Metabolizing Heartbreak Main Idea The day we broke up, I recorded my heartbeat. I have always been afraid to look back on those losses, sorrows, betrayals and pains. But each time I truly do, it gives me a sense of release about things that are not eternal. The memory of that heartbreak in my heart is like a bowl of Meng Po soup - when I truly face it, that part has gradually faded away. I began to think: Could this memory be turned into a ritual of food? I encoded that day’s heartbeat into an ATGC sequence, implanted it into probiotics, and let it enter my intestines. The stomach has always been an organ of emotion - when people feel nervous and anxious, it is always the first to react. If the memory I swallowed could be transformed into a calming substance there, helping me release and relax, and ensuring I never repeat the same mistakes - that would be the Meng Po soup in the sense of synthetic biology.
L-Protein Engineering The idea is to transform L-Protein into a self-stabilizing, autonomously localized structure, eliminating the need for DNAJ assistance. This will improve the stability of L-Protein. STEP 1 Gather Information about Lysis Protein /Sequence /DNAj Sequence / Conserved sites if any Known mutational effects from research
Subsections of Projects
Individual Final Project
Metabolizing Heartbreak
Main Idea
The day we broke up, I recorded my heartbeat.
I have always been afraid to look back on those losses, sorrows, betrayals and pains. But each time I truly do, it gives me a sense of release about things that are not eternal. The memory of that heartbreak in my heart is like a bowl of Meng Po soup - when I truly face it, that part has gradually faded away.
I began to think: Could this memory be turned into a ritual of food? I encoded that day’s heartbeat into an ATGC sequence, implanted it into probiotics, and let it enter my intestines. The stomach has always been an organ of emotion - when people feel nervous and anxious, it is always the first to react. If the memory I swallowed could be transformed into a calming substance there, helping me release and relax, and ensuring I never repeat the same mistakes - that would be the Meng Po soup in the sense of synthetic biology.
system logic
Mengpo Soup is an engineered probiotic system. Users record their heartbeats during a moment of emotional breakdown, and this heartbeat data is encoded into a DNA sequence and edited into the plasmid of E. coli Nissle 1917. This strain of bacteria carries a molecular sensing circuit: when the host re-enters a high-stress state, the concentration of norepinephrine in the gut increases, activating the sensing system. The heartbeat sequence begins to be transcribed into RNA, triggering the toehold switch to open, and the downstream GAD gene is expressed, producing GABA, making the body feel calm.
The Process
Encoding the Body: From Heartbeat to DNA
On March 29, 2026, 100 heart rate readings were recorded via Apple Watch across a single day — a day of personal significance. The data spans 12:21 to 22:45, with a several-hour gap in the middle that coincides with the most emotionally intense period of the day.
Step 1 — Modeling the rhythm
The heart rate data is fitted to a Simple Harmonic Motion equation:
x(t) = mean + A · cos(ωt + φ)
This treats the heartbeat as a biological oscillator, extracting three parameters that together describe the rhythm of that day:
∙ A = 24.46 BPM — the amplitude of emotional fluctuation
∙ ω = 0.2848 rad/hr — the frequency, corresponding to a full cycle of approximately 22 hours
∙ φ = −0.568 rad — the phase offset, shaped by the silence in the middle
The gap in recording is not treated as missing data. It is preserved in the model as a structural trace — embedded in the phase parameter as a period of arrested motion.
Step 2 — Quantization
Each parameter is normalized within a defined biological range and mapped to an integer between 0 and 255, using 8 bits of precision.
Step 3 — Binary to nucleotide
Each integer is converted to 8-bit binary. Every two bits are then translated into a nucleotide base:
00 → A
01 → T 10 → G
11 → C
The sequence
The three parameters produce a 12-base sequence:
TCCTAGTTGGA
Flanked by neutral spacers for biological stability:
AAAA TCCTAGTTGGA AAAA
Step 4 — Inserted into GFP
This sequence has been inserted into the non-coding region of a GFP reporter plasmid (pZE21-GFPaav, Addgene #26643), downstream of the rrnB T1 terminator — a location where it coexists with the fluorescent protein machinery without interfering with its function.
What this sequence holds
The encoding is fully reversible. Given only these 12 bases, the original SHM parameters can be reconstructed, and from them, the heart rate curve of that day can be redrawn.
The 22-hour cycle encoded in ω is not coincidental. It is the duration of the emotional arc of that day — from the peak at 12:29, through the silence, to the quiet of late evening. One oscillation. One day. One ending.
Group Final Project
L-Protein Engineering
The idea is to transform L-Protein into a self-stabilizing, autonomously localized structure, eliminating the need for DNAJ assistance. This will improve the stability of L-Protein.
STEP 1
Gather Information about Lysis Protein /Sequence /DNAj Sequence / Conserved sites if any Known mutational effects from research
Lysis Protein Sequence (UniProtKB ID: https://www.uniprot.org/uniprotkb/P03609/entry)
LS dipeptide: Positions 44 and 45 (Leucine-Serine) in the MS2 L protein are crucial.
Domain division: The L protein is divided into four domains. Domain 1 (N-terminus), while positively charged and important, is not essential for the cleavage function itself (primarily responsible for binding to the host chaperone protein DnaJ); while Domains 2 to 4 (C-terminal half), containing the LS motif, are the key components for performing the cleavage function.
Therefore, the design mainly focuses on the Domain 1 region and replaces the water-soluble amino acids in it to improve its hydrophobicity and make it stable to generate spontaneous folding.
STEP 2
Select an approach to make sequence variants
Plan 1: METRFPQQSQQTPASTNRRRPFKHEDYPCRRQQRSSTLLVLIFLAIFLSLFTNQLLLSLLEAVIRTVTTLQQLLT
Design Actions: According to the LLR score, the K mutation at position 50, changing to L, yields a score of 2.56. Replacing with L (leucine) significantly enhances the hydrophobic anchoring force at the Domain 2/4 junction. Changing the Y at position 39 to L, located in Domain 1, yields a score of 2.24. Y contains a polar hydroxyl group; replacing it with L makes the transmembrane helix purer and more stable.
Plan 1.5: METRFPQQSQQTPASTNRRRPFKHEDYPRRRQQRSSTLLVLIFLAIFLSLFTNQLLLSLLEAVIRTVTTLQQLLT
Design Actions: According to the LLR, the C mutation, changing to R, yields a score of 2.39.
Principle: Increasing positive charge enhances the protein’s autonomous attraction to the negatively charged cell membrane, thereby reducing dependence on DNAJ escort.
Plan 2: METRFPQQQQQTPASTNRRRPFKHEDYPRRRQQRSSTLLVLIFLAIFLSLFTNQLLLSLLEAVIRTVTTLQQLLT
Design Action: According to LLR, mutating S to Q results in a score as high as 2.39.
Principle: Increasing the rigidity of Domain 1 allows it to fold into a helical state.
