Biology subjects

Sahin, M. A.

Publications and source records attributed to Sahin, M. A..

6 recordsLinked to original sources

bioRxiv2026

Lab on a Capillary: Instrument-Free Compartmentalization Using Photopatterned Hydrogel Rings Embedded inside a Glass Capillary for Amplified Bioassays

Sensitive and low-cost protein biomarker detection is critical for disease diagnosis. Advanced microfluidic systems can generate miniature reaction compartments for a high-sensitivity assay. However, these platforms often require external instruments, skilled operators, and complex setups. Here, we develop a Lab on a Capillary (LabCap) platform that integrates photopatterned hydrogel rings within a glass capillary using a reconfigurable stop-flow lithography system. During sample loading and unloading steps, nanoliter-scale aqueous droplets (torodrops) are spontaneously formed around the hydrogel rings, creating isolated reaction compartments without the need for external instruments or an immiscible oil phase. The LabCap platform enables quantitative detection of clinically relevant biomarkers, including C-reactive protein (CRP) and N-terminal pro-B-type natriuretic peptide (NT-proBNP). By adjusting the incubation protocol, assay speed and sensitivity can be tuned to meet different analytical requirements. A periodic medium exchange protocol enables biomarker detection at concentrations as low as 1 ng/mL, whereas prolonged static incubation extends detection to 0.1 ng/mL. In addition, LabCap offers practical advantages, including low fabrication cost (<{euro}1 per device), low reagent consumption (<100 L per assay step), and minimal wash-buffer usage (1 mL). These results demonstrate that LabCap is a simple, cost-effective, and versatile platform for biomarker detection.

bioengineering↗

bioRxiv2026

Acoustofluidic Active Flow Sculpting Enables Dynamic, Reconfigurable Cross-Sectional Patterning

Soft materials created with flow lithography exhibit distinct functionality depending on the shape and material composition of the precursor fluids, enabling applications ranging from tissue engineering to anti-counterfeiting. However, current manufacturing techniques largely rely on static nozzle geometries or passive hydrodynamic focusing, which commit to a fixed structure during fabrication and limit the ability to actively reconfigure material architecture in continuous flow. Here, we introduce ActiSculpt, an acoustofluidic platform that replaces physical constructions with dynamic, programmable, non-invasive elements to configure the continuous flow. By exploiting the interplay between laminar stability and acoustic streaming, we decouple deterministic fluid deformation from chaotic mixing, enabling the precise sculpting of cross-sectional flow structures. We demonstrate the high-throughput generation of a diverse library of hydrogel particles with continuously tunable moments of inertia. We further demonstrate continuous fiber fabrication in which acoustic parameters are varied in real time, using temporal control to encode structural variation along the fiber's length. Finally, we translate this platform into a motion-controlled 3D printer, establishing printability of fully-curable and half-curable fiber configurations and confirming that acoustically programmed cross-sections, along with their capacity for multi-fiber structural assembly, are preserved in the printed output. The result is a platform that overcomes the one-device, one-geometry constraint of existing techniques, enabling not only on-demand reconfiguration between fabrication runs but real-time control of material architecture within a single continuous flow, extending from bench-scale characterization to an operating additive manufacturing process. This spatiotemporal control establishes a new design axis for engineering soft materials with programmable mechanical and functional properties.

bioengineering↗

bioRxiv2025

3D Hydrodynamic Flow Lithography

Continuous- and stop-flow lithography has been widely used for the fabrication of ingenious multi-dimensional microstructures, including fibers and microparticles. The flow profile of multiple co-flowing streams during the process, as one of the dimensions, dictates the cross-sectional morphology of the microstructures. Here, we introduce a three-dimensional hydrodynamic flow lithography (3D HFL) approach that enables rapid and programmable generation of desired flow profiles and their conversion into solid microstructures. By strategically combining multiple flow sculpting strategies, including variable inlet configurations, intra-channel pillar configurations, and outlet configurations, we achieved precise and versatile control over flow sculpting, as validated by computational fluid dynamics simulations and experimental production of microparticles and fibers, offering unparalleled design flexibility. Importantly, the flow sculpting device is fabricated using low-cost 3D-printed molds to cast PDMS channels with precisely aligned inlets and complex geometries that are difficult or impossible to achieve using conventional soft lithography. Our 3D HFL approach effectively overcomes the limitations of existing microfabrication techniques in device complexity, structural diversity, multi-material integration, and production throughput. Furthermore, we demonstrated the capability of this platform to produce anisotropic multi-material microparticles and fibers tailored for specific applications, such as amphiphilic particles for uniform microdroplet capture, biocompatible patterned hydrogels for controlled cell adhesion, and dual-layer fibers for temperature sensing. The simplicity of device fabrication, combined with the broad design flexibility, establishes this platform as a scalable, high-throughput, and versatile solution for engineering anisotropic microparticles and fibers with tailored functionalities, providing powerful tools for a wide range of downstream fields.

