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Untangling the Mysteries of Knots with Quantum Computers

What Quantum Advantage actually looks like

March 25, 2025

By Konstantinos Meichanetzidis

One of the greatest privileges of working directly with the world’s most powerful quantum computer at ԹϺ is building meaningful experiments that convert theory into practice. The privilege becomes even more compelling when considering that our current quantum processor – our H2 system – will soon be enhanced by Helios, a quantum computer potentially a stunning trillion times more powerful, and due for launch in just a few months. The moment has now arrived when we can build a timeline for applications that quantum computing professionals have anticipated for decades and which are experimentally supported.

ԹϺ’s applied algorithms team has released an end-to-end implementation of a quantum algorithm to solve a central problem in knot theory. Along with an efficiently verifiable benchmark for quantum processors, it allows for concrete resource estimates for quantum advantage in the near-term. The research team, included ԹϺ researchers Enrico Rinaldi, Chris Self, Eli Chertkov, Matthew DeCross, David Hayes, Brian Neyenhuis, Marcello Benedetti, and Tuomas Laakkonen of the Massachusetts Institute of Technology. In this article, Konstantinos Meichanetzidis, a team leader from ԹϺ’s AI group who led the project, writes about the problem being addressed and how the team, adopting an aggressively practical mindset, quantified the resources required for quantum advantage:

Knot theory is a field of mathematics called ‘low-dimensional topology’, with a rich history, stemming from a wild idea proposed by Lord Kelvin, who conjectured that chemical elements are different knots formed by vortices in the aether. Of course, we know today that the aether theory was falsified by the Michelson-Morley experiment, but mathematicians have been classifying, tabulating, and studying knots ever since. Regarding applications, the pure mathematics of knots can find their way into cryptography, but knot theory is also intrinsically related to many aspects of the natural sciences. For example, it naturally shows up in certain spin models in statistical mechanics, when one studies thermodynamic quantities, and the magnetohydrodynamical properties of knotted magnetic fields on the surface of the sun are an important indicator of solar activity, to name a few examples. Remarkably, physical properties of knots are important in understanding the stability of macromolecular structures. This is highlighted by work of Cozzarelli and Sumners in the 1980’s, on the topology of DNA, particularly how it forms knots and supercoils. Their interdisciplinary research helped explain how enzymes untangle and manage DNA topology, crucial for replication and transcription, laying the foundation for using mathematical models to predict and manipulate DNA behavior, with broad implications in drug development and synthetic biology. Serendipitously, this work was carried out during the same decade as Richard Feynman, David Deutsch, and Yuri Manin formed the first ideas for a quantum computer.

Most importantly for our context, knot theory has fundamental connections to quantum computation, originally outlined by Witten’s work in topological quantum field theory, concerning spacetimes without any notion of distance but only shape. In fact, this connection formed the very motivation for attempting to build topological quantum computers, where anyons – exotic quasiparticles that live in two-dimensional materials – are braided to perform quantum gates. The relation between knot theory and quantum physics is the most beautiful and bizarre facts you have never heard of.

The fundamental problem in knot theory is distinguishing knots, or more generally, links. To this end, mathematicians have defined link invariants, which serve as ‘fingerprints’ of a link. As there are many equivalent representations of the same link, an invariant, by definition, is the same for all of them. If the invariant is different for two links then they are not equivalent. The specific invariant our team focused on is the Jones polynomial.

Four equivalent representations of the trefoil knot, the simplest non-trivial knot.
They all have the same Jones polynomial, as it is an invariant.
These knots have different Jones polynomials, so they are not equivalent.

The mind-blowing fact here is that any quantum computation corresponds to evaluating the Jones polynomial of some link, as shown by the works of Freedman, Larsen, Kitaev, Wang, Shor, Arad, and Aharonov. It reveals that this abstract mathematical problem is truly quantum native. In particular, the problem our team tackled was estimating the value of the Jones polynomial at the 5th root of unity. This is a well-studied case due to its relation to the infamous Fibonacci anyons, whose braiding is capable of universal quantum computation.

