arXiv subjects

Xiaojun Yao

Publications and source records attributed to Xiaojun Yao.

At least 19 recordsLinked to original sources

arXiv2026

Computationally Efficient Description of Medium Response to Jets in Heavy Ion Collisions

We develop an Efficient Wake procedure for computing the distribution of hadrons originating from jet wakes in heavy ion collisions - the hydrodynamic response of a droplet of quark-gluon plasma to the energy and momentum deposited in it by high-energy partons propagating through it. The procedure employs the linearity of linearized hydrodynamics and takes account of the effects of both longitudinal expansion and transverse radial flow on the hydrodynamic evolution of the wakes and on the resulting particle production at the freezeout hypersurface. It makes repeated use of template solutions to linearized hydrodynamics in a Bjorken flow background with no transverse flow, templates that need only be computed once, and uses suitable rotations and boosts to map fluctuations from these templates to fluctuations at a point on the freezeout hypersurface in a way that incorporates the effects of the radial flow. We benchmark this procedure by comparing its results to results obtained from full $(3+1)$-dimensional nonlinear hydrodynamics calculations, find reasonable agreement, and find that our Efficient Wake procedure yields a much better description of the distribution of hadrons originating from jet wakes than does the older oversimplified procedure employed in the Hybrid Model. And, the Efficient Wake procedure is computationally efficient: it is at least tens of thousands of times faster than full nonlinear hydrodynamics calculations. Hence, we anticipate that when our new procedure is implemented in Monte Carlo analyses of jets in heavy ion collisions, for example in the Hybrid Model, it will greatly improve the description of the soft component of many jet and jet substructure observables as compared to experimental data.

hep-ph↗

arXiv2026

Local Thermalization of SU(2) Lattice Gauge Fields on Quantum Computers

We simulate the local thermalization dynamics for minimally truncated SU(2) pure gauge theory on linear plaquette chains with up to 151 plaquettes using IBM quantum computers. We study the time dependence of the entanglement spectrum, Rényi-2 entropy and anti-flatness on small subsystems. The quantum hardware results obtained after error mitigation agree with extrapolated classical simulator results for chains consisting of up to 101 plaquettes. Our results demonstrate the feasibility of local thermalization studies for chaotic quantum systems, such as nonabelian lattice gauge theories, on current noisy quantum computing platforms.

hep-lat↗

arXiv2026

Quantum Simulation of QCD in Axial Gauge

We study quantum simulation of SU(3) non-Abelian gauge theory dynamically coupled with fundamental fermions in $3+1$ dimensions by employing the lattice Hamiltonian in axial gauge that avoids Gauss's law constraints. The temporal component of the gauge field is analytically solved in terms of independent field degrees of freedom and a lattice regulated Green's function. The axial gauge condition is trivially maintained in time evolution, even under Trotterization. The gauge field degrees of freedom are expressed in the local field basis and can be efficiently transformed into the canonical conjugate momentum basis by local quantum Fourier transforms. We prove the number of qubits needed for describing all states up to an energy $E$ with an accuracy $ε$ on a lattice of volume $V$ at bare coupling $g$ is bounded as $16n_A V + 12n_f V$, where $n_A \approx \log_2 (\frac{64 E' V^{4/3}}{π^2ε} + \frac{32\sqrt{2}g n_f E'^{1/2} V^{7/6}}{\sqrt{3}π^3ε^{1/2}} ) $ is the number of qubits needed for each independent gauge field per site with a shifted energy $E'$, and $n_f$ denotes the number of fermion flavors. We then analyze a quantum algorithm for time evolution that is based on Trotterization, quantum Fourier transform, and Jordan-Wigner transformation, for which quantum circuits can be explicitly constructed under arbitrary gauge field truncation and digitization. We find the numbers of CNOT and single-qubit rotation gates both scale as $O(n_A^4 V^{4/3}) + O(V^{5/3})$ per Trotter step for fixed $n_f\leq 6$. We conclude that quantum resources needed for simulating real-time dynamics of lattice QCD scale polynomially with volume, energy, time, accuracy, and bare Hamiltonian parameters.

