) = (1 - (0.95)^(n+1))/0.05;
     y2(n+1) = n + 1;
 end
+
+% Plot output of system for input x[n] = 0.95^n u[n]
 figure(1)
 n=0:1:99;
 stem(n,y1)
 xlabel('n')
 ylabel('y(n)')
+
+% Plot output of system for input x[n] = u[n]
 figure(2)
 n=0:1:99;
 stem(n,y2)

8th-Semester-Spring-2025/clinic-consultant/labs/lab-3/lab3q5.py

@@ -0,0 +1,23 @@
+import numpy as np
+import scipy as sp
+import matplotlib.pyplot as plt
+
+def main():
+    n = np.arange(100)              # First 100 samples
+
+    y_1 = (1 - 0.95**(n+1))/0.05    # Output of system for input x[n] = 0.95^n u[n]
+    y_2 = n + 1                     # Output of system for input x[n] = u[n]
+
+    plt.stem(n, y_1)                # Plot y_1[n]
+    plt.xlabel("n")
+    plt.ylabel("y[n]")
+    plt.show()
+
+    plt.stem(n, y_2)                # Plot y_2[n]
+    plt.xlabel("n")
+    plt.ylabel("y[n]")
+    plt.show()
+
+
+if __name__ == "__main__":
+    main()

8th-Semester-Spring-2025/frontiers/references/10.1038_s41467-017-01104-3-citation.ris

@@ -0,0 +1,18 @@
+TY  - JOUR
+AU  - Al Ouahabi, Abdelaziz
+AU  - Amalian, Jean-Arthur
+AU  - Charles, Laurence
+AU  - Lutz, Jean-François
+PY  - 2017
+DA  - 2017/10/17
+TI  - Mass spectrometry sequencing of long digital polymers facilitated by programmed inter-byte fragmentation
+JO  - Nature Communications
+SP  - 967
+VL  - 8
+IS  - 1
+AB  - In the context of data storage miniaturization, it was recently shown that digital information can be stored in the monomer sequences of non-natural macromolecules. However, the sequencing of such digital polymers is currently limited to short chains. Here, we report that intact multi-byte digital polymers can be sequenced in a moderate resolution mass spectrometer and that full sequence coverage can be attained without requiring pre-analysis digestion or the help of sequence databases. In order to do so, the polymers are designed to undergo controlled fragmentations in collision-induced dissociation conditions. Each byte of the sequence is labeled by an identification tag and a weak alkoxyamine group is placed between 2 bytes. As a consequence of this design, the NO-C bonds break first upon collisional activation, thus leading to a pattern of mass tag-shifted intact bytes. Afterwards, each byte is individually sequenced in pseudo-MS3 conditions and the whole sequence is found.
+SN  - 2041-1723
+UR  - https://doi.org/10.1038/s41467-017-01104-3
+DO  - 10.1038/s41467-017-01104-3
+ID  - Al Ouahabi2017
+ER  - 

8th-Semester-Spring-2025/frontiers/references/achs_jacsat137_5629.bib

@@ -0,0 +1,38 @@
+
+
+
+
+
+
+
+
+
+@article{doi:10.1021/jacs.5b02639,
+author = {Al Ouahabi, Abdelaziz and Charles, Laurence and Lutz, Jean-Fran{\c{c}}ois},
+title = {Synthesis of Non-Natural Sequence-Encoded Polymers Using Phosphoramidite Chemistry},
+journal = {Journal of the American Chemical Society},
+volume = {137},
+number = {16},
+pages = {5629-5635},
+year = {2015},
+doi = {10.1021/jacs.5b02639},
+    note ={PMID: 25851514},
+
+URL = { 
+    
+        https://doi.org/10.1021/jacs.5b02639
+    
+    
+
+},
+eprint = { 
+    
+        https://doi.org/10.1021/jacs.5b02639
+    
+    
+
+}
+
+}
+
+

8th-Semester-Spring-2025/frontiers/references/acs.macromol.5b00890.ris

@@ -0,0 +1,24 @@
+
+
+
+
+TY  - JOUR
+T1  - Coding Macromolecules: Inputting Information in Polymers Using Monomer-Based Alphabets
+AU  - Lutz, Jean-François
+Y1  - 2015/07/28
+PY  - 2015
+DA  - 2015/07/28
+N1  - doi: 10.1021/acs.macromol.5b00890
+DO  - 10.1021/acs.macromol.5b00890
+T2  - Macromolecules
+JF  - Macromolecules
+JO  - Macromolecules
+SP  - 4759
+EP  - 4767
+VL  - 48
+IS  - 14
+PB  - American Chemical Society
+SN  - 0024-9297
+M3  - doi: 10.1021/acs.macromol.5b00890
+UR  - https://doi.org/10.1021/acs.macromol.5b00890
+ER  - 

8th-Semester-Spring-2025/frontiers/references/siam_140962486.bib

@@ -0,0 +1,35 @@
+
+
+
+
+
+
+@article{doi:10.1137/140962486,
+author = {Acharya, Jayadev and Das, Hirakendu and Milenkovic, Olgica and Orlitsky, Alon and Pan, Shengjun},
+title = {String Reconstruction from Substring Compositions},
+journal = {SIAM Journal on Discrete Mathematics},
+volume = {29},
+number = {3},
+pages = {1340-1371},
+year = {2015},
+doi = {10.1137/140962486},
+
+URL = { 
+    
+        https://doi.org/10.1137/140962486
+    
+    
+
+},
+eprint = { 
+    
+        https://doi.org/10.1137/140962486
+    
+    
+
+}
+,
+    abstract = { Motivated by mass-spectrometry protein sequencing, we consider the problem of reconstructing a string from the multisets of its substring composition. We show that all strings of length 7, one less than a prime and one less than twice a prime, can be reconstructed uniquely up to reversal. For all other lengths, we show that unique reconstruction is not always possible and provide sometimes-tight bounds on the largest number of strings with given substring compositions. The lower bounds are derived by combinatorial arguments, while the upper bounds follow from algebraic approaches that lead to precise characterizations of the sets of strings with the same substring compositions in terms of the factorization properties of bivariate polynomials. Using results on the transience of multidimensional random walks, we also provide a reconstruction algorithm that recovers random strings over alphabets of size \$\ge4\$ from their substring compositions in optimal near-quadratic time. The problem considered is related to the well-known turnpike problem, and its solution may hence shed light on this longstanding open problem as well. }
+}
+
+