Building and improving on the work of Shor, Aharonov, Landau, Jones, and Kauffman, our team developed an efficient quantum algorithm that works end-to end. That is, given a link, it outputs a highly optimized quantum circuit that is readily executable on our processors and estimates the desired quantity. Furthermore, our team designed problem-tailored error detection and error mitigation strategies to achieve a higher accuracy.

Demonstration of the quantum algorithm on the H2 quantum computer for estimating the value of Jones polynomial of a link with ~100 crossings. The raw signal (orange) can be amplified (green) with error detection, and corrected via a problem-tailored error mitigation method (purple), bringing the experimental estimate closer to the actual value (blue).

In addition to providing a full pipeline for solving this problem, a major aspect of this work was to use the fact that the Jones polynomial is an invariant to introduce a benchmark for noisy quantum computers. Most importantly, this benchmark is efficiently verifiable, a rare property since for most applications, exponentially costly classical computations are necessary for verification. Given a link whose Jones polynomial is known, the benchmark constructs a large set of topologically equivalent links of varying sizes. In turn, these result in a set of circuits of varying numbers of qubits and gates, all of which should return the same answer. Thus, one can characterize the effect of noise present in a given quantum computer by quantifying the deviation of its output from the known result.

The benchmark introduced in this work allows one to identify the link sizes for which there is exponential quantum advantage in terms of time to solution against the state-of-the-art classical methods. These resource estimates indicate our next processor, Helios, with 96 qubits and at least 99.95% two-qubit gate-fidelity, is extremely close to meeting these requirements. Furthermore, ԹϺ’s hardware roadmap includes even more powerful machines that will come online by the end of the decade. Notably, an advantage in energy consumption emerges for even smaller link sizes. Meanwhile, our teams aim to continue reducing errors through improvements in both hardware and software, thereby moving deeper into quantum advantage territory.

Rigorous resource estimation of our quantum algorithm pinpoints the exponential quantum advantage quantified in terms of time-to-solution, namely the time necessary for the classical state-of-the-art to reach the same error as the achieved by quantum. The advantage crossover happens at large link sizes, requiring circuits with ~85 qubits and ~8.5k two-qubit gates, assuming 99.99% two-qubit gate fidelity and 30ms per circuit-layer. The classical algorithms are assumed to run on the Frontier Supercomputer.

The importance of this work, indeed the uniqueness of this work in the quantum computing sector, is its practical end-to-end approach. The advantage-hunting strategies introduced are transferable to other “quantum-easy classically-hard” problems. Our team’s efforts motivate shifting the focus toward specific problem instances rather than broad problem classes, promoting an engineering-oriented approach to identifying quantum advantage. This involves first carefully considering how quantum advantage should be defined and quantified, thereby setting a high standard for quantum advantage in scientific and mathematical domains. And thus, making sure we instill confidence in our customers and partners.

Edited

About ԹϺ

ԹϺ, the world’s largest integrated quantum company, pioneers powerful quantum computers and advanced software solutions. ԹϺ’s technology drives breakthroughs in materials discovery, cybersecurity, and next-gen quantum AI. With over 500 employees, including 370+ scientists and engineers, ԹϺ leads the quantum computing revolution across continents. 

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August 18, 2026
Teaching AI with Quantum Data

AI + quantum computing: ԹϺ, NVIDIA, and Pfizer have combined transformer-based generative AI with quantum computing to automatically generate high-quality quantum chemistry circuits more efficiently than traditional optimization methods.

Practical pharma impact: The approach was used to prepare molecular ground states and validated on ԹϺ’s Helios hardware, demonstrating a path toward larger-scale computational chemistry and drug discovery.

Long-term vision: The team aims to build quantum foundation models that learn from increasingly complex quantum data, eventually enabling AI to design circuits for molecules too large for classical simulation.