hep-lat↗

arXiv2026

The Utility of Sparse Error Detection in Quantum Simulations

The recent success of error detecting codes points toward their potential application to fault-tolerant simulations of nature. In this work, we examine the utility of sparse error detection for simulating lattice gauge theories using quantum computers. In particular, we study the time evolution of the lattice Schwinger model embedded into the Iceberg code family, $[[N+2, N, 2]]$, as well as the Hypercube code family, $[[2^N, N, 2]]$. The lattice of electrons and positrons in the axial gauge is embedded into a single code block or into multiple code blocks, and this work finds that large codeblocks are advantageous in the absence of connectivity constraints. Noisy classical simulations with realistic near-term error rates, infrequent syndrome measurements and physics-aware postselection are found to improve observable estimation. Under realistic noise rates for near-term quantum computers, this work finds that sparse error detection in quantum simulations has the potential to improve accuracy of observable estimation. Additional rounds of error detection are found to systematically drive errors in observables to the noise floor set by the code. These findings suggest that incorporating minimal implementations of fault tolerance in the near-term will enhance the performance of quantum simulations in nuclear physics and high-energy physics.

quant-ph↗

arXiv2026

Realizing Error Suppression in Partially Fault-Tolerant Quantum Simulations with IBM Quantum Computers

Quantum error-detecting codes offer a near-term path for improving the performance of quantum simulations on noisy hardware. Using IBM's superconducting quantum computer ibm_boston, we show that partially fault-tolerant encoded quantum simulations of the Ising model in 1+1D and 2+1D outperform their unencoded counterparts in estimating local observables. To represent 42 logical qubits on the heavy-hex quantum processor, 21 blocks of the [[4, 2, 2]] Iceberg code and up to 136 physical qubits are used. By pairing fault-tolerant syndrome extraction with non-fault-tolerant logical operations, this scheme preserves many of the benefits of error detection while avoiding the overhead typically required for a fully fault-tolerant logical gate set. The encoding's square logical connectivity, together with the freedom to place logical qubits within each block, enables simulations of a 2D spatial lattice with lower circuit depth than the unencoded implementation requires. We introduce Observable-Ranked Postselection, a selective-filtering technique based on syndrome correlations that recovers reliable results without the prohibitive shot loss of full syndrome postselection. Under the cumulative effect of device errors, this encoding improves local-observable accuracy over the unencoded baseline by 2-6% at intermediate times in 1+1D simulations, growing with circuit depth to over 200% in 2+1D at the latest times studied.

quant-ph↗

arXiv2026

Quantum Error Correction Codes for Truncated SU(2) Lattice Gauge Theories

We construct two quantum error correction codes for pure SU(2) lattice gauge theory in the electric basis truncated at the electric flux $j_{\rm max}=1/2$, which are applicable on quasi-1D plaquette chains, 2D honeycomb and 3D triamond and hyperhoneycomb lattices. The first code converts Gauss's law at each vertex into a stabilizer while the second only uses half of the vertices and is locally the carbon code. Both codes are able to correct single-qubit errors. The electric and magnetic terms in the SU(2) Hamiltonian are expressed in terms of logical gates in both codes. The logical-gate Hamiltonian in the first code exactly matches the spin Hamiltonian for gauge singlet states found in previous work.

quant-ph↗

arXiv2026

The Magic Barrier before Thermalization

We investigate the time dependence of anti-flatness in the entanglement spectrum, a measure for non-stabilizerness and lower bound for non-local quantum magic resource, on a subsystem of a linear SU(2) plaquette chain during thermalization. Tracing the time evolution of a large number of initial states, we find that the anti-flatness exhibits a barrier-like maximum during the time period when the entanglement entropy of the subsystem grows rapidly from the initial value to the microcanonical entropy. The location of the peak is strongly correlated with the time when the entanglement exhibits the strongest growth. This behavior is found for generic highly excited initial computational basis states and persists for coupling constants across the ergodic regime, revealing a universal structure of the entanglement spectrum during thermalization. We conclude that quantitative simulations of thermalization for nonabelian gauge theories require quantum computing. We speculate that this property generalizes to other quantum chaotic systems, a conjecture supported by analogous behavior observed in real-time simulations of the mixed-field Ising model.

