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Unified, Geometric Framework for Nonequilibrium Protocol Optimization

Controlling thermodynamic cycles to minimize the dissipated heat is a long-standing goal in thermodynamics, and more recently, a central challenge in stochastic thermodynamics for nanoscale systems. Here, we introduce a theoretical and computational framework for optimizing nonequilibrium control protocols that can transform a system between two distributions in a minimally dissipative fashion. These protocols optimally transport a system along paths through the space of probability distributions that minimize the dissipative cost of a transformation. Furthermore, we show that the thermodynamic metric—determined via a linear response approach—can be directly derived from the same objective function that is optimized in the optimal transport problem, thus providing a unified perspective on thermodynamic geometries. As a result, we investigate this unified geometric framework in two model systems and observe that our procedure for optimizing control protocols is robust beyond linear response.

36 MATERIALS SCIENCE↗

Tough Errors Are no Match (TEAM): Optimizing the Quantum Compiler for Noise Resilience

This report summarizes research performed under the Tough Errors Are no Match (TEAM) project. The primary focus of TEAM has been to research and develop a compilation toolbox leveraging techniques from quantum characterization and control, probabilistic programming, and approximate computing. Our goal was to develop robust protocols that can be integrated into quantum compilers to optimize and enhance the robustness of noisy computation. Here, we provide a summary of TEAM work focused on characterization and control of quantum systems.

97 MATHEMATICS AND COMPUTING↗

Marine Microeukaryote Metatranscriptomics: Sample Processing and Bioinformatic Workflow Recommendations for Ecological Applications

Microeukaryotes (protists) serve fundamental roles in the marine environment as contributors to biogeochemical nutrient cycling and ecosystem function. Their activities can be inferred through metatranscriptomic investigations, which provide a detailed view into cellular processes, chemical-biological interactions in the environment, and ecological relationships among taxonomic groups. Established workflows have been individually put forth describing biomass collection at sea, laboratory RNA extraction protocols, and bioinformatic processing and computational approaches. Here, we present a compilation of current practices and lessons learned in carrying out metatranscriptomics of marine pelagic protistan communities, highlighting effective strategies and tools used by practitioners over the past decade. We anticipate that these guidelines will serve as a roadmap for new marine scientists beginning in the realms of molecular biology and/or bioinformatics, and will equip readers with foundational principles needed to delve into protistan metatranscriptomics.

Cohen, Natalie R.↗

Certifying almost all quantum states with few single-qubit measurements

Certifying that an n -qubit state synthesized in the laboratory is close to a given target state is a fundamental task in quantum information science. However, existing rigorous protocols applicable to general target states have potentially prohibitive resource requirements in the form of either deep quantum circuits or exponentially many single-qubit measurements. Here we prove that almost all n -qubit target states, including those with exponential circuit complexity, can be certified from only O ( n 2 ) single-qubit measurements. Given access to the target state’s amplitudes, our protocol requires only O ( n 3 ) classical computation. This result is established by a technique that relates certification to the mixing time of a random walk. Our protocol has applications for benchmarking quantum systems, for optimizing quantum circuits to generate a desired target state and for learning and verifying neural networks, tensor networks and various other representations of quantum states using only single-qubit measurements. We show that such verified representations can be used to efficiently predict highly non-local properties of a synthesized state that would otherwise require an exponential number of measurements on the state. We demonstrate these applications in numerical experiments with up to 120 qubits and observe an advantage over existing methods such as cross-entropy benchmarking.

information theory and computation↗

Solving the Bernstein-Vazirani problem using Majorana-based topological quantum algorithms

Executing quantum algorithms using Majorana zero modes—a major milestone for the field of topological quantum computing—requires a platform that can be scaled to large quantum registers, can be controlled in real time and space, and a braiding protocol that uses the unique properties of these exotic particles. Here, we demonstrate the first successful simulation of a Majorana-based, fault-tolerant quantum algorithm to solve the Bernstein-Vazirani problem in two-dimensional magnet-superconductor hybrid structures from initialization to read-out of the final many-body state. Utilizing the Majorana zero modes’ topological properties, we introduce an optimized braiding protocol for the algorithm and a scalable architecture for its implementation with an arbitrary number of qubits. We visualize the algorithm protocol in real time and space by computing the non-equilibrium density of states, which is proportional to the time-dependent differential conductance, and the non-equilibrium charge density, which assigns a unique signature to each final state of the algorithm.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Universal energy-speed-accuracy trade-offs in driven nonequilibrium systems

