Individual Final Project

PiezoTone BioPatch

In Silico Peptide and DNA Construct Design for a Cutaneous Piezoelectric Biointerface

Figure 1

Figure 1. Cabrera, A. (2026f). Screenshot of later-stage construct visualization for piezoelectric biointerface design [Project documentation image]. GitHub.

Figure 2

Figure 2. Screenshot documenting a later project page or workflow visualization related to the synthetic biology and biointerface design process. Source: Cabrera (2026i).

Figure 3

Figure 3. Screenshot documenting the final or advanced project page visualization for the proposed piezoelectric biointerface workflow. Source: Cabrera (2026j).

1. Project Summary

A Synthetic Biology Approach to Piezoelectric Biomaterials for Soft Robotic Muscle Rehabilitation

I. Problem Statement

Muscle rehabilitation after stroke, spinal cord injury, or neuromuscular disease is complex.

Current electrostimulation tools are often coarse, relying on large impulses with limited adaptability.

Spasticity remains a major unresolved challenge: muscles are overactive and resist controlled movement.

Need: a gentle, adaptive, tissue-compatible interface that can modulate muscle tone and support recovery.

II. The Proposed Solution — Concept Overview

The proposed solution is a soft robotic wearable with a piezoelectric biomaterial interface.

The material sits between the device and the skin or muscle.

It can:

• Sense mechanical deformation
• Deliver targeted micro-electrical impulses
• Potentially sense temperature
• Provide vibrotactile feedback

Goal at this stage: muscle tone modulation, not full movement restoration.

III. The Material — Piezoelectric Biomaterials

What is piezoelectricity?
Piezoelectricity is the conversion between mechanical energy and electrical energy.

Biological piezoelectricity exists naturally in materials such as:

• Collagen
• Chitosan
• Bone
• Silk

This project proposes designing a synthetic piezoelectric protein by combining amino acid sequences from collagen and chitosan.

The material can be 3D printed, enabling layered device architectures, such as:

• A piezoelectric layer in contact with the skin
• Supporting or functional materials layered above

IV. The Biological Engineering — Plasmid Design

The biological engineering approach is to express the piezoelectric protein in E. coli using a synthetic construct.

Plasmid components

• Promoter, either constitutive or inducible
• Ribosome binding site, such as the Shine-Dalgarno sequence
• Target gene: piezoelectric protein sequence derived from collagen and chitosan
• Linker sequences
• Terminator

Tool used: Consensus / Benchling-style platform for sequence design.

Challenge: there is no existing validated plasmid for this specific piezoelectric construct. This makes the construct a novel contribution of the project.

V. Device Integration — Soft Robotics Interface

The soft robot provides the mechanical actuation, which may be:

• Pneumatic
• Hydraulic
• Cable-driven

The piezoelectric layer functions as the smart interface, converting robot movement into electrical signals delivered to the muscle.

Advantages over conventional electrostimulation

• Gentle, distributed impulses
• Conformability to body geometry
• Potential integration of sensing and actuation in one layer
• Possible sensing of pressure and temperature

Alternative delivery formats

• Patch
• Micro-injection
• Injectable hydrogel
• Implant

VI. Clinical Targets

Potential clinical targets include:

Spasticity

Modulating overactive muscle tone in conditions such as:

• Post-stroke spasticity
• Cerebral palsy
• Spinal cord injury

Muscle fatigue reduction

Supporting recovery during rehabilitation by reducing fatigue.

Muscle regeneration support

The material may act as a tissue scaffold while also providing stimulation.

Pelvic floor and fine motor applications

Highly customizable stimulation patterns could support applications requiring precise, localized modulation.

VII. Validation Plan

The validation plan includes:

• Confirm protein expression: SDS-PAGE gel electrophoresis
• Confirm protein identity: fluorescent protein tag, such as GFP, and western blot
• Quantify yield: protein quantification assay
• Characterize piezoelectric properties: measure electrical output under mechanical loading
• Future translation: progress from in vitro testing to in vivo evaluation

VIII. Challenges and Next Steps

Key challenges and next steps include:

• Completing the plasmid cassette, including promoter and terminator selection
• Selecting an appropriate E. coli strain for quaternary protein structure formation
• Translating the protocol from in vitro to in situ
• Customizing stimulation patterns according to patient needs and anatomy

IX. Conclusion

This project proposes a first step toward a biologically derived, 3D-printable piezoelectric interface for soft robotic rehabilitation devices.

