arXiv subjects

Kalyan Dasgupta

Publications and source records attributed to Kalyan Dasgupta.

8 recordsLinked to original sources

arXiv2026

Quantum Variational Approaches to the Maximum Independent Set Problem at Utility Scale

We study variational quantum algorithms for the Maximum Independent Set (MIS) problem on benchmark graphs of 64, 99, and 180 vertices. The Variational Quantum Eigensolver (VQE) and Quantum Approximate Optimization Algorithm (QAOA) are compared across SPSA and COBYLA optimizers at multiple circuit depths. A preprocessing pipeline comprising spectral graph reordering (via the Fiedler vector) and distance-based sparsification reduces circuit depth while preserving energy fidelity. Classical post-processing via history-guided bitstring correction and stepwise maximality extension recovers the exact MIS across all instances. With CVaR optimization, VQE with SPSArecovers up to 6 distinct MIS per run for the 64-node instance and up to 10 distinct MIS per run for the 99-node instance, sampling broadly from the optimal solution population. Repeated runs with different SPSA trajectories collectively enumerate a larger fraction of all MIS for each instance. For the 180-node instance, where standard approaches stall at size 14 (MIS is 15), we introduce ancilla-assisted superposition initialization: ancilla qubits prepare a uniform superposition over classically-found near-optimal solutions, and an excitation-preserving ansatz evolves this state while conserving Hamming weight. This novel construction enables quantum-parallel variational search over multiple seeds simultaneously, discovering the exact MIS where single-seed methods fail. The 180-qubit simulation represents, to our knowledge, the largest scale at which gate-based variational algorithms have solved MIS to optimality. Hardware validation on IBM Quantum hardware ibm_marrakesh confirms that converged simulator parameters transfer effectively to noisy quantum execution.

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arXiv2026

Hamiltonian-Guided Leverage Embedding: Robust Subspace Compression for Efficient QAOA Parameter Estimation

The Quantum Approximate Optimization Algorithm (QAOA) is a hybrid quantum-classical framework for combinatorial optimization on near-term quantum devices. A central bottleneck is the classical estimation of its variational parameters γ and β, which must be optimized over a high-dimensional, non-convex landscape corrupted by sampling noise. We observe that the classical feature matrices constructed from QAOA measurement samples exhibit pronounced low-rank structure, and exploit this property for noise-robust, reduced-dimension parameter search. We present the Hamiltonian-Guided Leverage Embedding (HGLE) algorithm - a hybrid pipeline that encodes low-energy quantum samples into a weighted Ising feature matrix and compresses it via leverage-score row sampling, provably preserving the dominant rank-rsubspace geometry. The compressed representation drives a classical trust-region loop for (γ, β) estimation at a fraction of the original cost. We provide formal guarantees for rank preservation and energy approximation error, and demonstrate robustness across problem types (Max-Cut, Maximum Independent Set) and graph topologies of varying density.

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arXiv2026

Accelerating De Novo Genome Assembly via Quantum-Assisted Graph Optimization with Bitstring Recovery

Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome assembly, which involves constructing an entire genome sequence from scratch without a reference genome, presents significant challenges due to its high computational complexity, affecting both time and accuracy. In this study, we propose a hybrid approach utilizing a quantum computing-based optimization algorithm integrated with classical pre-processing to expedite the genome assembly process. Specifically, we present a method to solve the Hamiltonian and Eulerian paths within the genome assembly graph using gate-based quantum computing through a Higher-Order Binary Optimization (HOBO) formulation with the Variational Quantum Eigensolver algorithm (VQE), in addition to a novel bitstring recovery mechanism to improve optimizer traversal of the solution space. A comparative analysis with classical optimization techniques was performed to assess the effectiveness of our quantum-based approach in genome assembly. The results indicate that, as quantum hardware continues to evolve and noise levels diminish, our formulation holds a significant potential to accelerate genome sequencing by offering faster and more accurate solutions to the complex challenges in genomic research.

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arXiv2025

Capturing Protein Free Energy Landscape using Efficient Quantum Encoding

Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is critical, as a protein's functionality is inherently linked to its final folded form. Misfolding can lead to severe diseases such as Alzheimer's and cystic fibrosis, highlighting the biological and clinical importance of understanding protein folding mechanisms. This work presents a novel turn based encoding optimization algorithm for predicting the folded structures of peptides and small proteins. Our approach builds upon our previous research, where our objective function focused on hydrophobic collapse, a fundamental phenomenon underlying the protein folding process. In this work, we extend that framework by not only incorporating hydrophobic interactions but also including all non bonded interactions modeled using the Miyazawa Jernigan potential. We constructed a Hamiltonian from the defined objective function that encodes the folding process on a three dimensional face centered cubic lattice, offering superior packing efficiency and a realistic representation of protein conformations. This Hamiltonian is then solved using classical and quantum solvers to explore the vast conformational space of proteins. To identify the lowest-energy folded configurations, we utilize the Variational Quantum Eigensolver implemented on IBM 133 qubit hardware. The predicted structures are validated against experimental data using root mean square deviation as a metric and compared against classical simulated annealing and molecular dynamics simulation results. Our findings highlight the promise of hybrid classical and quantum approaches in advancing protein folding predictions, particularly for sequences with low homology.