The connection between measure theoretic optimal transport and dissipative nonequilibrium dynamics provides a language for quantifying nonequilibrium control costs, leading to a collection of thermodynamic speed limits, which rely on the assumption that the target probability distribution is perfectly realized. This is almost never the case in experiments or numerical simulations, so here we address the situation in which the external controller is imperfect. We obtain a lower bound for the dissipated work in generic nonequilibrium control problems that (1) is asymptotically tight and (2) matches the thermodynamic speed limit in the case of optimal driving. Along with analytically solvable examples, we refine this imperfect driving notion to systems in which the controlled degrees of freedom are slow relative to the nonequilibrium relaxation rate, and identify independent energy contributions from fast and slow degrees of freedom. Furthermore, we develop a strategy for optimizing minimally dissipative protocols based on optimal transport flow matching, a generative machine learning technique. Furthermore, this latter approach ensures the scalability of both the theoretical and computational framework we put forth. Crucially, we demonstrate that we can compute the terms in our bound numerically using efficient algorithms from the computational optimal transport literature and that the protocols we learn saturate the bound.

59 BASIC BIOLOGICAL SCIENCES↗

Certified randomness using a trapped-ion quantum processor

Although quantum computers can perform a wide range of practically important tasks beyond the abilities of classical computers, realizing this potential remains a challenge. An example is to use an untrusted remote device to generate random bits that can be certified to contain a certain amount of entropy. Certified randomness has many applications but is impossible to achieve solely by classical computation. Here we demonstrate the generation of certifiably random bits using the 56-qubit Quantinuum H2-1 trapped-ion quantum computer accessed over the Internet. Our protocol leverages the classical hardness of recent random circuit sampling demonstrations: a client generates quantum ‘challenge’ circuits using a small randomness seed, sends them to an untrusted quantum server to execute and verifies the results of the server. We analyse the security of our protocol against a restricted class of realistic near-term adversaries. Using classical verification with measured combined sustained performance of 1.1 × 10 18 floating-point operations per second across multiple supercomputers, we certify 71,313 bits of entropy under this restricted adversary and additional assumptions. Our results demonstrate a step towards the practical applicability of present-day quantum computers.

computer science↗

Optimization of Water-Alternating-CO2 Injection Field Operations Using a Machine-Learning-Assisted Workflow

Summary This paper will present a robust workflow to address multiobjective optimization (MOO) of carbon dioxide (CO2)-enhanced oil recovery (EOR)-sequestration projects with a large number of operational control parameters. Farnsworth unit (FWU) field, a mature oil reservoir undergoing CO2 alternating water injection (CO2-WAG) EOR, will be used as a field case to validate the proposed optimization protocol. The expected outcome of this work would be a repository of Pareto-optimal solutions of multiple objective functions, including oil recovery, carbon storage volume, and project economics. FWU’s numerical model is used to demonstrate the proposed optimization workflow. Because using MOO requires computationally intensive procedures, machine-learning-based proxies are introduced to substitute for the high-fidelity model, thus reducing the total computation overhead. The vector machine regression combined with the Gaussian kernel (Gaussian-SVR) is used to construct proxies. An iterative self-adjusting process prepares the training knowledge base to develop robust proxies and minimizes computational time. The proxies’ hyperparameters will be optimally designed using Bayesian optimization to achieve better generalization performance. Trained proxies will be coupled with multiobjective particle swarm Optimization (MOPSO) protocol to construct the Pareto-front solution repository. The outcomes of this workflow will be a repository containing Pareto-optimal solutions of multiple objectives considered in the CO2-WAG project. The proposed optimization workflow will be compared with another established methodology using a multilayer neural network (MLNN) to validate its feasibility in handling MOO with a large number of parameters to control. Optimization parameters used include operational variables that might be used to control the CO2-WAG process, such as the duration of the water/gas injection period, producer bottomhole pressure (BHP) control, and water injection rate of each well included in the numerical model. It is proved that the workflow coupling Gaussian-SVR proxies and the iterative self-adjusting protocol is more computationally efficient. The MOO process is made more rapid by squeezing the size of the required training knowledge base while maintaining the high accuracy of the optimized results. The outcomes of the optimization study show promising results in successfully establishing the solution repository considering multiple objective functions. Results are also verified by validating the Pareto fronts with simulation results using obtained optimized control parameters. The outcome from this work could provide field operators an opportunity to design a CO2-WAG project using as many inputs as possible from the reservoir models. The proposed work introduces a novel concept that couples Gaussian-SVR proxies with a self-adjusting protocol to increase the computational efficiency of the proposed workflow and to guarantee the high accuracy of the obtained optimized results. More importantly, the workflow can optimize a large number of control parameters used in a complex CO2-WAG process, which greatly extends its utility in solving large-scale MOO problems in various projects with similar desired outcomes.

