Thesis Title: "Design and Fabrication of Nanofluidic Devices via Semiconductor Techniques for Single-Molecule Sensing and Computing "

Name of the Student: Mr. Muhammad Sajeer P

Degree Registered: Ph.D. Engineering

Advisor: Prof. Manoj Varma, CeNSE

Date: 23rd January 2026, (Friday), 4 PM

Venue: CeNSE Seminar Hall 


Abstract
Nano- and angstrom-scale fluidic devices, including nanopores (0D), nanotubes (1D), and nano-slits (2D), 
are pushing the fundamental limits of single-molecule sensing. These confinement regimes allow for the 
precise investigation of ionic transport, enabling applications that range from next-generation sequencing 
to novel computational applications. While biological alternatives of these devices have received significant
 attention and widely used for next generation sequencing applications, their solid-state counterparts had 
limited growth. There have been several practical and technical challenges hindering these including lack 
of scalability and limitations of ionic current based sensing technique itself. This thesis addresses several 
of these challenges through a four-phase framework: Building, Improving, Applying, and Reflecting.

Phase 1 (Building) establishes a robust and optimized protocol for solid-state nanopore fabrication 
and characterization. By standardizing fabrication workflows, this work lowers the barrier to entry 
for nanopore research and enables reliable in-house device development.

Phase 2 (Improving) focuses on active control and advanced readout. On the device side, we 
demonstrate solid-state nanopores integrated with microheaters to achieve thermal modulation of 
ionic conductance. On the measurement side, we introduce "nanopore electrometry," a self-referenced 
readout technique. This method presents a robust alternative to traditional ionic current sensing and 
is validated through the discrimination of amino acids using Molecular Dynamics and Multiphysics simulations.

Phase 3 (Applying) transitions to 2D material-based nanofluid devices such as nano-slits and nanochannels. 
We establish ultramicrotomy as a scalable, high-throughput technique for fabricating MoS2 nano-slits towards 
single-molecule DNA topology studies. Furthermore, we utilize van der Waals (vdW) assembled hBN-MoS2 nanochannels 
to explore biomimetic protein dynamics and demonstrate their potential for computational applications.

Phase 4 (Reflecting) situates these technological advances within a broader societal context by examining 
the ethical, legal, and societal implications (ELSI) of nanopore sequencing technologies. This analysis highlights 
the need for inclusive governance, ethical foresight, and responsible innovation as these technologies transition 
from laboratory research to widespread public use.

Together, this work advances the scalability, functionality, and societal awareness of solid-state nanofluidic 
technologies, contributing to their maturation as platforms for both fundamental research and real-world applications.