The novelty lies in combining:

• Synthetic biology, through custom protein design
• Soft robotics, through wearable and compliant actuation

The near-term goal is to:

1. Prove the construct
2. Characterize the material
3. Demonstrate muscle tone modulation

PiezoTone BioPatch is an in silico synthetic biology and biomaterials project that explores the design of a modular peptide and DNA construct for a future cutaneous piezoelectric hydrogel patch. The long-term motivation is to support research on pathological muscle-tone modulation, especially in conditions where abnormal tone, stiffness, or spasticity limits upper-limb movement, comfort, range of motion, and participation in daily life.

The project does not claim to directly treat spasticity or to prove therapeutic efficacy at this stage. Instead, it focuses on designing a molecular interface that could later be incorporated into a soft hydrogel patch placed on the skin. This cutaneous approach is safer and more feasible than an implantable scaffold because it avoids direct subcutaneous or intramuscular placement.

The project combines a chitosan–fibrin hydrogel concept, a collagen-like piezoelectric-inspired peptide motif, and cell-interface motifs such as RGD and IKVAV. The designed peptide was translated into a DNA coding sequence, annotated in Benchling, codon-optimized for E. coli, and developed toward a simulated expression cassette for future recombinant production.

2. Problematic and Research Gap

Pathological muscle tone is a complex rehabilitation challenge. In neurological conditions such as stroke, spinal cord injury, cerebral palsy, or other neuromotor disorders, abnormal tone may affect comfort, mobility, joint range of motion, and functional independence.

Across current studies, the main gap is not simply that the elbow or limb cannot be “de-spastic.” The larger gap is that elbow tone modulation is often:

• not measured objectively;
• not individualized to specific muscles;
• not adapted to specific ranges of motion;
• not clearly linked to sustained functional improvement;
• not embedded in multimodal rehabilitation strategies;
• not clearly connected to patient comfort, participation, and daily life.

Therefore, the project starts from the following idea:

The major gap is not only the lack of techniques to change limb muscle tone, but the lack of integrated, mechanism-informed, and patient-centered strategies that distinguish different sources of tone, target both central and peripheral contributors, and connect local tone changes to meaningful functional outcomes.

Muscle rehabilitation after stroke, spinal cord injury, or neuromuscular disease is complex.

Current electrostimulation tools are often coarse, relying on large impulses with limited adaptability.

Spasticity remains a major unresolved challenge: muscles are overactive and resist controlled movement.

Need: a gentle, adaptive, tissue-compatible interface that can modulate muscle tone and support recovery.

3. Opportunity

Piezoelectric biomaterials are interesting for rehabilitation and tissue-interface research because they can convert mechanical deformation into electrical signals. Available studies show that piezoelectric biomaterials can support nerve regeneration, reduce muscle atrophy, and improve motor recovery in animal models through self-powered or ultrasound-triggered electrical stimulation.

However, there is still no direct evidence that these materials reduce human muscle spasticity or pathological tone in neurological disorders. Therefore, this remains an important research gap.

This project uses that gap as an opportunity to ask:

Can a biofunctional cutaneous piezoelectric interface be designed in silico as a future platform for studying localized neuromuscular stimulation and pathological muscle-tone modulation?

4. Project Question

The main research question is:

How can an in silico synthetic biology design be used to create a modular peptide and DNA construct for a cutaneous piezoelectric hydrogel patch with future relevance for pathological muscle-tone modulation?

This question connects:

• synthetic biology;
• peptide design;
• DNA construct design;
• biomaterials;
• hydrogel patch design;
• piezoelectric interfaces;
• neuromuscular rehabilitation.

5. Broad Objective

The broad objective of this project is to design, in silico, a DNA-encoded modular peptide that could functionalize a future chitosan–fibrin piezoelectric hydrogel patch for skin-contact neuromuscular stimulation research.

