arXiv subjects

Emil Zak

Publications and source records attributed to Emil Zak.

13 recordsLinked to original sources

arXiv2026

BCover: An Electronic Structure-Based Scoring Suite for Reaction-Aware Covalent Docking

Covalent virtual screening requires ranking compounds according to both noncovalent recognition and their ability to adopt a reaction-competent geometry with an appropriately reactive warhead. Here, we introduce BCover, a reaction-aware scoring suite that combines pre-reactive docking with quantum-chemistry-derived ligand reactivity descriptors, the electrostatic properties of the protein pocket. Quantum-chemical descriptors are aggregated using a nonlinear tree-based scoring model. BCover was evaluated retrospectively on the COValid benchmark, comprising nine targets and ten reactive sites, and compared with AutoDock, DOCK6, DOCKovalent, AlphaFold3 with Rosetta rescoring, and AlphaFold3 confidence-based ranking. BCover achieved an average adjusted LogAUC of 31% (57% max), an average ROC-AUC of 0.88 (0.96 max), an average EF1 of 18 (33 max). Its average LogAUC exceeded those of the classical docking methods and AlphaFold3-Rosetta, although AlphaFold3-mPAE provided the strongest overall enrichment. At an average runtime of about 10~s per ligand, BCover was approximately 25-fold faster than the evaluated AlphaFold3 workflows and achieved the highest average time-adjusted virtual-screening productivity index. Redocking experiments further showed that the method recovered near-native ligand conformations. These results demonstrate that combining docking-derived geometry with ligand local electronic reactivity and pocket electrostatics provides an efficient and interpretable strategy for covalent ligand prioritization. BCover is intended as a high-throughput screening method that complements more computationally demanding QM/MM and free-energy calculations during subsequent lead optimization.

physics.chem-ph↗

arXiv2026

Fault-tolerant quantum simulation of the Pauli-Breit Hamiltonian for ab initio hybrid quantum-classical molecular design with applications to photodynamic therapy

Relativistic spin effects drive subtle molecular phenomena ranging from intersystem crossing in photodynamic therapy to spin-mediated catalysis and high-resolution spectroscopy. These effects are described by the Pauli-Breit Hamiltonian, which extends the nonrelativistic electronic Hamiltonian by including one- and two-electron spin-orbit and spin-spin interactions. First-principles simulations of the full Pauli-Breit Hamiltonian rapidly become intractable on classical computers due to the exponential growth of the Hilbert space and the complexity of two-body spin-dependent terms. We propose a fault-tolerant quantum algorithm for computing molecular energy levels and properties governed by the Pauli-Breit Hamiltonian. Our approach block-encodes the relativistic Hamiltonian in a second-quantized, doubly factorized representation. By reformulating the Hamiltonian in a symmetry-adapted Majorana basis, we construct efficient linear-combination-of-unitaries circuits that encode spin-orbit interactions without effective or mean-field approximations. We introduce spin-controlled Pauli-SWAP networks that decouple spin and orbital control logic, enabling a unified treatment of relativistic spin mixing with only modest overhead relative to spin-free simulations. We analyze quantum resources in terms of logical qubits and T-gate complexity, showing that explicit spin degrees of freedom do not worsen the asymptotic scaling. The prefactor is reduced by a factor of two compared to direct linear-combination-of-unitaries approaches. Finally, we outline a hybrid quantum-classical workflow for designing photodynamic therapy photosensitizers, artificial photosynthesis catalysts, and other systems where accurate relativistic spin effects are essential.

quant-ph↗

arXiv2025

Quantum algorithm for solving generalized eigenvalue problems with application to the Schr\"odinger equation

Accurate computation of multiple eigenvalues of quantum Hamiltonians is essential in quantum chemistry, materials science, and molecular spectroscopy. Estimating excited-state energies is challenging for classical algorithms due to exponential scaling with system size, posing an even harder problem than ground-state calculations. We present a quantum algorithm for estimating eigenvalues and singular values of parameterized matrix families, including solving generalized eigenvalue problems that frequently arise in quantum simulations. Our method uses quantum amplitude amplification and phase estimation to identify matrix eigenvalues by locating minima in the singular value spectrum. We demonstrate our algorithm by proposing a quantum-computing formulation of the pseudospectral collocation method for the Schr\"odinger equation. We estimate fault-tolerant quantum resource requirements for the quantum collocation method, showing favorable scaling in the size of the problem $N$ (up to $\widetilde{\mathcal{O}}(\sqrt{N})$) compared to classical implementations with $\widetilde{\mathcal{O}}(N)$, for certain well-behaved potentials. Additionally, unlike the standard collocation method, which results in a generalized eigenvalue problem requiring matrix inversion, our algorithm circumvents the associated numerical instability by scanning a parameterized matrix family and detecting eigenvalues through singular value minimization. This approach is particularly effective when multiple eigenvalues are needed or when the generalized eigenvalue problem involves a high condition number. In the fault-tolerant era, our method may thus be useful for simulating high-dimensional molecular systems with dense spectra involving highly excited states, such as those encountered in molecular photodynamics or quasi-continuum regimes in many-body and solid-state systems.

