The cost of quantum algorithms for biochemistry: A case study in metaphosphate hydrolysis
Ryan LaRose, Antonios M. Alvertis, Alan Bidart, Ben DalFavero, Sophia E. Economou, J. Wayne Mullinax, Mafalda Ramôa, Jeremiah Rowland, Brenda Rubenstein, Nicolas PD Sawaya, Prateek Vaish, Grant M. Rotskoff, Norm M. Tubman
quant-phcs.ETSubmitted Jan 27, 2026• Announced Jan 28, 2026• 1 citation• Revised Feb 11, 2026 (v2)
We evaluate the quantum resource requirements for ATP/metaphosphate hydrolysis, one of the most important reactions in all of biology with implications for metabolism, cellular signaling, and cancer therapeutics. In particular, we consider three algorithms for solving the ground state energy estimation problem: the variational quantum eigensolver, quantum Krylov, and quantum phase estimation. By utilizing exact classical simulation, numerical estimation, and analytical bounds, we provide a current and future outlook for using quantum computers to solve impactful biochemical and biological problems. Our results show that variational methods, while being the most heuristic, still require substantially fewer overall resources on quantum hardware, and could feasibly address such problems on current or near-future devices. We include our complete dataset of biomolecular Hamiltonians and code as benchmarks to improve upon with future techniques.
We evaluate the quantum resource requirements for ATP/metaphosphate hydrolysis, one of the most important reactions in all of biology with implications for metabolism, cellular signaling, and cancer therapeutics. In particular, we consider three algorithms for solving the ground state energy estimation problem: the variational quantum eigensolver, quantum Krylov, and quantum phase estimation. By utilizing exact classical simulation, numerical estimation, and analytical bounds, we provide a current and future outlook for using quantum computers to solve impactful biochemical and biological problems. Our results show that variational methods, while being the most heuristic, still require substantially fewer overall resources on quantum hardware, and could feasibly address such problems on current or near-future devices. We include our complete dataset of biomolecular Hamiltonians and code as benchmarks to improve upon with future techniques.
New approaches into computational quantum chemistry can be developed through the use of quantum computing. While universal, fault-tolerant quantum computers are still not available, and we want to utilize today's noisy quantum processors. One of their flagship applications is the variational quantum eigensolver (VQE)-an algorithm for calculating the minimum energy of a physical Hamiltonian. In this study, we investigate how various types of errors affect the VQE and how to efficiently use the available resources to produce precise computational results. We utilize a simulator of a noisy quantum device, an exact statevector simulator, and physical quantum hardware to study the VQE algorithm for molecular hydrogen. We find that the optimal method of running the hybrid classical-quantum optimization is to: (i) allow some noise in intermediate energy evaluations, using fewer shots per step and fewer optimization iterations, but ensure a high final readout precision; (ii) emphasize efficient problem encoding and ansatz parametrization; and (iii) run all experiments within a short time-frame, avoiding parameter drift with time. Nevertheless, current publicly available quantum resources are still very noisy and scarce/expensive, and even when using them efficiently, it is quite difficult to perform trustworthy calculations of molecular energies.