The project focuses on the molecular design stage, not on human testing.

6. Hypothesis

I hypothesize that a modular DNA-encoded peptide can be designed in silico to functionalize a chitosan–fibrin piezoelectric hydrogel patch, creating a skin-contact biointerface suitable for future studies of transcutaneous electroactive stimulation and pathological muscle-tone modulation.

7. Why a Cutaneous Patch?

The original concept considered a scaffold that could potentially interact with muscle or connective tissue. However, for implementation, a cutaneous patch is more feasible and safer as a first step.

A cutaneous patch would be placed on the skin rather than implanted under it.

Conceptually:

text Skin surface ↓ Soft adhesive or hydrogel contact layer ↓ Peptide-functionalized chitosan–fibrin hydrogel ↓ Piezoelectric or collagen-inspired material layer ↓ Flexible protective backing

References: Kamel, N. A. (2022). Bio-piezoelectricity: fundamentals and applications in tissue engineering and regenerative medicine. Biophysical Reviews, 14(3), 717–733. https://doi.org/10.1007/s12551-022-00969-z

Yogeswaran, N., Dang, W., Navaraj, W. T., Shakthivel, D., Khan, S., Polat, E. O., Gupta, S., Heidari, H., Kaboli, M., Lorenzelli, L., Cheng, G., & Dahiya, R. (2015). New materials and advances in making electronic skin for interactive robots. Advanced Robotics, 29(21), 1359–1373. https://doi.org/10.1080/01691864.2015.1095653

A related study demonstrated that biodegradable 3D piezoelectric scaffolds can deliver ultrasound-driven, wirelessly powered electrical stimulation and promote spinal cord injury repair in a rat model, supporting the relevance of piezoelectric biomaterials for regenerative neurorehabilitation (Chen et al., 2022).

Project Documentation Figures

The following screenshots document the development process of the synthetic sequence design, codon optimization, and plasmid-design workflow for the proposed piezoelectric biointerface construct.

Figure 4

Figure 4. Initial codon optimization and synthetic sequence design workflow for the proposed piezoelectric biointerface construct. Source: Cabrera (2026a).

Figure 5

Figure 5. Later stage of the sequence design workflow, including additional construct visualization or annotation. Source: Cabrera (2026b).

Figure 6

Figure 6. Refinement of the synthetic construct design and related sequence information. Source: Cabrera (2026c).

Figure 7

Figure 7. Continued development of the plasmid-design or sequence-design workflow. Source: Cabrera (2026d).

Figure 8

Figure 8. Updated design stage of the synthetic biology workflow for the biointerface construct. Source: Cabrera (2026e).

Figure 9

Figure 9. Final or later-stage visualization of the proposed construct design workflow. Source: Cabrera (2026f).

Figure 10

Figure 10. Additional stage of the project page or workflow for the proposed piezoelectric biointerface construct. Source: Cabrera (2026g).

Figure 11

Figure 11. Continued stage of the project page or workflow development. Source: Cabrera (2026h).

Project Title

Genetic Design of a Silk-Inspired Protein Module for Future Rehabilitation Biomaterials

SECTION 1: ABSTRACT

This project addresses a key challenge in wearable rehabilitation and soft robotics: many assistive devices still rely on rigid or non-biological materials that can limit comfort, adaptability, and integration with the body. Soft robotic systems offer a promising alternative, but there is still a gap in how biological material principles can be translated into programmable and manufacturable biomaterials for future wearable actuation. The overall objective of this project is to design and assemble a DNA construct encoding a protein-inspired material building block based on motifs from Bombyx mori silk fibroin and elastic protein domains, as a first step toward engineered biomaterials for soft rehabilitation devices.

The central hypothesis is that a genetically encoded silk-inspired or silk-elastin-like protein sequence can serve as a rational platform for future bio-derived films, fibers, or coatings with useful mechanical properties such as flexibility, resilience, and hierarchical assembly. To test this idea, the project will complete sequence design, codon optimization, plasmid planning, overlap design, Gibson Assembly, bacterial transformation, and clone validation. Methods include Benchling-based DNA design, PCR amplification, Gibson Assembly, E. coli transformation, colony screening, and sequence verification.