Energy & Fuels↗

Perfect quantum state transfer on diamond fractal graphs

In the quest for designing novel protocols for quantum information and quantum computation, an important goal is to achieve perfect quantum state transfer for systems beyond the well-known one- dimensional cases, such as 1D spin chains. Here, we use methods from fractal analysis and probability to find a new class of quantum spin chains on fractal-like graphs (known as diamond fractals) which support perfect quantum state transfer and which have a wide range of different Hausdorff and spectral dimensions. The resulting systems are spin networks combining Dyson hierarchical model structure with transverse permutation symmetries of varying order.

97 MATHEMATICS AND COMPUTING↗

High-Performance Semiempirical Excited-State Molecular Dynamics Powered by Graphics Processing Units

Here, this Letter introduces excited-state molecular dynamics in PYSEQM, a GPU-accelerated semiempirical quantum chemistry engine implemented in PyTorch. The new module enables Born–Oppenheimer molecular dynamics (BOMD) using configuration-interaction singles and random phase approximation for excited states, allowing long trajectories and large statistical ensembles to be simulated efficiently on a single GPU. We also implement an extended Lagrangian excited-state BOMD (XL-ESMD) scheme that propagates auxiliary electronic variables, enabling relaxed ground and excited-state convergence thresholds without compromising energy conservation. The excited-state BOMD implementation scales smoothly from small chromophores to a nearly 900-atom dendrimer (taking 6.5 s per MD step). PYSEQM also supports batched execution, allowing many geometries or trajectories to be evaluated in a single GPU launch, substantially increasing throughput and making ensemble-based protocols routine. As a demonstration, we compute absorption, emission, and infrared spectra from trajectories propagated on the ground and first excited states. The XL-ESMD scheme yields identical spectra at significantly lower computational cost, establishing the role of extended Lagrangian based dynamics for efficient excited-state BOMD simulations. Beyond raw performance, PYSEQM’s PyTorch foundation provides automatic differentiation for forces, efficient GPU batching, and seamless interfacing with machine learning models. These capabilities position PYSEQM as a practical platform for machine learning-augmented excited-state dynamics and lay the foundation for future data-driven nonadiabatic excited-state dynamics modeling of ultrafast spectroscopic probes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Calibration of energy density functionals with deformed nuclei

Nuclear density functional theory is the prevalent theoretical framework for accurately describing nuclear properties at the scale of the entire chart of nuclides. Given an energy functional and a many-body scheme (e.g., single- or multireference level), the predictive power of the theory depends strongly on how the parameters of the energy functionals have been calibrated with experimental data. Expanded algorithms and computing power have enabled recent optimization protocols to include data in deformed nuclei in order to optimize the coupling constants of the energy functional. The primary motivation of this work is to test the robustness of such protocols with respect to some of the technical and numerical details of the underlying calculations, especially when the calibration explores a large parameter space. To this end, we quantify the effect of these uncertainties on both the optimization and statistical emulation of composite objective functions. We also emphasize that Bayesian calibration can provide better estimates of the theoretical errors used to define objective functions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

OLCF Summit Supercomputer GPU Snapshots During Double-Bit Errors and Normal Operations

As we move into the exascale era, the power and energy footprints of high-performance computing (HPC) systems have grown significantly larger. Due to the harsh power and thermal conditions the system, components are exposed to extreme operating conditions. Operation of such modern HPC systems requires deep insights into long term system behavior to maintain its efficiency as well as its longevity. To help the HPC community to gain such insights, we provide double-bit errors using system telemetry data and logs collected from the Summit supercomputer, equipped with 27,648 Tesla V100 GPUs with 2nd-generation high-bandwidth memory (HBM2). The dataset relies on Nvidia XID records internally collected by GPU firmware at the time of failure occurrence, on the reboot-time logs of each Summit node, on node-level job scheduler records collected after each job termination, and on a 1Hz data rate from the baseboard management controllers (BMCs) of each Summit compute node using the OpenBMC event subscription protocol. Technical details can be found in the paper Oles et. al “Understanding GPU Memory Corruption at Extreme Scale: The Summit Case Study” ICS’24 (https://doi.org/10.1145/3650200.3656615).