quant-ph↗

arXiv2025

Controlling rovibrational state populations of polar molecules in inhomogeneous electric fields of the Stark deceleration: molecular dynamics and quantum chemistry simulations

We propose a modified Stark-chirped rapid adiabatic passage technique for a robust rovibrational population transfer in the gas phase molecules in the presence of certain inhomogeneous electric fields. As an example application, the new state switching scheme is shown to greatly enhance the process of slowing polar ammonia molecules in the Stark decelerator. High-level quantum mechanical simulations show that a virtually complete population inversion between a selected pair of weak-field and strong-field seeking states of NH$_3$ can be achieved. Strong dc electric fields within the Stark decelerator are used as part of the rovibrational population transfer protocol. Classical-dynamics simulations for ammonia demonstrate notable improvements in the longitudinal phase space acceptance of the Stark decelerator upgraded with the state switching and an increased deceleration efficiency with respect to the standard Stark deceleration technique.

physics.atom-ph↗

arXiv2025

Quantum Discrete Variable Representations

We present a fault-tolerant quantum algorithm for implementing the Discrete Variable Representation (DVR) transformation, a technique widely used in simulations of quantum-mechanical Hamiltonians. DVR provides a diagonal representation of local operators and enables sparse Hamiltonian structures, making it a powerful alternative to the finite basis representation (FBR), particularly in high-dimensional problems. While DVR has been extensively used in classical simulations, its quantum implementation, particularly using Gaussian quadrature grids, remains underexplored. We develop a quantum circuit that efficiently transforms FBR into DVR by following a recursive construction based on quantum arithmetic operations, and we compare this approach with methods that directly load DVR matrix elements using quantum read-only memory (QROM). We analyze the quantum resources, including T-gate and qubit counts, required for implementing the DVR unitary and discuss preferable choices of QROM-based and recursive-based methods for a given matrix size and precision. This study lays the groundwork for utilizing DVR Hamiltonians in quantum algorithms such as quantum phase estimation with block encoding.

quant-ph↗

arXiv2025

Higher order tensor factorizations for block encoding vibrational and vibronic Hamiltonians

Fault tolerant quantum simulation via the phase estimation algorithm and qubitization has a T-gate count that scales proportionally to the 1-norm of the Hamiltonian, the cost of block encoding the Hamiltonian, and inversely proportionally to the desired accuracy. Tensor factorization methods have been successfully used to reduce T-gate counts in the ground state electronic structure problem. Here we introduce the use of tensor factorization methods to reduce the T-gate count of quantum phase estimation. In particular, we show how Canonical Polyadic and Tucker decompositions of the tensors representing the vibrational and vibronic Hamiltonians can be utilized to rewrite the Hamiltonian in terms of linear combination of bosonic position operators representing nuclear vibrations. We demonstrate the use of these factorization methods on the water and monodeutered methane molecules.

quant-ph↗

arXiv2024

Utilizing redundancies in Qubit Hilbert Space to reduce entangling gate counts in the Unitary Vibrational Coupled-Cluster Method

We present a new method for state preparation using the Unitary Vibrational Coupled-Cluster (UVCC) technique. Our approach utilizes redundancies in the Hilbert space in the direct mapping of vibrational modes into qubits. By eliminating half of the qubit controls required in the Trotterized UVCC ansatz, our method achieves up to a 50% theoretical reduction in the entangling gate count compared to other methods and up to a 28% reduction compared practically useful approaches. This improvement enhances the fidelity of UVCC state preparation, enabling more efficient and earlier implementation of complex quantum vibrational structure calculations on near-term quantum devices. We experimentally demonstrate our method on Quantinuum's H1-1 quantum hardware, achieving significantly higher fidelities for 6- and 8-qubit systems compared to existing implementations. For fault-tolerant architectures, eliminating half of the control qubits in multi-controlled rotations incurs an additional Toffoli gate overhead elsewhere in the circuit. Thus, the overall performance gain depends on the specific decomposition method used for multi-controlled gates.

quant-ph↗

arXiv2024

Simultaneously optimizing symmetry shifts and tensor factorizations for cost-efficient Fault-Tolerant Quantum Simulations of electronic Hamiltonians

In fault-tolerant quantum computing, the cost of calculating Hamiltonian eigenvalues using the quantum phase estimation algorithm is proportional to the constant scaling the Hamiltonian matrix block-encoded in a unitary circuit. We present a method to reduce this scaling constant for the electronic Hamiltonians represented as a linear combination of unitaries. Our approach combines the double tensor-factorization method of Burg et al. with the the block-invariant symmetry shift method of Loaiza and Izmaylov. By extending the electronic Hamiltonian with appropriately parametrized symmetry operators and optimizing the tensor-factorization parameters, our method achieves a 25% reduction in the block-encoding scaling constant compared to previous techniques. The resulting savings in the number of non-Clifford T-gates, which are an essential resource for fault-tolerant quantum computation, are expected to accelerate the feasiblity of practical Hamiltonian simulations. We demonstrate the effectiveness of our technique on Hamiltonians of industrial and biological relevance, including the nitrogenase cofactor (FeMoCo) and cytochrome P450.