quant-ph↗

arXiv2026

Tame the Umklapp Processes in Real-Time Lattice Simulation for Hydrodynamics: An Ising Field Theory Study

We calculate the real-time symmetric correlation function of the stress-energy tensor for a non-integrable Ising field theory consisting of three stable scalar particles via lattice Hamiltonian simulation. Using classical exact diagonalization and the matrix product state tensor network methods, we find that in the scaling region of the lattice theory, Umklapp processes are suppressed and the sound modes of relativistic hydrodynamics emerge at long wavelength and late time. The extracted ratio of bulk viscosity to entropy density is $ζ/s=14.19\pm 0.90$ and the speed of sound is $c_s/c=0.76 \pm 0.02$ at the temperature $T\approx 7.14$ in units of the lowest stable particle's mass. Our study demonstrates the utility of real-time lattice Hamiltonian simulation for describing hydrodynamization and calculating transport coefficients nonperturbatively.

hep-lat↗

arXiv2026

Eigenstate Thermalization in 1+1-Dimensional SU(2) Lattice Gauge Theory Coupled with Dynamical Fermions

We test the eigenstate thermalization hypothesis (ETH) in 1+1-dimensional SU(2) lattice gauge theory (LGT) with one flavor of dynamical fermions. Using the loop-string-hadron framework of the LGT with a bosonic cut-off, we exactly diagonalize the Hamiltonian for finite size systems and calculate matrix elements (MEs) in the eigenbasis for both local and non-local operators. We analyze different indicators to identify the parameter space for quantum chaos at finite lattice sizes and investigate how the ETH behavior emerges in both the diagonal and off-diagonal MEs. Our investigations allow us to study various time scales of thermalization and the emergence of random matrix behavior, and highlight the interplays of the several diagnostics with each other. Furthermore, from the off-diagonal MEs, we extract a smooth function that is closely related to the spectral function for both local and non-local operators. We find numerical evidence of the spectral gap and the memory peak in the non-local operator case. Finally, we investigate aspects of subsystem ETH in the lattice gauge theory and identify certain features in the subsystem reduced density matrix that are unique to gauge theories.

hep-th↗

arXiv2026

GeoCycler: Reward-Aligned 3D Diffusion for Constraint-Conditioned Cyclic Peptide Design

Cyclic peptides are attractive therapeutic modalities because their closed-ring topology can improve stability and target specificity. However, de novo cyclic peptide design remains challenging for diffusion generators, as macrocyclization requires satisfying sparse, non-smooth, and compositional geometric constraints. Existing constraint-conditioned methods largely rely on inference-time guidance, which can steer samples toward desired closures but does not directly change the learned generative distribution. We propose GeoCycler, a reward-weighted diffusion alignment framework for training conditional latent diffusion models toward macrocyclization feasibility. GeoCycler introduces a type-gated stair reward that activates distance-based shaping only when prerequisite residue or linker types are satisfied, providing dense geometric feedback while avoiding misleading signals from chemically incompatible anchors. Together with positive-only reward weighting and replay-based stabilization, GeoCycler aligns a single generator across multiple cyclization topologies. On the LNR benchmark, GeoCycler improves pass@5 closure success over strong guidance-based baselines across stapled, head-to-tail, disulfide, and bicyclic settings. In particular, it improves head-to-tail success by 20.8 percentage points over CP-Composer while maintaining comparable amino-acid and backbone-dihedral statistics. These results suggest that training-time alignment to sparse geometric constraints is a promising alternative to relying solely on post hoc sampling-time correction for cyclic peptide generation.