Quantum computing has long promised a future that expands what we can do with compute — for example, in molecular simulation, materials discovery, or pharmaceuticals development. But between that promise and practical utility sits a stubborn bottleneck: quantum state preparation.

To run any algorithm on a quantum computer, you must first put the qubits in the right starting state. Think of it like setting up a Rube Goldberg machine- except in this case, you’re not sure exactly which initial setup will give you the results you want. This is what makes quantum state preparation so important: your choice of initial state dictates the accuracy and cost of the rest of the calculation.

We teamed up with NVIDIA and Pfizer to tackle this problem, with an eye towards developing meaningful industrial workflows. The result is a new generative quantum AI framework, called ADAPT-GQE, which we consider to be a canonical instance of GenQAI. ADAPT-GQE uses quantum data to train transformer models that ultimately synthesize quantum chemistry circuits faster, with better outcomes, in a sort of ‘virtuous cycle’.

Ultimately, this means we have developed a new interface between quantum computing and AI. By treating quantum circuit generation as a language modelling problem, we now have a system that can generate high-quality ground-state preparation circuits - with comparable or improved state preparation accuracy.

The Magic – and Difficulty – of Computational Chemistry

The goal of computational chemistry is to learn about chemical properties without performing expensive, time-consuming, and sometimes dangerous “wet-lab” experiments.

In principle, you can replace the majority of your physical experiments with computer simulations, saving billions of dollars and years of time.

In reality, computational chemistry is very tricky. To accurately simulate a chemical inside of a computer, you have to build it from the ground up. You start with a collection of atoms (in the case of imipramine, you have 19 Carbon atoms, 24 Hydrogen atoms, and 2 Nitrogen atoms). Then, like Nature’s ‘lego’, you assemble those atoms into a molecule: you set bond lengths, strengths, angles, interactions, and so on.

This is not straightforward: a single molecule can exist in many forms; with different angles, rotations, etc. We will call these different forms ‘conformations’.

Then, to actually estimate chemical properties, or to explore chemical reaction pathways, you have to reproduce the detailed physics that goes on at the atomic level: take your chosen conformation then figure out how each orbital is occupied, how the electrons are interacting with each other or the atomic nuclei, how is the addition of heat or a catalyst going to affect things.... it gets complicated, quickly.

Despite all this, computational chemistry is a powerhouse in pharmaceutical development. Right now, pharmaceutical companies save money and time by simulating as much as they can on computers, avoiding time consuming and expensive laboratory experiments. However, even with ~50 years of development, the existing classical methods have very real limitations.

This is where quantum computing comes in: this new computational paradigm can elide those limitations because it has many of the “hard parts” (like superposition or entanglement) natively encoded. Used correctly, quantum computing promises to break old barriers, further improving margins for pharma companies across the globe while contributing to meaningful, impactful, discoveries.

A Virtuous Cycle: Using Quantum Data to Train AI, Which Then Designs Better Quantum Circuits

While quantum computational chemistry is one of the strongest candidates for near-term quantum advantage, current hardware is still in the earlier stages of development. With limited qubits and error rates, algorithm designers need to make every gate count, keep circuits shallow, and be able to tolerate some level of noise.

This is where generative AI enters the picture.

Instead of hand-designing chemistry circuits and laboriously experimenting to see how well they run, there is another idea: what if we trained an AI to solve the problems that quantum computational chemistry faces?

Using this approach, not only can we save time and resources; but we can shorten the timeline to realize practical results. With better state prep and other circuits, applications that were once considered far in the future come into view.

Our first attempt at this is called ADAPT-GQE. The central idea behind ADAPT-GQE is deceptively simple: instead of laboriously searching for good quantum circuits from scratch, train a transformer model to generate them directly.

Importantly, the framework is model-agnostic, which we showed by deploying it on complementary transformer architectures - (a pretrained LLM) and (trained from scratch).