quant-ph↗

arXiv2022

The nuclear-spin-forbidden rovibrational transitions of water from first principles

The water molecule occurs in two nuclear-spin isomers that differ by the value of the total nuclear spin of the hydrogen atoms, i.e., $I=0$ for para-H$_2$O and $I=1$ for ortho-H$_2$O. Spectroscopic transitions between rovibrational states of ortho and para water are extremely weak due to the tiny hyperfine nuclear-spin-rotation interaction of only $\sim30$ kHz and so far were not observed. We report the first comprehensive theoretical investigation of the hyperfine effects and ortho-para transitions in H$_2$$^{16}$O due to nuclear-spin-rotation and spin-spin interactions. We also present the details of our newly developed general variational approach to the simulation of hyperfine effects in polyatomic molecules. Our results for water suggest that the strongest ortho-para transitions with room-temperature intensities on the order of $10^{-31}$ cm/molecule are about an order of magnitude larger than previously predicted values and should be detectable in the mid-infrared $\nu_2$ and near-infrared $2\nu_1+\nu_2$ and $\nu_1+\nu_2+\nu_3$ bands by current spectroscopy experiments.

physics.atom-ph↗

arXiv2019

Field-induced diastereomers for chiral separation

A novel approach for the state-specific enantiomeric enrichment and the spatial separation of enantiomers is presented. Our scheme utilizes techniques from strong-field laser physics, specifically an optical centrifuge in conjunction with a static electric field, to create a chiral field with defined handedness. Molecular enantiomers experience unique rotational excitation dynamics and this can be exploited to spatially separate the enantiomers using electrostatic deflection. Notably, the rotational-state-specific enantiomeric enhancement and its handedness is fully controllable. To explain these effects, we introduce the conceptual framework of $field\text{-}induced~diastereomers$ of a chiral molecule and perform robust quantum mechanical simulations on the prototypical chiral molecule propylene oxide (C$_3$H$_6$O), for which ensembles with an enantiomeric excess of up to $30~\%$ were obtained.

physics.chem-ph↗

arXiv2018

The ExoMol database: molecular line lists for exoplanet and other hot atmospheres

The ExoMol database (www.exomol.com) provides extensive line lists of molecular transitions which are valid over extended temperatures ranges. The status of the current release of the database is reviewed and a new data structure is specified. This structure augments the provision of energy levels (and hence transition frequencies) and Einstein $A$ coefficients with other key properties, including lifetimes of individual states, temperature-dependent cooling functions, Landé $g$-factors, partition functions, cross sections, $k$-coefficients and transition dipoles with phase relations. Particular attention is paid to the treatment of pressure broadening parameters. The new data structure includes a definition file which provides the necessary information for utilities accessing ExoMol through its application programming interface (API). Prospects for the inclusion of new species into the database are discussed.

astro-ph.GA↗

arXiv2016

A room temperature CO$_2$ line list with ab initio computed intensities

Atmospheric carbon dioxide concentrations are being closely monitored by remote sensing experiments which rely on knowing line intensities with an uncertainty of 0.5% or better. We report a theoretical study providing rotation-vibration line intensities substantially within the required accuracy based on the use of a highly accurate {\it ab initio} dipole moment surface (DMS). The theoretical model developed is used to compute CO$_2$ intensities with uncertainty estimates informed by cross comparing line lists calculated using pairs of potential energy surfaces (PES) and DMS's of similar high quality. This yields lines sensitivities which are utilized in reliability analysis of our results. The final outcome is compared to recent accurate measurements as well as the HITRAN2012 database. Transition frequencies are obtained from effective Hamiltonian calculations to produce a comprehensive line list covering all $^{12}$C$^{16}$O$_2$ transitions below 8000 cm$^{-1}$ and stronger than 10$^{-30}$ cm / molecule at $T=296$~K

physics.chem-ph↗

arXiv2016

Normal modes. The true story

The aim of this article is a comprehensive description of normal modes of molecular vibrations. The starting point is chosen to be a general molecular system with separated center of mass and an arbitrary embedding of body-fixed axes. This allows to focus on internal degrees of freedom only, leaving the problem of rotational motion behind. Nevertheless, for the sake of completeness we first introduce a general quantum-mechanical Hamiltonian in Eckart-Watson representation, to make a quick leap into a simplified harmonic description for internal motion and rigid rotor for rotational degrees of freedom. This regime constitutes a basis for more sophisticated calculations.

quant-ph↗