arXiv subjects

Victor S. Batista

Publications and source records attributed to Victor S. Batista.

At least 19 recordsLinked to original sources

arXiv2026

Project Ariadne: Prompt-Conditioned Route Generation for Synthesis Planning

Retrosynthetic planning seeks to connect a target molecule to commercially available starting materials through a multistep route. Classical planners construct such routes by iteratively applying single-step reaction models within a search procedure; constrained variants often require specialized algorithms or architectural changes. Direct route generation reframes retrosynthesis as sequence generation, but existing direct-generation methods still train separate models for different planning specifications. We introduce Ariadne, a decoder-only route generator that represents the target, optional constraints, and route in one prompt-completion sequence. On the RetroCast/PaRoutes mkt-cnv-160 benchmark family, one 24-layer checkpoint follows route-depth and required-starting-material prompts: adding the corresponding prompt fields raises Solv-0 by 13.7 points for depth constraints and 31.2 points for required-leaf constraints. Ariadne also improves over DESP, a bidirectional search planner, on required-leaf Top-10 and Solv-0 in 24 GPU-minutes versus 6.8 GPU-hours. On standard reconstruction, Ariadne is comparable to DMS Explorer XL at about half the reported inference time. Across additional target-only benchmarks, Ariadne's clearest gains are on route-holdout reconstruction, whereas AiZynthFinder MCTS remains stronger on several Solv-0 comparisons. These results extend sequence generation from specialist retrosynthesis models to prompt-conditioned structural route generation. We release the codebase and training scripts to support further work, but do not introduce Tier-1--3 route checkers; those remain the main bottleneck before models of this kind can become useful to experimental chemists.

cs.LG↗

arXiv2026

Steady-state spectral kissing and dissipative phase transitions

Spectral kissing, recently realized in a Kerr parametric oscillator (KPO), refers to the merging of pairs of energy levels and arises as a manifestation of an excited-state quantum phase transition (ESQPT). Here, we show that this phenomenon has a dissipative counterpart encoded in the spectrum of the steady-state density matrix. Using a dissipative KPO as a representative example, we demonstrate that, in the weak-dissipation regime, the eigenvalues of the steady-state density matrix organize into quasi-degenerate pairs that mirror the spectral kissing of the corresponding closed system. As the dissipation strength increases, this pairing gradually disappears. By analyzing the classical limit of the system, we derive analytical expressions for the critical lines governing both the onset of steady-state spectral kissing and its disappearance at a dissipative phase transition.

quant-ph↗

arXiv2026

Solving Constrained Optimization Problems Using Hybrid Qubit-Qumode Quantum Devices

Variational Quantum Algorithms (VQAs) provide a promising framework for tackling complex optimization problems on near-term quantum hardware. Here, we demonstrate that hybrid qubit--qumode quantum devices offer an efficient route to solving Quadratic Unconstrained Binary Optimization (QUBO) problems using the Echoed Conditional Displacement Variational Quantum Eigensolver (ECD-VQE). Leveraging circuit quantum electrodynamics (cQED) architectures, we encode QUBO instances across multiple qumodes weakly coupled to a single qubit and extract binary solutions directly from photon-number measurements. We apply ECD-VQE to the Binary Knapsack Problem and show that it outperforms the Quantum Approximate Optimization Algorithm (QAOA) implemented on conventional qubit circuits, achieving higher-quality solutions with dramatically fewer resources. We also demonstrate that ECD-VQE can be extended to chemically motivated tasks such as active-space selection for multireference electronic structure methods. These results highlight the utility of hybrid qubit-qumode platforms for a broad class of NP-hard and chemistry-related optimization problems, and demonstrate that variational ECD ansatz can realize expressive state preparation with significantly shallower circuits than qubit-only architectures, positioning qubit-qumode gates as compelling candidates for constrained optimization in early fault-tolerant quantum computing.

quant-ph↗

arXiv2026

Asymmetry Control in a Parametric Oscillator for the Quantum Simulation of Chemical Activation