The expected outcome is a validated recombinant DNA construct that demonstrates the feasibility of integrating synthetic biology and protein design into a material-centered design workflow for future soft robotic textile applications. This project therefore functions as an enabling step between biomolecular design and the long-term development of adaptive rehabilitation wearables.

SECTION 2: PROJECT AIMS

Aim 1: Experimental Aim

The first aim of my final project is to design, assemble, and validate a recombinant DNA construct encoding a silk-inspired or silk-elastin-like protein module by utilizing Benchling for sequence design, codon optimization, PCR, Gibson Assembly, bacterial transformation, and colony validation workflows. This aim focuses on creating a feasible genetic starting point for future biomaterial development and demonstrates how DNA design can be incorporated into a design research process for rehabilitation-oriented material systems.

Aim 2: Development Aim

The second aim of the project is to express and characterize the engineered protein material after successful plasmid validation, including small-scale protein production, purification, and exploratory material formation into films, coatings, or fibers. A successful Aim 1 would enable the next stage of testing whether the designed sequence shows desirable material behaviors such as film formation, flexibility, and compatibility with textile substrates.

Aim 3: Visionary Aim

The third aim of the project is to contribute to a long-term vision in which genetically designed protein materials become programmable components of wearable soft robotic systems for rehabilitation. If fully realized, this concept could support a new class of biomaterial-based soft actuators or structural interfaces that are lighter, more adaptive, and more biologically integrated than many current rehabilitation devices.

SECTION 3: BACKGROUND

Background and Literature Context

Soft robotics for rehabilitation is a rapidly growing field because soft devices can better conform to the body and reduce joint misalignment compared with rigid systems. Textile-based and soft actuator approaches are especially promising because they offer comfort, safety, and better integration into everyday life. However, important material challenges remain, including durability, controllability, biocompatibility, and the ability to closely adapt to the body while maintaining function.

At the same time, silk fibroin is highly relevant for biomaterial design because it combines strength, flexibility, hierarchical organization, and biocompatibility. Silk-inspired materials have strong potential for biomedical engineering and wearable systems. Synthetic biology methods such as Gibson Assembly also provide a practical way to construct recombinant sequences that encode designed protein materials. Despite progress in soft robotics and silk-based biomaterials, the integration of DNA-level protein design into rehabilitation-oriented material design is still underexplored. This project addresses that gap by positioning genetic design as the starting point of a future material system for wearable rehabilitation.

Two Peer-Reviewed Research Citations Relevant to the Project

Citation 1:
Sanchez, V., Walsh, C. J., and Wood, R. J. Textile Technology for Soft Robotic and Autonomous Garments (2021).

This paper reviews how textile structures can function as robotic substrates rather than passive coverings. It shows that knitting, weaving, multilayer structures, and fiber orientation can contribute directly to sensing, actuation, and body-conforming performance in soft robotic garments. For this project, the paper is important because it supports the idea that future rehabilitation systems can benefit from material architectures inspired by biological systems, especially when movement and compliance are designed into the textile itself. It also helps justify why a biomaterial building-block approach could eventually feed into wearable actuator design rather than remaining purely molecular.

Citation 2:
Recent review literature on silk fibroin-derived biomaterials for biomedical applications.

This body of research explains that silk fibroin-derived materials are highly versatile for regenerative and biomedical uses because they offer favorable mechanical properties, processability, and biocompatibility. The literature also highlights future directions involving intelligent biomaterials, sensors, and wearable health applications. For my project, this supports the use of Bombyx mori silk fibroin as a model for designing recombinant or inspired protein materials that may later be translated into films, fibers, or interfaces for soft systems. It therefore provides a bridge between molecular material design and rehabilitation-oriented device thinking.

Novelty and Innovation

This project is innovative because it does not begin with the actuator as the primary design object. Instead, it begins with the genetic design of a material building block that could later support soft robotic and textile applications. Rather than only using existing elastomers or fabrics, it explores whether protein-inspired sequence design can become part of a material-centered workflow for rehabilitation technology. The work is also novel because it connects synthetic biology tools such as Gibson Assembly with a design research question rooted in biomaterials, soft robotics, and future wearable rehabilitation systems.