From Iterative Optimization to Generative Models

The initial goal here is to find the ‘ground state’ of the molecule imipramine (this is the electronic state with the smallest amount of energy stored inside it). To do this, you have to find the right ‘state preparation circuit’, as described above.

Until now, a leading method for finding the ground state with quantum computers was the ‘Variational Quantum Eigensolver (VQE)’, a hybrid quantum-classical approach. The VQE process starts with a ‘guess’ circuit for a particular conformation of the molecule. The quantum computer runs the circuit to measure the associated energy of the molecule. This result is fed back into a classical optimizer that then tweaks the circuit parameters, hopefully resulting in one with a lower molecular energy. This loop repeats until a minimum energy is found.

Unfortunately, VQE has a few severe limitations that make it infeasible for widespread use. The recently proposed ADAPT-VQE was a crucial step forward meant to address some of the issues with “plain” VQE. In ADAPT-VQE, instead of starting with a guess for the initial circuit, the process builds a circuit in steps by selecting operators from a pool(typically using gradient information) and optimizing. This approach can be more effective, but unfortunately still grows too large too quickly.

This is where the joint team jumped in.

Combining the best of all worlds, the team’s new framework, ADAPT-GQE, combines AI with the ADAPT-VQE to create something entirely new – and something that, so far, is a scalable, hardware-validated pathway toward automated quantum circuit synthesis.

First, transformers (in this case, Nemotron and Gemma) are trained via supervised fine-tuning on ADAPT-VQE data. In this way, the old method isn’t thrown away but is instead treated as a high-quality data-producing “oracle”.

Then, once the transformer has been initially trained, it defines a distribution over circuits, each one with some probability of corresponding to the ground state. This distribution can be used in a fine-tuning loop, for example, reinforcement learning. In reinforcement learning, the framework takes a circuit from that distribution, runs it, and measures the energy. It feeds the results back into the transformer, which adjusts its distribution. Over time, the model learns to prioritize circuits that prepare increasingly accurate ground states.

Crucially, reinforcement learning allows the system to surpass its original training data instead of merely imitating it. The model is no longer acting as a compressed lookup table for ADAPT-VQE. It begins exploring novel circuit configurations that may outperform the teacher algorithm itself. This is one of the most important conceptual shifts in the project.

In this case, instead of running all the initial circuits on ԹϺ’s Helios, the reinforcement learning circuits were run using NVIDIA accelerated computing and the CUDA-Q platform, simulating a quantum processor.

Finally, once the transformers are optimized via reinforcement learning, the best resulting circuits are validated for accuracy and feasibility, by running them using InQuanto and on ԹϺ’s newest hardware, Helios. With InQuanto v5.2, users can now with both the Helios quantum computer and the Selene quantum emulator through Nexus.

This powerful combination of InQuanto and Nexus enabled the execution one of the largest AI-generated quantum chemistry circuits to date on a quantum computer; helping to turn the promise of quantum computing into a practical tool for pharmaceutical development.

Teaching a Transformer

Looking farther in the future, the researchers envision something much larger than a single molecular benchmark.

For bigger and more complex molecules, ADAPT-VQE won’t work in the first place as the initial training “oracle”. In addition, the molecular energy calculations used in the reinforcement learning grow too large for classical systems simulating quantum computers, so the quantum processor becomes essential.

Luckily, this is not a problem. The ultimate goal of the ADAPT-GQE framework is to develop a “curriculum” for the transformers. This means instead of re-training them for every new molecule, you instead keep what you already learned, and expand your knowledge from there.

By initially teaching it on molecules that are smaller, and that can be fully simulated, you ensure it learns on good data that can be double checked using known methods. From there, you can carefully build up the complexity to see how the transformer learns. Eventually, you hope to train it on molecules that can’t be simulated classically, using purely quantum data, all the while getting closer to the complexity levels you’re chasing.

