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Our Work
The SParK Lab aims to tackle real-world problems with simplest and easily implementable biochemistry solutions, engineered to work in the most efficient ways.
Details about the Ongoing Projects
Biomolecular Engineering for Critical Mineral Recovery
There is a growing need for rare earth elements (REEs) due to their widespread use in diverse industries such as electronics, catalysis, magnets, batteries, glass, and phosphors. India possesses the world’s most extensive shoreline heavy mineral placer deposits, spanning over 6000 km. Although the country holds substantial reserves of REEs, the key challenge lies in obtaining highly pure elements through conventional, often non-sustainable, extraction processes.
Current technologies involved in the separation of REEs from a mixture of various ions include:
(1) Solvent Extraction, (2) Ion Exchange, (3) Precipitation and (4) Membrane separation.
Although effective these processes are capital heavy, require large amounts of toxic and hazardous waste, including organic solvents that can pose significant environmental risks. There is a clear need to develop technologies that can overcome the above mentioned limitations.
The group is designing peptides that selectively bind and separate REEs from mixtures of ions. Peptides are attractive ligands because they exhibit a broad range of physicochemical properties even with relatively short amino acid sequences (typically fewer than 20 residues), allowing their selectivity to be finely tuned for specific REEs. Moreover, peptides are biodegradable and do not introduce toxic by-products into the environment. Advances in peptide synthesis and genetic engineering further enable the production of tailored peptides with desired binding properties in a straightforward and cost-effective manner.
A Synthetic Biology Approach to Design Next-Generation Biopolymers
The group’s research focuses on developing sustainable, protein-based materials that can serve as next-generation alternatives to petroleum-derived plastics. By strategically engineering proteins with site-specific amino acid mutations—particularly involving cysteine residues—the lab constructs covalently crosslinked, biodegradable hydrogels and coatings with tunable mechanical strength and customized functionality.
These designer protein networks combine the robustness and versatility of synthetic polymers with the advantages of biodegradability and environmental compatibility. Additionally, by integrating selective metal-ion sequestration capabilities, the materials can address pressing challenges such as water contamination and scarcity. Through this synthetic biology-driven approach, the lab aims to create environmentally responsible biomaterials that unite the principles of biotechnology, molecular engineering, and sustainable material science.
Synthetic Biology Driven Melanin Deposition for Wood Coating
Wood is inherently strong, lightweight, and renewable, making it one of the most versatile materials in construction and design. However, conventional coloring and coating techniques typically rely on resource-intensive and environmentally harmful synthetic chemicals.
To create a sustainable alternative, the group is developing a bioinspired technique that utilizes living systems to directly generate natural melanin pigment coatings on wood surfaces. The resulting melanin layer not only enhances aesthetic appeal but also improves moisture retention and imparts photothermal responsiveness, all while preserving the wood’s compressive strength.
This integration of synthetic biology with materials science opens new opportunities for eco-friendly, functional wood coatings in sustainable architecture, interior design, and thermal management applications.
On-Demand Manufacturing of Proteins through Light-Activated Molecular Purification (LAMP)
This research aims to develop a device-based system that integrates synthetic biology techniques, cell-free protein synthesis, and a light-stimulated purification method known as LAMP (Light-Activated Molecular Purification).
Cell-free systems employ flash-frozen crude cell lysates combined with essential additives (energy sources, amino acids, nucleotides, and cofactors) and a DNA template to produce proteins within hours. The in-house LAMP technique is designed to purify a wide range of proteins using a photocleavable tag, PhoCl1, which breaks upon exposure to ~405 nm light, thereby releasing the target protein from Ni-NTA resin.
The ultimate goal is to develop a continuous, automated device capable of producing proteins from frozen components and purifying them using light activation, enabling rapid and scalable on-demand protein manufacturing.
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Refining Peptide Design for Surface Binding
Solid-binding peptides (SBPs) are short amino acid sequences that exhibit strong affinity toward organic or inorganic surfaces, enabling surface modification without the use of harsh chemicals. This property is particularly valuable for applications such as biosensing, where high precision and specificity are essential for accurate detection.
The group adopts a computational approach to identify improved SBPs, addressing the limitations of traditional experimental screening methods that often introduce biases or miss peptides with strong binding affinities. The methodology involves conducting Molecular Dynamics (MD) simulations to model peptide–surface interactions within water-solvated environments, offering deeper insights into binding mechanisms and peptide conformational behavior.
Through this approach, the lab seeks to advance the rational design of peptide–surface interfaces for use in biosensors, catalysis, and nanomaterial development.
L-Cysteine Mediated Synthesis of Selenium Nanoparticles for Agricultural Enhancement
The formation of selenium nanosheets can be achieved through a simple and environmentally friendly chemical reduction process at room temperature, using L-cysteine as both a reducing and stabilizing agent. In this method, a selenium precursor such as sodium selenite is introduced into an aqueous solution of L-cysteine, followed by the addition of CTAB to promote thin-layer nanosheet formation.
The sulfhydryl (-SH) group of L-cysteine facilitates the reduction of selenite ions (Se⁴⁺) to elemental selenium (Se⁰). Simultaneously, L-cysteine molecules bind to the surface of the forming selenium particles via their carboxyl and amino groups, acting as a soft template that prevents aggregation and controls size and morphology, resulting in stable nano-selenium structures.
These engineered selenium nanomaterials show great promise in agricultural applications, particularly for biofortification—enhancing the selenium content of crops—and improving plant stress tolerance due to selenium’s vital role in antioxidant defense and overall physiological health.
Studying Fluorescent Peptide Aggregation Dynamics to Develop a Tag for Imaging Biomolecular Condensates
The project investigates the aggregation dynamics of fluorescent C-terminal peptide fragments, employing a suite of biophysical techniques to unravel their structure–function relationships. By integrating solvatochromism assays, Dynamic Light Scattering (DLS), and Circular Dichroism (CD) spectroscopy, we systematically characterize the spectral and structural properties of these peptides in a range of solvent environments. Insights from these studies are being leveraged to design and validate a novel fluorescent tag for the imaging of liquid-liquid phase separation (LLPS), enhancing our ability to visualize and quantify biomolecular condensates in complex biological systems.
De Novo Protein Design for Advancements in Material Sciences
The design of novel proteins with functions not yet observed in nature has become possible through de novo protein design. This research focuses on computationally designing proteins for diverse applications in material science, leveraging cutting-edge algorithms and machine learning models to create biomolecules with tailored properties.
Rare earth elements (REEs) are challenging to extract using conventional methods due to their environmental impact. As a sustainable alternative, biohydrometallurgy offers an eco-friendly approach to metal recovery. Naturally occurring proteins such as lanmodulin (LanM) exhibit high binding affinity toward lanthanides but lack specificity among individual elements. Through de novo protein design, it is possible to achieve selective and specific recognition of REEs, overcoming the limitations of naturally evolved systems.
The design principles are grounded in understanding amino acid propensities and higher-order protein structures. The typical workflow involves backbone generation using diffusion-based image models, followed by deep learning–driven sequence design and three-dimensional structure prediction of the generated proteins. This rational, computational design pipeline enables precise control at the side-chain level of each residue, thereby allowing fine-tuning of the protein’s structure and functionality.
Funding agencies