cs.CE↗

arXiv2026

Gluon Entanglement Entropy inside a Nucleon: A Toy Model

We construct a toy model of a nucleon, in which three static quarks interact via a SU(3) gauge field on a planar honeycomb lattice. The dynamics of the gauge field is described by the Kogut-Susskind Hamiltonian, truncated to the lowest three SU(3) irreducible representations. We show that the internal structure of the toy nucleon reflects salient features of the physical nucleon state. We then find the entanglement entropy of the gauge field within the nucleon state and compute its time evolution after a quench, in which all three valence quarks are suddenly removed. We show that the entanglement entropy in the final state is dominated by the dynamically generated contribution rather than the initial state entropy.

hep-ph↗

arXiv2026

CA-DEL: An Open Multi-Target, Multi-Modal Benchmark for Learning from DNA-Encoded Library Screens

The success of machine learning in drug discovery hinges on learning the relationship between a chemical structure and its biological activity. While DNA-Encoded Library (DEL) technology can generate the massive datasets required for this task, its primary signal -- sequencing read counts -- is an indirect and often noisy proxy for true molecular binding affinity. To address the scarcity of public benchmarks for developing robust models that can overcome this data challenge, we introduce CA-DEL, a multi-dimensional public benchmark featuring screens against three homologous carbonic anhydrase isoforms. While recent benchmarks like KinDEL have introduced 3D poses for kinase targets, CA-DEL distinguishes itself by focusing on the selectivity challenge among homologous Carbonic Anhydrase isoforms (CAII, CAIX, CAXII). Unlike benchmarks relying solely on noisy enrichment scores, CA-DEL integrates a rigorous validation set of experimentally determined binding affinities ($K_i$) from ChEMBL, establishing a critical Sim-to-Real evaluation paradigm: training on noisy DEL screens and testing on high-fidelity biophysical data.

q-bio.BM↗

arXiv2026

Quantum Simulation of QED in Coulomb Gauge

A recent work considered quantum simulation of Quantum Electrodynamics on a lattice in the Coulomb gauge with gauge degrees of freedom represented in the occupation basis in momentum space. Here we consider the more efficient representation of the gauge degrees of freedom in field basis in position space and develop a quantum algorithm for real-time simulation. We show that the continuum Coulomb gauge Hamiltonian is equivalent to the temporal gauge Hamiltonian when acting on physical states consisting of fermion and transverse gauge fields. The Coulomb gauge Hamiltonian is discretized by using the Green's function of the discrete Laplacian operator under the Dirichlet boundary conditions. Both the continuum Coulomb gauge Hamiltonian and the discretized one proposed here guarantee that the unphysical longitudinal gauge fields are decoupled and commute with the corresponding Hamiltonian. Thus there is no need to impose any constraint. The local gauge field basis and the canonically conjugate variable basis are swapped efficiently using the quantum Fourier transform. We prove that the qubit cost to represent physical states and the gate count for real-time simulation scale polynomially with the lattice size, energy, time, accuracy, and Hamiltonian parameters in lattice units. The gate cost here for implementing the time evolution of the gauge field is reduced at least by a factor on the order of $10^8$ for modest lattice size and accuracy level compared with the previous work.

quant-ph↗

arXiv2026

Minimally Truncated SU(3) Lattice Gauge Theory and String Tension

We study SU(3) gauge theory on small lattices in the minimal (qutrit) electric field truncation retaining only the ${\bf 1}, {\bf 3}, {\bf \overline{3}}$ representations for the link variables. Explicit expressions are given for the Kogut-Susskind Hamiltonian for the square plaquette chain and the two-dimensional honeycomb lattice. Our formalism can be easily extended to the minimally truncated general SU($N_c$) gauge theory. The addition of (static) quarks is discussed. We present results for the energy spectrum of the gauge field on these lattices by exact diagonalization of the Hamiltonian and analyze its statistical properties. We also compute the SU(3) string tension and discuss how it is modified by vacuum fluctuations. Finally, we calculate the potential energies of a static quark-antiquark pair and three static quarks and study their screening at finite temperature.