In ab-initio quantum chemistry, solving the electronic structure problem of a molecular system of interest to obtain an approximation of the ground and, in some cases, the excited state energies is a core and central task in various quantum chemistry processes. These include, but certainly not limited to, the calculation of the activation energy–that is the minimal energy required to launch a given chemical reaction–, the dipole and multipole moments which describe the polarity of the molecule, performing the optimization of the geometry of the molecule and searching for transition states. Furthermore, many quantum chemistry applications are predicated, not merely on the approximation of the ground state energy, but also on the corresponding first order derivatives. The body of literature of classical algorithms approximating the ground state energy and its first order derivative is extensively rich with a plethora of methods such as self-consistent mean-field methods, coupled-cluster methods, density matrix renormalization group and many more, each of which has intrinsic set of properties and characteristics that makes it suitable for specific tasks and cases. However, classical methods face a practically insurmountable challenge: the efficient computation of high accuracy approximation of ground state energies of large system sizes. This is fundamentally because the electronic structure problem provably belongs to the complexity class of QMA-hard problems. Which also means that it is out of reach for quantum algorithms as well in general. However, with certain assumptions that are expected to hold molecules of interest–that so far proved to be classically challenging because the required accuracy set by the standard of chemical accuracy threshold (generally held in quantum chemistry)– quantum algorithms can efficiently treat such cases. While originally theorized by Richard Feynmann as a potentially efficient way of simulating some classically intractable many-body systems, quantum computing has since proven to have a stronger and richer potential paving the way for the inception of new algorithms such as Shor’s algorithm for integer factorization, HHL for solving linear system of equation and Grover’s algorithm for constrained binary search, just to name a few. These algorithms provably exhibit an improvement rate that goes respectively exponentially and quadratically in the time complexity. Quantum chemistry is considered a prominent candidate to benefit from quantum computing given the variety of quantum algorithms put forth to solve the electronic structure problem of particular systems of interest. These quantum algorithm proposals can be broadly categorized in three main categories that span the spectrum: from noisy intermediate scale quantum (NISQ) computers to early and full scale fault tolerant quantum ((E)FTQC) computers. Firstly, the variational quantum eigensolver (VQE) family of quantum algorithms which variationally search for the ground state energy through the optimization of the energy of a parametrized state prepared in a quantum computer using an ansatz. Secondly, the quantum Krylov subspace diagonalization (QKSD) methods, which generate a subspace of the original Hilbert space and efficiently produce the lowest energy in said subspace as its output. Lastly, we have the quantum phase estimation (QPE) algorithms, which provably produce the ground state energy in Heisenberg scaling presenting hence a provable efficient solution. In this thesis, we firstly set to work on the problem of efficient Hamiltonian linear combination of unitaries (LCU) representation. This is mainly motivated by the wide-range impact an efficient compression of the Hamiltonian can potentially have on several quantum algorithms such as VQE, QPE...etc. We designed a method that efficiently compress the Hamiltonian representation in a way that is beneficially impactful across the set of the aforementioned quantum algorithms. Namely, we motivate and present in Sections 1.3 and 1.4 respectively, the regularized compressed double-factorization (RC-DF) and show how it reduces the energy measurement complexity both in terms of number of distinct observables and number of samples. Moreover, it also reduces the total depth of the quantum phase estimation circuit thanks to its low normalization factor. Secondly, given the importance of the energy derivatives, in Sections 2.1 and 2.2, we introduce and present an efficient quantum algorithm for the calculation of the analytic gradient of VQE energies of double-factorized Hamiltonians. Furthermore, in Section 2.1, we expand on the utility of RC-DF by presenting a quantum algorithm that determines the analytic gradient of energies measured with respect to RC-DF Hamiltonains. Third, in Section 3.1, we summarize the theoretical results of purification error-mitigation techniques, namely echo verification and virtual distillation. In Section 3.2, we report on the results of the experimental bench mark, of said techniques, performed on on Google’s Sycamore device to validate the theoretical scaling of error suppression and extrapolate the resources needed for classically intractable system sizes. Fourth, in Section 4 we establish the challenges of computing energy gradients in a quantum Krylov frame work. To overcome the problem, we provide, in Section 4.3, an efficient quantum algorithm for calculating energy derivative obtained through QKSD procedures. Our approach shows how the QKSD ground state can be prepared using quantum signal processing (QSP) and reduces the number of observables to O(1) per reduced density matrix (RDM). Lastly, in light of the importance of quantum RAMs due to their utility in a variety of quantum algorithms that require efficient initial state preparation, as explained in Section 5.5, we address the problematic exponential depth of the bucket-brigade QRAM (when decomposed). We present in Section 5.6 a very efficient Clifford+T decomposition of the bucket-brigade QRAM, which preserves the linear scaling of the depth of the circuit without introducing any additional ancilla.
This article presents a comprehensive survey of the current frontier in quantum computing for computational sciences, evaluating the technical requirements to translate theoretical asymptotic speedups into practical utility in the areas of chemistry, biochemistry, and materials science. We review foundational algorithms, including the quantum Fourier transform, quantum phase estimation, and the quantum linear-system solver, along with variational heuristics such as variational quantum eigensolver and quantum approximate optimization algorithm. Particular emphasis is placed on near-optimal Hamiltonian simulation frameworks, specifically qubitization and quantum signal processing. Furthermore, we shed light on the current advances in quantum error correction codes, quantum hardware, and quantum software platforms. We then provide a comprehensive review of the application of quantum algorithms in four computational science domains that collectively represent the most compelling near-term targets for quantum advantage. This article aims to provide a clear and balanced perspective on the current state of the field and its future potential for advancing computational science.