97 MATHEMATICS AND COMPUTING↗

Parallel-in-time quantum simulation via Page and Wootters quantum time

In the past few decades, researchers have created a veritable zoo of quantum algorithms by drawing inspiration from classical computing, information theory, and even from physical phenomena. Here, we present quantum algorithms for parallel-in-time simulations that are inspired by the Page and Wootters formalism. In this framework, and thus in our algorithms, the classical time variable of quantum mechanics is promoted to the quantum realm by introducing a Hilbert space of “clock” qubits that are then entangled with the “system” qubits. We show that our algorithms can compute temporal properties over 𝑁 different times of many-body systems by only using log⁡(𝑁) clock qubits. As such, we achieve an exponential trade-off between time and spatial complexities. In addition, we rigorously prove that the entanglement created between the system qubits and the clock qubits has operational meaning, as it encodes valuable information about the system’s dynamics. We also provide a circuit depth estimation of all the protocols, showing a running time advantage in computation times over traditional sequential-in-time algorithms. In particular, for the case when the dynamics are determined by the Aubry-Andre model, we present a hybrid method for which our algorithms have a depth that only scales as 𝒪⁡(log⁡(𝑁)⁢𝑛). As a by-product, we can relate the previous schemes to the problem of equilibration of an isolated quantum system, thus indicating that our framework enables a new dimension for studying dynamical properties of many-body systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Sparse Phase Ansatzes for Resource-Efficient Qudit State Preparation via the SNAP-Displacement Protocol

Efficient preparation of nonclassical bosonic states is a central requirement for quantum computing, simulation, and precision metrology. We study resource-efficient quantum state preparation in bosonic qudit systems using the SNAP-displacement (SD) protocol. Existing SD-based approaches typically require a large number of gates and SNAP phases, resulting in complex control pulses with longer ansatz durations and amplified impact of photon-loss and control errors. In this work, we focus on the near- to medium-term regime, in which noisy quantum devices impose trade-offs on the fidelity that can be achieved, which must be taken into account. Specifically, we propose to optimize only a subset of the SNAP phases and introduce three progressively more general sparse ansatzes. To provide fine-grained control and identify the most suitable ansatz for a given target fidelity, we further employ a scalarized multi-objective optimization that trades off fidelity against either the number of phases or the duration of the ansatz. Numerical results for several target states and qudit dimensions up to $d=64$, evaluated through the hypervolume of the Pareto frontiers, show that these sparse ansatzes achieve favorable trade-offs over the fully parameterized SD protocol in both ideal and noisy settings. The advantage is strongest and most consistent when minimizing the number of phases, while improvements in ansatz duration are smaller and more dependent on the target-state family and noise level, suggesting a practical route to more efficient near- and medium-term bosonic state preparation.

Ferrari Dacrema, Maurizio [Milan Polytechnic] (ORC↗

Modbus RTU for Embedded Cyber Secure Inverter Controller

The Modbus communication protocol is a widely adopted communication standard in industrial control systems. This communication protocol is known for being reliable and straightforward to implement while being versatile in terms of its operating parameters while supporting multiple formats over various hardware infrastructures and architectures. Many intelligent devices such as Programmable Logic Controllers (PLCs), Human-Machine Interfaces (HMIs), Internet-of-Things (IoT), and various Operational Technologies (OT) utilize Modbus for their communication systems. These types of systems must communicate with each other through a standardized and central communication process. To support the integration of these modular systems, a Field-Programmable Gate Array (FPGA) can act as an embedded central routing fabric for this communication to take place. Embedded systems are versatile enough to interface with various devices and systems to accomplish various goals. Additionally, embedded systems require relatively small physical designs to minimize the required resources to facilitate the intended application by providing low-level system access. This minimization of system resources goes hand in hand with reducing the financial cost of a proposed solution or system. As remotely collaborating researchers often use FPGAs to prototype designs that are required to have a method for data transmission among systems, it is imperative to provide a baseline standard for communications among devices and systems. A typical method of implementing the Modbus RTU communication protocol in an embedded environment is using integrated logic architectures within the FPGA called “Intellectual Property (IP) cores.” IP cores can be designed using integrated logic or circuit designs to function as an embedded processor. These IP cores can then perform the required computational actions to support the Modbus RTU communication protocol by utilizing high-level programming languages such as the C programming language. The hardware description language of Very High-Speed Integrated Circuit Hardware Description Language (VHDL) allows for the control of real hardware at the logic gate and signal level. These logic gates and signals can be designed and controlled to perform desired actions based on the system design. Programming an FPGA using VHDL allows an individual to access the lowest abstraction level of the system during FPGA development. This level of abstraction is referred to as the register-transfer level (RTL), which gives access to manipulating values and variables at the register level. This register-level manipulation provides precision over creating the logical circuit within the FPGA, thus minimizing the required code to perform desired operations. The Modbus RTU communication protocol can be implemented within an FPGA using VHDL programming to establish a standardized and embedded serial communication pathway. This implementation provides a standardized communication protocol to streamline research efforts among researchers, thus increasing the efficiency of research efforts. Additionally, this Modbus RTU implementation requires fewer resources when compared to typical communication protocol implementations that utilize an IP core, reducing the hardware requirement for effective research efforts.