8th-Semester-Spring-2025/rapid-prototyping/clock-breadboard/citations.bib

@@ -0,0 +1,26 @@
+@manual{CD4073BE,
+	organization = {Texas Instruments},
+	url = {https://www.ti.com/lit/ds/symlink/cd4081b.pdf?ts=1741984790984&ref_url=https%253A%252F%252Fsearch.brave.com%252F},
+	title = {CMOS AND Gates},
+	number = {CD4073B, CD4081B, CD4082B},
+	month = {September},
+	year = {2003}
+}
+
+@manual{INND-TS30,
+	organization = {Inolux},
+	url = {https://www.inolux-corp.com/datasheet/Display/Through-Hole-Display/SingleDigit/INND-TS30%20Series_V1.0.pdf},
+	title = {INND-TS30 Series 0.3” Through Hole Single Digit Display},
+	number = {INND-TS30},
+	month = {July},
+	year = {2017}
+}
+
+@manual{CD4026BE,
+	organization = {Texas Instruments},
+	url = {https://www.ti.com/lit/ds/symlink/cd4026b.pdf},
+	title = {CMOS Decade Counters/Dividers},
+	number = {CD4026B, CD4033B},
+	month = {July},
+	year = {2003}
+}

8th-Semester-Spring-2025/rapid-prototyping/clock-breadboard/clock-breadboard.md

@@ -0,0 +1,66 @@
+---
+title: Project 2A - Clock Breadboard
+subtitle: ECE09402 - Rapid Prototyping and Fabrication
+author:
+	- Aidan Sharpe (916373346)
+	- Michelle Frolio
+	- Karl Dyer
+date: March 14th, 2025
+geometry: margin=1in
+bibliography: citations.bib
+---
+
+\newpage
+
+# Introduction
+The goal of this project is to prototype a single digit from a seven segment display-based digital clock. Once functionality is verified, the circuit will be adapted for a printed circuit board (PCB).
+
+# Design Requirements
+1. Display brightness shall be the same regardless of the digit being displayed
+2. The digit shall be incremented with a momentary switch
+	a. The output of the momentary switch shall be debounced
+3. The digit shall support rolling over from 9 to 0
+4. The digit shall also support rolling over from 5 to 0
+5. The display shall be an INND-TS30RCB
+6. The display shall be driven with a CD4026BE decade counter
+7. The design shall utilize a CD4073BE three-channel, three-input AND gate
+
+# Results
+The final breadboard layout configured for rolling over from 5 to 0 is seen in the figure below. The wire colors represent the following:
+
+* Red: +5v
+* Black: ground 
+* Purple clock input
+* Yellow: roll over logic inputs to the AND gate (segments E, F, G)
+* Blue: display driver and AND gate outputs
+* White: button output
+
+
+To switch to 9 to 0 roll over mode, the diode (highlighted as D1 below) should be removed, and the reset pin (pin 15) of the CD4026BE should be tied to ground [@CD4026BE].
+
+![Final circuit top view](./diode.png){width=100%}
+
+In this mode, the system was tested with a signal generator set up to output a 50% duty cycle, 1Hz, 5v square wave. The signal generator setup is seen below.
+
+![Signal generator setup](./sig-gen.png){width=50%}
+
+Momentary switches can bounce when pressed or released, which has the effect of multiple pulses. In the case of this design, the bouncing of the button will cause CD4026BE to count multiple times. This behavior is undesirable, but can be resolved with a de-bouncing circuit. The de-bounce circuit implemented is simply a low pass filter with a pull down resistor to discharge the capacitor. The final design is seen in figure \ref{fig:debounce}.
+
+![Debounce schematic \label{fig:debounce}](./debounce.png){width=50%}
+
+![](./5to0roll.mp4)
+
+![](./9to0roll.mp4)
+
+# Reflection
+Integrated circuits such as the INND-TS30 seven segment display with a 300mil spacing between the inline pins must be bent to fit into the breadboard [@INND-TS30]. Bending the pins in this way makes it very easy for the IC to pop out or to make poor electrical contact with the breadboard.
+
+Planning ahead is critical to breadboarding. In this case, I planned out the best orientations of the seven segment display with respect to its driver. Importantly, the pins on the driver [@CD4026BE] are not in the same order or always on the same side of the IC as the display [@INND-TS30].
+
+We also learned that sometimes devices do not behave as expected. The CD4073BE that was originally distributed was part of a faulty batch. The expected behavior is that when pins 11, 12, and 13 are logic high, pin 10 is also logic high [@CD4073BE]. During our testing, we noticed that the faulty chips did not exhibit this behavior, with the output remaining low regardless of the input state. Unfortunately, these issues are difficult to debug and can really only be remedied with a different batch of parts.
+
+Finally, we learned that there are a lot of first order RC low-pass filter topologies for the debounce circuit. We used the design in figure \ref{fig:debounce} as it debounced on both the rising and falling edges. The initial design we implemented only debounced the falling edge, but during testing, the rising edge would sometimes trigger multiple clock pulses.
+
+\newpage
+
+# References