Quantum chemistry and materials is one of the most promising applications of quantum computing. Yet much work is still to be done in matching industry-relevant problems in these areas with quantum algorithms that can solve them. Most previous efforts have carried out resource estimations for quantum algorithms run on large-scale fault-tolerant architectures, which include the quantum phase estimation algorithm. In contrast, few have assessed the performance of near-term quantum algorithms, which include the variational quantum eigensolver (VQE) algorithm. Recently, a large-scale benchmark study [Gonthier et al. 2020] found evidence that the performance of the variational quantum eigensolver for a set of industry-relevant molecules may be too inefficient to be of practical use. This motivates the need for developing and assessing methods that improve the efficiency of VQE. In this work, we predict the runtime of the energy estimation subroutine of VQE when using robust amplitude estimation (RAE) to estimate Pauli expectation values. Under conservative assumptions, our resource estimation predicts that RAE can reduce the runtime over the standard estimation method in VQE by one to two orders of magnitude. Despite this improvement, we find that the runtimes are still too large to be practical. These findings motivate two complementary efforts towards quantum advantage: 1) the investigation of more efficient near-term methods for ground state energy estimation and 2) the development of problem instances that are of industrial value and classically challenging, but better suited to quantum computation.
With quantum computers on the horizon, it is essential to understand what problems they can be used to solve. One potential application is simulating quantum systems, in particular, systems with many interacting electrons. However, there is a disparity between the computational resources required to study these problems and the capabilities of modern experimental quantum devices. In this thesis, we make progress toward closing this gap by reducing the cost of quantum simulation of quantum chemistry on a number of fronts. In the first half, we develop three improved quantum simulation algorithms by approximating time evolution under the Hamiltonian using a truncated Taylor series rather than the Trotter-Suzuki decomposition. We do this first for the molecular electronic structure Hamiltonian in two representations, obtaining asymptotic improvements in terms of both the number of orbitals and the required precision. We also apply the truncated Taylor series paradigm to quantum simulation in real space, where we consider simulation of general wave functions discretized on a uniform grid. In the second half, by working with Hamiltonians tailored specifically to quantum algorithms, we demonstrate that Trotter steps of the electronic structure Hamiltonian can be simulated in exactly N depth and with only linear connectivity, where N is the number of spin-orbitals. This resolves the problem of non-locality in fermion-to-qubit mappings, and has wide-ranging applications for variational and phase estimation-based quantum simulation of quantum chemistry. We further study this algorithm on an error-corrected quantum computer using the surface code. Benchmarking it alongside other product formula approaches, we show that quantum simulation of scientifically important instances of the electronic structure problem that are classically intractable can be performed with only a few hundred thousand physical qubits and fewer than one billion costly fault-tolerant gates. Finally, we study the effect of using randomized Hamiltonians in iterative phase estimation, and how this allows us to reduce the costs of simulation as well as to exploit knowledge of the ground state in how we design our simulation algorithm.
Quantum chemistry is among the most promising applications of quantum computing, offering the potential to solve complex electronic structure problems more efficiently than classical approaches. A critical component of any quantum algorithm is the measurement step, where the desired properties are extracted from a quantum computer. This review focuses on recent advancements in quantum measurement techniques tailored for quantum chemistry, particularly within the second quantized framework suitable for current and near-term quantum hardware. We provide a comprehensive overview of measurement strategies developed primarily for the Variational Quantum Eigensolver (VQE) and its derivatives. These strategies address the inherent challenges posed by the complexity of the electronic Hamiltonian operator. Additionally, we examine methods for estimating excited states and one- and two-electron properties, extending the applicability of quantum algorithms to broader chemical phenomena. Key aspects of the review include approaches for constructing measurement operators with reduced classical preprocessing and quantum implementation costs, techniques to minimize the number of measurements required for a given accuracy, and error mitigation strategies that leverage symmetries and other properties of the measurement operators. Furthermore, we explore measurement schemes rooted in Quantum Phase Estimation (QPE), which are expected to become viable with the advent of fault-tolerant quantum computing. This review emphasizes foundational concepts and methodologies rather than numerical benchmarks, serving as a resource for researchers aiming to enhance the efficiency and accuracy of quantum measurements in quantum chemistry.