Why This Project Matters and What Impact It Could Have

This project matters because rehabilitation devices are often limited by discomfort, poor adaptability, and a mismatch between rigid engineered materials and the soft, dynamic nature of the human body. Soft robotics has improved this situation, but there is still a major barrier in developing materials that combine compliance, structure, biocompatibility, and designability in one platform. By exploring recombinant protein design inspired by silk fibroin and elastic domains, this project proposes an upstream strategy for creating future materials that are programmable at the sequence level.

If successful, this work could contribute to new scientific and technical capabilities in the design of biologically inspired fibers, coatings, or composite interfaces for rehabilitation systems. Beyond the immediate project, the approach could help expand synthetic biology into design-led biomaterial development, opening possibilities in wearable health, biomedical manufacturing, and adaptive assistive technologies. At a field level, achieving these aims could shift part of soft robotics research from selecting existing materials toward encoding material function directly into designed biological sequences.

Ethical Implications

This project raises ethical questions related to responsibility, beneficence, and care. Because it uses genetic design and cloning methods, even at a small and non-pathogenic laboratory scale, it must be conducted with care regarding biosafety, containment, and responsible communication. Another ethical issue is translational overclaim: it would be inappropriate to suggest that an early-stage recombinant material construct is already a safe rehabilitation technology for patients. There are also broader concerns about access and fairness. If protein-designed biomaterials eventually enable advanced rehabilitation devices, those technologies should not become available only to well-funded laboratories or privileged health systems.

To ensure the project is ethical, the experimental scope should be limited to standard non-pathogenic laboratory strains, non-harmful recombinant sequences, and institutionally approved cloning practices. The project should clearly state that this work is a foundational material-design study, not a clinical intervention. Potential unintended consequences include failed assumptions about expression, folding, or material behavior, as well as overestimating the translational relevance of silk-inspired sequences. Alternatives include using non-recombinant silk fibroin, commercially available biomaterials, or simulation-based design approaches if biological uncertainty becomes too high. Ethical conduct in this project therefore requires transparent reporting of uncertainties, proportional claims, and attention to long-term access, sustainability, and safety in future applications.

SECTION 4: EXPERIMENTAL DESIGN, TECHNIQUES, TOOLS, AND TECHNOLOGY

Experimental Hypothesis

A recombinant DNA construct encoding a silk-inspired or silk-elastin-like protein module can be rationally designed and assembled using Gibson Assembly, creating a validated genetic platform for future biomaterial development relevant to rehabilitation-oriented soft systems.

Detailed Experimental Plan

1. Define the design target and functional logic
   In the first half day, I will define the biological rationale for the construct: a short recombinant protein containing a silk fibroin-inspired repetitive domain and, optionally, an elastic motif to introduce flexibility.
   Expected result: a clear design brief linking sequence motifs to desired material behavior.

2. Select protein motif sources from literature
   Over half a day to one day, I will review silk fibroin sequence features from Bombyx mori and identify a simplified motif suitable for classroom-scale DNA design. If appropriate, I will compare this with elastin-like motifs such as VPGXG repeats as a complementary domain.
   Expected result: a shortlist of feasible amino acid motifs for construct design.

3. Draft the protein architecture
   Over half a day, I will choose a modular protein layout such as His-tag + linker + silk-inspired repeat block + optional elastin-like block + stop codon.
   Expected result: a protein design schematic with module order and approximate length.

4. Codon-optimize the DNA sequence for E. coli
   In half a day, I will use Benchling or a similar design platform to codon-optimize the sequence for bacterial expression while minimizing problematic repeats or secondary structures when possible.
   Expected result: a codon-optimized DNA sequence ready for synthesis or PCR-based assembly.

5. Choose an expression plasmid backbone
   In half a day, I will select an appropriate plasmid backbone already available in class or lab, ideally one with a bacterial promoter, antibiotic resistance marker, and affinity-tag compatibility.
   Expected result: a plasmid map and insertion strategy.