Dissipative tunneling remains a cornerstone effect in quantum mechanics. In chemistry, it plays a crucial role in governing the rates of chemical reactions, often modeled as the motion along the reaction coordinate from one potential well to another. The relative positions of energy levels in these wells strongly influence the reaction dynamics. Chemical research will benefit from a fully adjustable, asymmetric double-well equipped with precise measurement capabilities of the tunneling rates. In this paper, we show a quantum simulator system that consists of a continuously driven Kerr parametric oscillator with a third order non-linearity that can be operated in the quantum regime to create a fully tunable asymmetric double-well. Our experiment leverages a low-noise, all-microwave control system with a high-efficiency readout, based on a tunnel Josephson junction circuit, of the which-well information. We explore the reaction rates across the landscape of tunneling resonances in parameter space. We uncover two new and counter-intuitive effects: (i) a weak asymmetry can significantly decrease the activation rates, even though the well in which the system is initialized is made shallower, and (ii) the width of the tunneling resonances alternates between narrow and broad lines as a function of the well depth and asymmetry. We predict by numerical simulations that both effects will also manifest themselves in ordinary chemical double-well systems in the quantum regime. Our work is a first step for the development of analog molecule simulators of proton transfer reactions based on quantum parametric processes.

quant-ph↗

arXiv2026

Nonadiabatic H-Atom Scattering Channels on Ge(111) Elucidated by the Hierarchical Equations of Motion

Atomic and molecular scattering at semiconductor interfaces plays a central role in surface chemistry and catalysis, yet predictive simulations remain challenging due to strong nonadiabatic effects causing the breakdown of the Born-Oppenheimer approximation. Here, we present fully quantum simulations of H-atom scattering from the Ge(111)c(2x8) rest site using the hierarchical equations of motion (HEOM) with matrix product states (MPS). The system is modeled by mapping a density functional theory (DFT) potential energy surface onto a Newns-Anderson Hamiltonian. Our simulations reproduce the experimentally observed bimodal kinetic energy distributions, capturing both elastic and energy-loss channels. By systematically examining atom-surface coupling, incident energy, and isotope substitution, we identify the strong-coupling regime required to recover the experimental energy-loss profile. This regime suppresses the elastic peak, implying additional site-specific scattering channels in the observed elastic peak. Deuterium substitution further produces a subtle shift in the energy-loss peak, consistent with experiment. These results establish HEOM as a rigorous framework for quantum surface scattering, capable of capturing nonadiabatic dynamics beyond electronic friction and perturbative approaches.

cond-mat.mtrl-sci↗

arXiv2026

FragmentRetro: A Quadratic Retrosynthetic Method Based on Fragmentation Algorithms

Retrosynthesis, the process of deconstructing a target molecule into simpler precursors, is crucial for computer-aided synthesis planning (CASP). Widely adopted tree-search methods often suffer from exponential computational complexity. In this work, we introduce FragmentRetro, a novel retrosynthetic method that leverages fragmentation algorithms, specifically BRICS and r-BRICS, combined with stock-aware exploration and pattern fingerprint screening to achieve quadratic complexity. FragmentRetro recursively combines molecular fragments and verifies their presence in a building block set, providing sets of fragment combinations as retrosynthetic solutions. We present the first formal computational analysis of retrosynthetic methods, showing that tree search exhibits exponential complexity $O(b^h)$, DirectMultiStep scales as $O(h^6)$, and FragmentRetro achieves $O(h^2)$, where $h$ represents the number of heavy atoms in the target molecule and $b$ is the branching factor for tree search. Evaluations on PaRoutes, USPTO-190, and natural products demonstrate that FragmentRetro achieves high solved rates with competitive runtime, including cases where tree search fails. The method benefits from fingerprint screening, which significantly reduces substructure matching complexity. While FragmentRetro focuses on efficiently identifying fragment-based solutions rather than full reaction pathways, its computational advantages and ability to generate strategic starting candidates establish it as a powerful foundational component for scalable and automated synthesis planning.

cs.AI↗

arXiv2025

Procrustean Bed for AI-Driven Retrosynthesis: A Unified Framework for Reproducible Evaluation

Progress in computer-aided synthesis planning (CASP) is obscured by the lack of standardized evaluation infrastructure and the reliance on metrics that prioritize topological completion over chemical validity. We introduce RetroCast, a unified evaluation suite that standardizes heterogeneous model outputs into a common schema to enable statistically rigorous, apples-to-apples comparison. The framework includes a reproducible benchmarking pipeline with stratified sampling and bootstrapped confidence intervals, accompanied by SynthArena, an interactive platform for qualitative route inspection. We utilize this infrastructure to evaluate leading search-based and sequence-based algorithms on a new suite of standardized benchmarks. Our analysis reveals a divergence between "solvability" (stock-termination rate) and route quality; high solvability scores often mask chemical invalidity or fail to correlate with the reproduction of experimental ground truths. Furthermore, we identify a "complexity cliff" in which search-based methods, despite high solvability rates, exhibit a sharp performance decay in reconstructing long-range synthetic plans compared to sequence-based approaches. We release the full framework, benchmark definitions, and a standardized database of model predictions to support transparent and reproducible development in the field.