communication↗

Privacy-Preserving Knowledge Transfer with Bootstrap Aggregation of Teacher Ensembles

There is a need to transfer knowledge among institutions and organizations to save effort in annotation and labeling or in enhancing task performance. However, knowledge transfer is difficult because of restrictions that are in place to ensure data security and privacy. Institutions are not allowed to exchange data or perform any activity that may expose personal information. With the leverage of a differential privacy algorithm in a high-performance computing environment, we propose a new training protocol, Bootstrap Aggregation of Teacher Ensembles (BATE), which is applicable to various types of machine learning models. The BATE algorithm is based on and provides enhancements to the PATE algorithm, maintaining competitive task performance scores on complex datasets with underrepresented class labels.We conducted a proof-of-the-concept study of the information extraction from cancer pathology report data from four cancer registries and performed comparisons between four scenarios: no collaboration, no privacy-preserving collaboration, the PATE algorithm, and the proposed BATE algorithm. The results showed that the BATE algorithm maintained competitive macro-averaged F1 scores, demonstrating that the suggested algorithm is an effective yet privacy-preserving method for machine learning and deep learning solutions.

Yoon, Hong-Jun↗

Heterogeneous Multi-Domain Dataset Synthesis to Facilitate Privacy and Risk Assessments in Smart City IoT

The emergence of the Smart Cities paradigm and the rapid expansion and integration of Internet of Things (IoT) technologies within this context have created unprecedented opportunities for high-resolution behavioral analytics, urban optimization, and context-aware services. However, this same proliferation intensifies privacy risks, particularly those arising from cross-modal data linkage across heterogeneous sensing platforms. To address these challenges, this paper introduces a comprehensive, statistically grounded framework for generating synthetic, multimodal IoT datasets tailored to Smart City research. The framework produces behaviorally plausible synthetic data suitable for preliminary privacy risk assessment and as a benchmark for future re-identification studies, as well as for evaluating algorithms in mobility modeling, urban informatics, and privacy-enhancing technologies. As part of our approach, we formalize probabilistic methods for synthesizing three heterogeneous and operationally relevant data streams—cellular mobility traces, payment terminal transaction logs, and Smart Retail nutrition records—capturing the behaviors of a large number of synthetically generated urban residents over a 12-week period. The framework integrates spatially explicit merchant selection using K-Dimensional (KD)-tree nearest-neighbor algorithms, temporally correlated anchor-based mobility simulation reflective of daily urban rhythms, and dietary-constraint filtering to preserve ecological validity in consumption patterns. In total, the system generates approximately 116 million mobility pings, 5.4 million transactions, and 1.9 million itemized purchases, yielding a reproducible benchmark for evaluating multimodal analytics, privacy-preserving computation, and secure IoT data-sharing protocols. To show the validity of this dataset, the underlying distributions of these residents were successfully validated against reported distributions in published research. We present preliminary uniqueness and cross-modal linkage indicators; comprehensive re-identification benchmarking against specific attack algorithms is planned as future work. This framework can be easily adapted to various scenarios of interest in Smart Cities and other IoT applications. By aligning methodological rigor with the operational needs of Smart City ecosystems, this work fills critical gaps in synthetic data generation for privacy-sensitive domains, including intelligent transportation systems, urban health informatics, and next-generation digital commerce infrastructures.

IoT↗