hep-lat↗

arXiv2025

Theory of Quarkonia as Probes for Deconfinement

This is a plenary talk given at Quark Matter 2025, summarizing recent theoretical developments for the understanding of quarkonium production in relativistic heavy ion collisions and how quarkonium uniquely probes the deconfined phase of QCD matter.

hep-ph↗

arXiv2025

CONFIDE: Hallucination Assessment for Reliable Biomolecular Structure Prediction and Design

Reliable evaluation of protein structure predictions remains challenging, as metrics like pLDDT capture energetic stability but often miss subtle errors such as atomic clashes or conformational traps reflecting topological frustration within the protein folding energy landscape. We present CODE (Chain of Diffusion Embeddings), a self evaluating metric empirically found to quantify topological frustration directly from the latent diffusion embeddings of the AlphaFold3 series of structure predictors in a fully unsupervised manner. Integrating this with pLDDT, we propose CONFIDE, a unified evaluation framework that combines energetic and topological perspectives to improve the reliability of AlphaFold3 and related models. CODE strongly correlates with protein folding rates driven by topological frustration, achieving a correlation of 0.82 compared to pLDDT's 0.33 (a relative improvement of 148\%). CONFIDE significantly enhances the reliability of quality evaluation in molecular glue structure prediction benchmarks, achieving a Spearman correlation of 0.73 with RMSD, compared to pLDDT's correlation of 0.42, a relative improvement of 73.8\%. Beyond quality assessment, our approach applies to diverse drug design tasks, including all-atom binder design, enzymatic active site mapping, mutation induced binding affinity prediction, nucleic acid aptamer screening, and flexible protein modeling. By combining data driven embeddings with theoretical insight, CODE and CONFIDE outperform existing metrics across a wide range of biomolecular systems, offering robust and versatile tools to refine structure predictions, advance structural biology, and accelerate drug discovery.

q-bio.BM↗

arXiv2025

Entanglement Properties of SU(2) Gauge Theory

We review recent and present new results on thermalization of nonabelian gauge theory obtained by exact numerical simulation of the real-time dynamics of $(2+1)$-dimensional SU(2) lattice gauge theory. We discuss: (1) tests confirming the Eigenstate Thermalization Hypothesis; (2) the entanglement entropy of sublattices, including the Page curve, the transition from area to volume scaling with increasing energy of the eigenstate and its time evolution that shows thermalization of localized regions to be a two-step process; (3) the absence of quantum many-body scars when higher gauge field representations are taken into account; (4) the spectral form factor, which exhibits the expected slope-ramp-plateau structure for late times; (5) the entanglement Hamiltonian for SU(2), which has properties in accordance with the Bisognano-Wichmann theorem; and (6) a measure for non-stabilizerness or ``magic'' that is found to reach its maximum during thermalization. We conclude that the thermalization of nonabelian gauge theories is a promising process to establish quantum advantage.

hep-lat↗

arXiv2025

Improved Honeycomb and Hyperhoneycomb Lattice Hamiltonians for Quantum Simulations of Non-Abelian Gauge Theories

Improved Kogut-Susskind Hamiltonians for quantum simulations of non-Abelian Yang-Mills gauge theories are developed for honeycomb (2+1D) and hyperhoneycomb (3+1D) spatial tessellations. This is motivated by the desire to identify lattices for quantum simulations that involve only 3-link vertices among the gauge field group spaces in order to reduce the complexity in applications of the plaquette operator. For the honeycomb lattice, we derive a classically ${\cal O}(b^2)$-improved Hamiltonian, with $b$ being the lattice spacing. Tadpole improvement via the mean-field value of the plaquette operator is used to provide the corresponding quantum improvements. We have identified the (non-chiral) hyperhoneycomb as a candidate spatial tessellation for 3+1D quantum simulations of gauge theories, and determined the associated ${\cal O}(b)$-improved Hamiltonian.

hep-lat↗