cs.LG↗

arXiv2025

Qumode-Based Variational Quantum Eigensolver for Molecular Excited States

We introduce the Qumode Subspace Variational Quantum Eigensolver (QSS-VQE), a hybrid quantum-classical algorithm for computing molecular excited states using the Fock basis of bosonic qumodes in circuit quantum electrodynamics (cQED) devices. This approach harnesses the native universal gate sets of qubit-qumode architectures to construct highly expressive variational ansatze, offering potential advantages over conventional qubit-based methods. In QSS-VQE, the electronic structure Hamiltonian is first mapped to a qubit representation and subsequently embedded into the Fock space of bosonic qumodes, enabling efficient state preparation and reduced quantum resource requirements. We demonstrate the performance of QSS-VQE through simulations of molecular excited states, including dihydrogen and a conical intersection in cytosine. Additionally, we explore a bosonic model Hamiltonian to assess the expressivity of qumode gates, identifying regimes where qumode-based implementations outperform purely qubit-based approaches. These results highlight the promise of leveraging bosonic degrees of freedom for enhanced quantum simulation of complex molecular systems.

quant-ph↗

arXiv2025

Error-Mitigation Enabled Multicomponent Quantum Simulations Beyond the Born-Oppenheimer Approximation

We introduce a multicomponent unitary coupled cluster framework for quantum simulations of molecular systems that incorporate both electronic and nuclear quantum effects beyond the Born-Oppenheimer approximation. Using the nuclear-electronic orbital formalism, we construct mcUCC ansätze for positronium hydride and molecular hydrogen with a quantum proton, and analyze hardware requirements for different excitation truncations. To further reduce resource costs effectively, we employ the local unitary cluster Jastrow ansatz and implement it experimentally on IBM Q's Heron superconducting hardware. With the Physics-Inspired Extrapolation error mitigation protocol, the computed ground-state energies remain within chemical accuracy, consistent with the stated uncertainty level. These results provide the first demonstration of error-mitigated multicomponent correlated simulations on quantum hardware and outline a path toward scalable algorithms unifying electronic and nuclear degrees of freedom.

quant-ph↗

arXiv2025

A Perspective on Quantum Computing Applications in Quantum Chemistry using 25--100 Logical Qubits

The intersection of quantum computing and quantum chemistry represents a promising frontier for achieving quantum utility in domains of both scientific and societal relevance. Owing to the exponential growth of classical resource requirements for simulating quantum systems, quantum chemistry has long been recognized as a natural candidate for quantum computation. This perspective focuses on identifying scientifically meaningful use cases where early fault-tolerant quantum computers, which are considered to be equipped with approximately 25--100 logical qubits, could deliver tangible impact. While recent advances in classical computing have pushed the boundaries of tractable simulations to unprecedented scales, this logical-qubit regime represents the first window where quantum devices can pursue qualitatively distinct strategies, such as polynomial-scaling phase estimation, direct simulation of quantum dynamics, and active-space embedding, that remain challenging for classical solvers, for instance, multireference charge-transfer and conical-intersection states central to photochemistry and materials design. We highlight near-term opportunities in algorithm and software design, discuss representative chemical problems suited for quantum acceleration, and propose strategic roadmaps and collaborative pathways for advancing practical quantum utility in quantum chemistry.

quant-ph↗

arXiv2025

The Quantum Ensemble Variational Optimization Algorithm: Applications to Molecular Inverse Design