This penultimate result is called a ‘foundation model’, which is a massive AI neural network trained on vast, broad datasets that can be adapted to a wide variety of downstream tasks. In this case, the team is building the very ‘foundations’ of a model that can solve the ‘electronic structure problem’, which is the core computational challenge lying at the heart of quantum (and classical) computational chemistry.

A New Interface Between AI and Quantum Computing

What makes this work particularly interesting is that it treats quantum circuit generation as a language modeling problem: circuits become sequences, transformers learn distributions over those sequences, and reinforcement learning optimizes them against physical reward functions.

The result is an AI system capable of proposing quantum circuits that were never explicitly programmed by humans.

That does not mean generative AI is replacing physics or chemistry. Instead, it is becoming a new interface layer for navigating unimaginably large search spaces that traditional optimization methods struggle to explore efficiently.

For quantum chemistry, that could become transformative.

If successful, frameworks like ADAPT-GQE may eventually allow researchers to synthesize useful quantum circuits for molecular systems too large for classical computation, accelerating everything from materials discovery to pharmaceutical design.

The broader implication is difficult to ignore: foundation models may eventually extend beyond language, images, and code — and into the fabric of physical reality itself.

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August 17, 2026
Accuracy Is the Foundation of Meaningful Quantum Computing

Recently, industry peers—including ԹϺ’s Startup Program Partners and , as well as our partner —published a exploring quantum magnetism that “extends beyond the reach of the state-of-the-art classical methods considered;” evidence of a quantum advantage result. Interestingly, the team validated their results on ԹϺ machines (both Helios and System Model H2).

In 2025, ), exploring a similar system - also at scales that frustrate classical computation. This got us thinking: with more successes like this in the literature, what does this mean for the ecosystem at large? What are the key lessons to learn from these early demonstrations? And, perhaps most importantly, what’s next?

We Are Entering the Era of ‘What’, Not ‘When’

The answer to the first question, ‘what does this mean for the ecosystem at large’, is a delight to answer. After decades of promises, we are finally in the era where quantum computing is matched with, if not outright exceeding, classical HPC and supercomputing.

Examples of (complexity-theory proven) quantum advantage are already common, usually in the form of . This was extended to , which was one of the earliest commercial applications of quantum computing.

Since then, we have seen a number of results from different groups that push the limits of classical computing while exploring ‘real’ problems; these range from papers exploring (as mentioned above), to papers exploring things like or

Whether or not these are definitively ‘quantum advantage’ results is almost beside the point. They mark a distinct place on the path towards broad scale quantum utility, when quantum computers will be widely useful for researchers and industry alike. More importantly, these papers all speak to a certain level of ‘technological readiness’, showing that quantum computers are now proven to work on problems that are relevant (to some people, at least), at scales that aren’t easily reproduced elsewhere.

Accuracy is a Baseline Requirement  

One of the key lessons we can learn from all these demonstrations is that hardware accuracy is paramount. Without accuracy, quantum computers are very expensive noise generators, unable to move the needle beyond HPC. Happily, we are finding that current generation machines are still capable of quite a lot, thanks to baseline physical accuracy, optionally coupled with clever error mitigation on top.

In general, we are very pleased to see how error mitigation can significantly reduce the impact of hardware errors and improve the quality of computed results by applying sophisticated post-processing techniques. However, error mitigation is not free. As hardware noise increases, mitigation becomes increasingly computationally expensive, and the techniques themselves can skew the results. If the underlying hardware is insufficiently accurate, it becomes more difficult to distinguish genuine physical phenomena from artifacts introduced via mitigation.

This is precisely where hardware quality matters. The validation on ԹϺ systems provided an important independent confirmation that the mitigated results from another vendor reflected real physical behavior rather than bias introduced through the mitigation process. Because ԹϺ's hardware operates with substantially lower native error rates, it served as a high-confidence reference point for validating scientific results. Importantly, this validation was about confirming the underlying physics, not validating a claim of quantum advantage.