bioengineering↗

bioRxiv2024

Spatiotemporal control of a multilayered co-axial flow in a 3D printed microchannel with cascaded nozzles

Sculpting and stopping multilayered co-flowing streams is challenging due to inhomogeneous pressure distribution within a fluidic circuit composed of multiple interconnected microchannels having variable flow resistances. Here, we have investigated three different flow control methods to effectively stop a multilayered flow inside a 3D-printed microfluidic channel by bringing the average flow velocity from >100 mm s-1 to below a critical velocity of 200 {micro}m s-1 within a certain delay time tD of [~]2s. Firstly, we 3D printed a sequence of three concentric nozzles ([~]75 {micro}m) embedded serially inside the microchannel ([~]200 {micro}m) using a two-photon polymerization (2PP) method. Secondly, we used the 2PP-based 3D printed device to produce a structured coaxial flow of four streams with individual layer thicknesses of O(10 {micro}m) within the outlet section of the microchannel. Thirdly, we removed the pressure gradient across the fluidic circuit, from > 2 bar to [~]0 bar, to stop the multilayered flow and measured tD to assess the performance of the three stop flow methods. During the stop-flow phase, an inhomogeneous pressure gradient across different inlets resulted in a backflow to inlet channels with lower pressures. In the three stop-flow methods investigated, we systemically managed the fluidic capacitance to minimize a dimensionless backflow index (BFI) value from [~]0.3 (worst case) to [~]0.03 (best case) for a total flow rate ranging from 16.8 {micro}l min-1 to 168 {micro}l min-1. Finally, we have recommended the best stop-flow conditions, which resulted in a minimal delay time of tD [~] 2s and a BFI < 0.05.

bioengineering↗

bioRxiv2024

Tunable picoliter-scale dropicle formation using amphiphilic microparticles with patterned hydrophilic patches

Microparticle-templated droplets or dropicles have recently gained interest in the fields of diagnostic immunoassays, single-cell analysis, and digital molecular biology. Amphiphilic particles have been shown to spontaneously capture aqueous droplets within their cavities upon mixing with an immiscible oil phase, where each particle templates a single droplet. Here, we fabricated an amphiphilic microparticle with four discrete hydrophilic patches embedded at the inner corners of a square-shaped hydrophobic outer ring of the particle (4C particle). 3D computational fluid dynamics simulations predicted droplet formation dynamics and differing equilibrium conditions depending on the patterning configuration. Experiments recapitulated equilibrium conditions enabling tunable dropicle configurations with reproducible volumes down to [~]200pL templated by the amphiphilic particles. The dropicle configurations depended predominantly on the size of the hydrophilic patches of the 4C particles. This validated modeling approach can inform the design of dropicles with varying volumes and numbers per particle, which can be harnessed in new amplified bioassays for greater sensitivity, dynamic range, and statistical confidence.

bioengineering↗

bioRxiv2023

Fabrication of size-coded amphiphilic particles with a configurable 3D-printed microfluidic device for the formation of particle-templated droplets

Compartmentalizing an aqueous media into numerous nanoliter-scale droplets has substantially improved the performance of amplification assays. Particle-templated droplets or dropicles offer a user-friendly workflow for creating uniform volume compartments upon simple mixing of reagents and particles by using common laboratory apparatus. Amphiphilic shape-coded particles have been demonstrated to spontaneously hold aqueous droplets within hydrophilic cavities for multiplexed diagnostic assays. Here, we have proposed a configurable 3D-printed microfluidic device for the tunable fabrication of amphiphilic size-coded particles. The device was configured with multiple outlet tubings of different diameters and photomasks of variable slit lengths to fabricate a wide range of size-coded particles. We have fabricated >10 unique particle codes using a single reconfigurable device. The cross-sectional profile of the particles was further engineered by tuning the flow rate ratios of precursor streams to vary the inner and outer diameters of the particles and the thicknesses of the inner hydrophilic and outer hydrophobic layers. A range of cavity diameters and particle lengths enabled dropicle volumes of [~]1nL to [~]30nL. The fabricated particles were characterized by their ability to hold uniform droplet volumes and to orient themselves facing upwards or sideways in a well plate based on their aspect ratios.

bioengineering↗