Designing molecules with optimized properties remains a fundamental challenge due to the intricate relationship between molecular structure and properties. Traditional computational approaches that address the combinatorial number of possible molecular designs become unfeasible as the molecular size increases, suffering from the so-called `curse of dimensionality' problem. Recent advances in quantum computing hardware present new opportunities to address this problem. Here, we introduce the Quantum Ensemble Variational Optimization (QEVO) method for near-term and early fault-tolerant quantum computing platforms. QEVO efficiently maps molecular structures onto an orthonormal basis of Pauli strings and samples from a superposition state generated by a variational ansatz. The ansatz is iteratively optimized to identify molecular candidates with the desired property. Our numerical simulations demonstrate the potential of QEVO in designing drug-like molecules with anticancer properties, employing a shallow quantum circuit that requires only a modest number of qubits. We envision that QEVO could be applied to a wide range of complex problems, offering practical solutions to problems with combinatorial complexity.

quant-ph↗

arXiv2025

A Hybrid Transformer Architecture with a Quantized Self-Attention Mechanism Applied to Molecular Generation

The success of the self-attention mechanism in classical machine learning models has inspired the development of quantum analogs aimed at reducing computational overhead. Self-attention integrates learnable query and key matrices to calculate attention scores between all pairs of tokens in a sequence. These scores are then multiplied by a learnable value matrix to obtain the output self-attention matrix, enabling the model to effectively capture long-range dependencies within the input sequence. Here, we propose a hybrid quantum-classical self-attention mechanism as part of a transformer decoder, the architecture underlying large language models (LLMs). To demonstrate its utility in chemistry, we train this model on the QM9 dataset for conditional generation, using SMILES strings as input, each labeled with a set of physicochemical properties that serve as conditions during inference. Our theoretical analysis shows that the time complexity of the query-key dot product is reduced from $\mathcal{O}(n^2 d)$ in a classical model to $\mathcal{O}(n^2\log d)$ in our quantum model, where $n$ and $d$ represent the sequence length and embedding dimension, respectively. We perform simulations using NVIDIA's CUDA-Q platform, which is designed for efficient GPU scalability. This work provides a promising avenue for quantum-enhanced natural language processing (NLP).

quant-ph↗

arXiv2025

DirectMultiStep: Direct Route Generation for Multistep Retrosynthesis

Traditional computer-aided synthesis planning (CASP) methods rely on iterative single-step predictions, leading to exponential search space growth that limits efficiency and scalability. We introduce a series of transformer-based models, that leverage a mixture of experts approach to directly generate multistep synthetic routes as a single string, conditionally predicting each transformation based on all preceding ones. Our DMS Explorer XL model, which requires only target compounds as input, outperforms state-of-the-art methods on the PaRoutes dataset with 1.9x and 3.1x improvements in Top-1 accuracy on the n$_1$ and n$_5$ test sets, respectively. Providing additional information, such as the desired number of steps and starting materials, enables both a reduction in model size and an increase in accuracy, highlighting the benefits of incorporating more constraints into the prediction process. The top-performing DMS-Flex (Duo) model scores 25-50% higher on Top-1 and Top-10 accuracies for both n$_1$ and n$_5$ sets. Additionally, our models successfully predict routes for FDA-approved drugs not included in the training data, demonstrating strong generalization capabilities. While the limited diversity of the training set may affect performance on less common reaction types, our multistep-first approach presents a promising direction towards fully automated retrosynthetic planning.

cs.LG↗

arXiv2025

Impact of chaos on the excited-state quantum phase transition of the Kerr parametric oscillator

The driven Kerr parametric oscillator, of interest to fundamental physics and quantum technologies, exhibits an excited state quantum phase transition (ESQPT) originating in an unstable classical periodic orbit. The main signature of this type of ESQPT is a singularity in the level density in the vicinity of the energy of the classical separatrix that divides the phase space into two distinct regions. The quantum states with energies below the separatrix are useful for quantum technologies, because they show a cat-like structure that protects them against local decoherence processes. In this work, we show how chaos arising from the interplay between the external drive and the nonlinearities of the system destroys the ESQPT and eventually eliminates the cat states. Our results demonstrate the importance of the analysis of theoretical models for the design of new parametric oscillators with ever larger nonlinearities.

quant-ph↗

arXiv2025

Proposal for many-body quantum chaos detection

In this work, the term ``quantum chaos'' refers to spectral correlations similar to those found in the random matrix theory. Quantum chaos can be diagnosed through the analysis of level statistics using e.g.~the spectral form factor, which detects both short- and long-range level correlations. The spectral form factor corresponds to the Fourier transform of the two-point spectral correlation function and exhibits a typical slope-dip-ramp-plateau structure (aka correlation hole) when the system is chaotic. We discuss how this structure could be detected through the quench dynamics of two physical quantities accessible to experimental many-body quantum systems: the survival probability and the spin autocorrelation function. The survival probability is equivalent to the spectral form factor with an additional filter. When the system is small, the dip of the correlation hole reaches sufficiently large values at times which are short enough to be detected with current experimental platforms. As the system is pushed away from chaos, the correlation hole disappears, signaling integrability or localization. We also provide a relatively shallow circuit with which the correlation hole could be detected with commercially available quantum computers.