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arXiv2024

Encoding lattice structures in Quantum Computational Basis States

Lattice models or structures are geometrical objects with mathematical forms, that are used to represent physical systems. They have been used widely in diverse fields, namely, in condensed matter physics, to study degrees of freedom of molecules in chemistry and in studying polymer dynamics and protein structures to name a few. In this article we discuss an encoding methodology of lattice structures in computational basis states of qubits (as used in quantum computing algorithms). We demonstrate a specific use case of lattice models in protein structure prediction. We do not propose any quantum algorithm to solve the protein structure prediction problem, instead, we propose a generic encoding methodology of lattice structures.

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arXiv2023

An approach to solve the coarse-grained Protein folding problem in a Quantum Computer

Protein folding, which dictates the protein structure from its amino acid sequence, is half a century old problem of biology. The function of the protein correlates with its structure, emphasizing the need of understanding protein folding for studying the cellular and molecular mechanisms that occur within biological systems. Understanding protein structures and enzymes plays a critical role in target based drug designing, elucidating protein-related disease mechanisms, and innovating novel enzymes. While recent advancements in AI based protein structure prediction methods have solved the protein folding problem to an extent, their precision in determining the structure of the protein with low sequence similarity is limited. Classical methods face challenges in generating extensive conformational samplings, making quantum-based approaches advantageous for solving protein folding problems. In this work we developed a novel turn based encoding algorithm that can be run on a gate based quantum computer for predicting the structure of smaller protein sequences using the HP model as an initial framework, which can be extrapolated in its application to larger and more intricate protein systems in future. The HP model best represents a major step in protein folding phenomena - the hydrophobic collapse which brings the hydrophobic amino acid to the interior of a protein. The folding problem is cast in a 3D cubic lattice with degrees of freedom along edges parallel to the orthogonal axes, as well as along diagonals parallel to the axial planes. While, the original formulation with higher order terms can be run on gate based quantum hardwares, the QUBO formulation can give results on both classical softwares employing annealers and IBM CPLEX as well as quantum hardwares.

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arXiv2023

A Proposed Quantum Hamiltonian Encoding Framework for Time Evolution Operator Design of Potential Energy Function

The exploration of potential energy operators in quantum systems holds paramount significance, offering profound insights into atomic behaviour, defining interactions, and enabling precise prediction of molecular dynamics. By embracing the Born-Oppenheimer picture, we delve into the intricate quantum evolution due to potential energy, facilitating accurate modelling and simulation of atomic phenomena with improved quantum fidelity. This research delves into time evolution operation due to potential energy functions for applications spanning quantum chemistry and condensed matter physics. Challenges in practical implementation, encompassing the formidable curse of dimensionality and intricate entangled interactions, are thoughtfully examined. Drawing upon seminal works, we lay a robust foundation for comprehensive investigations into potential energy landscapes with two proposed algorithms. In one methodology, we have shown a systematic decomposition of the potential energy function into Hadamard bases with composite construction of Pauli-Z, identity and RZ gates which can construct the unitary time evolution operator corresponding to the potential energy with a very high fidelity. The other method is a trade-off between complexity and fidelity, where we propose a novel quantum framework that can reduce the gate complexity from Θ(2n) to Θ(nCr ) (for some r < n). The proposed quantum algorithms are capable of efficiently simulating potential energy operators. The algorithms were implemented in simulators and IBM quantum hardware to prove their efficacy

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arXiv2022

Loading Probability Distributions in a Quantum circuit

Quantum circuits generating probability distributions has applications in several areas. Areas like finance require quantum circuits that can generate distributions that mimic some given data pattern. Hamiltonian simulations require circuits that can initialize the wave function of a physical quantum system. These wave functions, in several cases, are identical to some very well known probability distributions. In this paper we discuss ways to construct parameterized quantum circuits that can generate both symmetric as well as asymmetric distributions. We follow the trajectory of quantum states as single and two qubit operations get applied to the system, and find out the best possible way to arrive at the desired distribution. The parameters are optimized by a variational solver. We present results from both simulators as well as real IBM quantum hardwares.

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