6. Design Gibson overlaps
   In half a day, I will design 20–40 bp overlapping homology regions between insert and vector so the construct can be assembled by Gibson Assembly.
   Expected result: finalized primer or fragment overlap plan.

7. Plan fragment generation strategy
   In half a day, I will decide whether the insert will be obtained by gene synthesis, ordered fragment, or PCR amplification from designed oligos or templates, depending on course resources.
   Expected result: a practical build strategy and reagent list.

8. Prepare DNA fragments by PCR
   Over one day, I will amplify the vector backbone and/or insert fragments using a high-fidelity polymerase such as Phusion in order to reduce sequence errors.
   Expected result: visible DNA bands of expected size after gel verification.

9. Purify amplified DNA fragments
   In half a day, PCR products will be cleaned using spin-column purification or gel extraction if nonspecific bands are present.
   Expected result: purified DNA fragments suitable for assembly.

10. Perform Gibson Assembly reaction
    In half a day, purified overlapping fragments will be combined in the Gibson Assembly reaction according to the recommended molar ratios.
    Expected result: assembled plasmid molecules containing the designed insert.

11. Transform assembled plasmid into competent E. coli
    In half a day plus overnight incubation, I will transform the assembly product into competent E. coli and plate the cells on selective agar.
    Expected result: antibiotic-resistant colonies indicating successful uptake of plasmid DNA.

12. Screen colonies by colony PCR
    Over half a day to one day, several colonies will be screened using primers flanking the insertion site to identify clones with the expected insert size.
    Expected result: one or more positive colonies with the correct amplicon length.

13. Miniprep positive clones
    In half a day, promising colonies will be grown in liquid culture and plasmid DNA will be isolated using a miniprep protocol.
    Expected result: purified plasmid DNA from candidate correct clones.

14. Sequence-verify the construct
    Over two to four days depending on turnaround time, I will submit the plasmid for Sanger sequencing to verify insert identity and reading-frame integrity.
    Expected result: confirmed plasmid sequence matching the designed construct.

15. Analyze construct quality and feasibility
    In half a day, I will compare the sequencing result against the original design and note any mutations, assembly issues, or repeat instability.
    Expected result: a validated final plasmid map and a build assessment.

16. Optional expression test
    If time allows, over one to two days I will run a small exploratory expression test in E. coli and evaluate crude lysate or SDS-PAGE evidence of a protein band at the expected size.
    Expected result: preliminary indication of whether the construct is compatible with bacterial expression.

17. Interpretation for biomaterial relevance
    In half a day, I will relate the verified construct back to the larger design question: how sequence-defined biological materials could eventually support films, fibers, coatings, or reinforcement elements for wearable soft systems.
    Expected result: a design-oriented conclusion rather than only a cloning result.

18. Document the workflow visually
    In half a day, I will prepare a figure showing sequence design, plasmid assembly, clone validation, and future material translation.
    Expected result: a clear workflow figure for the report and presentation.

Approximate Timeline

• Design and literature selection: 5 days
• Sequence planning, codon optimization, and overlap design: 5 days
• PCR, cleanup, and Gibson Assembly: 10 days
• Transformation and colony growth: 1 day theory
• Colony PCR and miniprep: 1 day theory
• Sanger confirmation: 2–4 days theory
• Optional expression test and interpretation: 1–2 days theory

Specific Methods, Tools, Technologies, and Concepts

• Benchling for DNA and plasmid design
• Codon optimization for bacterial expression
• High-fidelity PCR
• Gibson Assembly
• E. coli transformation
• Colony PCR
• Miniprep and Sanger sequencing
• Protein-inspired biomaterial design
• Silk fibroin motif abstraction from Bombyx mori
• Optional modular design using silk-elastin-like protein logic

Expected Overall Results

The most realistic expected result for this course is a bioispired output verified recombinant plasmid encoding a protein-inspired biomaterial module. A strong outcome would be a sequence-confirmed construct with correct assembly and a clear rationale for future expression and material testing. If expression screening is possible, an additional expected result would be preliminary evidence that the construct is compatible with bacterial production, although this would be considered a stretch goal rather than a requirement.