cond-mat.stat-mech↗

arXiv2025

A Model-Centric Review of Deep Learning for Protein Design

Deep learning has transformed protein design, enabling accurate structure prediction, sequence optimization, and de novo protein generation. Advances in single-chain protein structure prediction via AlphaFold2, RoseTTAFold, ESMFold, and others have achieved near-experimental accuracy, inspiring successive work extended to biomolecular complexes via AlphaFold Multimer, RoseTTAFold All-Atom, AlphaFold 3, Chai-1, Boltz-1 and others. Generative models such as ProtGPT2, ProteinMPNN, and RFdiffusion have enabled sequence and backbone design beyond natural evolution-based limitations. More recently, joint sequence-structure co-design models, including ESM3, have integrated both modalities into a unified framework, resulting in improved designability. Despite these advances, challenges still exist pertaining to modeling sequence-structure-function relationships and ensuring robust generalization beyond the regions of protein space spanned by the training data. Future advances will likely focus on joint sequence-structure-function co-design frameworks that are able to model the fitness landscape more effectively than models that treat these modalities independently. Current capabilities, coupled with the dizzying rate of progress, suggest that the field will soon enable rapid, rational design of proteins with tailored structures and functions that transcend the limitations imposed by natural evolution. In this review, we discuss the current capabilities of deep learning methods for protein design, focusing on some of the most revolutionary and capable models with respect to their functionality and the applications that they enable, leading up to the current challenges of the field and the optimal path forward.

cs.LG↗

arXiv2025

Simulating electronic structure on bosonic quantum computers

Quantum harmonic oscillators, or qumodes, provide a promising and versatile framework for quantum computing. Unlike qubits, which are limited to two discrete levels, qumodes have an infinite-dimensional Hilbert space, making them well-suited for a wide range of quantum simulations. In this work, we focus on the molecular electronic structure problem. We propose an approach to map the electronic Hamiltonian into a qumode bosonic problem that can be solved on bosonic quantum devices using the variational quantum eigensolver (VQE). Our approach is demonstrated through the computation of ground potential energy surfaces for benchmark model systems, including H$_2$ and the linear H$_4$ molecule. The preparation of trial qumode states and the computation of expectation values leverage universal ansatzes based on the echoed conditional displacement (ECD), or the selective number-dependent arbitrary phase (SNAP) operations. These techniques are compatible with circuit quantum electrodynamics (cQED) platforms, where microwave resonators coupled to superconducting transmon qubits can offer an efficient hardware realization. This work establishes a new pathway for simulating many-fermion systems, highlighting the potential of hybrid qubit-qumode quantum devices in advancing quantum computational chemistry.

quant-ph↗

arXiv2025

Simulating Non-Markovian Quantum Dynamics on NISQ Computers Using the Hierarchical Equations of Motion

Quantum computing offers promising new avenues for tackling the long-standing challenge of simulating the quantum dynamics of complex chemical systems, particularly open quantum systems coupled to external baths. However, simulating such non-unitary dynamics on quantum computers is challenging since quantum circuits are specifically designed to carry out unitary transformations. Furthermore, chemical systems are often strongly coupled to the surrounding environment, rendering the dynamics non-Markovian and beyond the scope of Markovian quantum master equations like Lindblad or Redfield. In this work, we introduce a quantum algorithm designed to simulate non-Markovian dynamics of open quantum systems. Our approach enables the implementation of arbitrary quantum master equations on noisy intermediate-scale quantum (NISQ) computers. We illustrate the method as applied in conjunction with the numerically exact hierarchical equations of motion (HEOM) method. The effectiveness of the resulting quantum HEOM algorithm is demonstrated as applied to simulations of the non-Lindbladian electronic energy and charge transfer dynamics in models of the carotenoid-porphyrin-\ce{C60} molecular triad dissolved in tetrahydrofuran and the Fenna-Matthews-Olson complex.

quant-ph↗