Hardware Accuracy Improves Computational Efficiency

All the above reflects our systems' strong native performance: when hardware begins with exceptionally high fidelity, there is simply less error to overcome. However, error mitigation remains an interesting and valuable approach: high-quality hardware establishes the baseline, and software extends what is possible.

However, native accuracy affects more than scientific confidence—it also influences computational efficiency. As program complexity and size increases, hardware error rates increase, and successful error mitigation generally requires more sampling, more processing, and more computational resources. The lower the physical fidelity, the greater the overhead required before arriving at trustworthy results.

By starting with significantly lower native error rates, ԹϺ systems reduce the amount of mitigation needed to achieve comparable scientific outcomes. This creates a practical advantage in computational cost while helping to preserve confidence in the resulting data.

Accuracy is the Foundation for Fault Tolerance

Finally, we can answer the question of what comes next. This may seem obvious, but it’s multifaceted. What’s next is large-scale fault tolerant quantum computing. But the real question is, what does that look like?

A truly large-scale fault tolerant quantum computer will operate with error correction embedded into the workflow, working on the ‘logical’ level. That means that programmers will write their code to operate on logical qubits, with all the mechanisms of error correction hidden under the hood. The result will be error rates low enough to run some truly behemoth workflows.

We are well along the path to realizing this : we have demonstrated , have world-leading , and have a platform as they are invented; a crucial advantage in a quickly-evolving landscape. All of this is enabled by our high native accuracy; the accomplishments listed would be impossible without hardware that wasn’t ultra-low error to begin with.

However, even with the full force of error correction, error mitigation may still play an important role in the post fault-tolerance era. While error correction will be applied broadly to all workflows, there will still be some special cases where error mitigation may stretch the hardware further, always ensuring we stay on our front foot as computational power grows.

Progress Is the Real Milestone

Scientific breakthroughs matter because they move the field forward. But lasting enterprise value will come from quantum computers that consistently deliver results organizations can trust.

With Helios—the world's most accurate commercial quantum computer[1]—and a growing ecosystem of partners building complementary technologies, ԹϺ is creating the accurate, scalable foundation needed to transform scientific achievements into practical quantum computing.

[1] Based on two qubit gate fidelity, as of December 31, 2025.

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July 29, 2026
Scaling the Signal: What a Larger QFT Says About Quantum Progress
  • Mitsui & Co. and Mitsubishi Electric demonstrated one of the world’s largest approximate Quantum Fourier Transforms (QFT) on ԹϺ Helios, scaling from prior records to 98 physical qubits.
  • The collaboration also implemented a logical QFT using a QEC (Quantum Error Correction) code with up to 12 logical qubits.
  • The work highlights ԹϺ’s accuracy and flexible architecture.

While there is ongoing debate around the pace of quantum computing’s development, a more grounded way to assess progress is through concrete demonstrations of foundational algorithms at meaningful scale. In this context, Mitsui & Co. and Mitsubishi Electric are taking a pragmatic view of quantum progress—focusing on how close the field is to executing core algorithmic primitives that underpin many potential industrial applications, rather than relying on abstract milestones or timelines.

, the industrial giants teamed up with ԹϺ to measure how close we are to running the Quantum Fourier Transform (QFT), a widely-used algorithmic primitive, at scales necessary for industrial applications. In the process, the team successfully ran one of the largest instances of the approximate QFT ever demonstrated. This achievement matters because the QFT is an essential primitive that underpins many of the quantum algorithms expected to deliver practical advantages.

You may have heard of the (classical) Fourier transform (FT), due to its ubiquity throughout modern computing. The FT is essential in everything from image analysis to data compression, with almost limitless applications in between. The quantum Fourier transform (QFT) is similar; it’s used in everything from chemistry to finance.

Because the QFT is a foundational primitive underpinning many quantum algorithms, demonstrating it at larger scales and higher fidelity is a practical way to measure quantum computing readiness. This is exactly the type of benchmarking that organizations should consider to understand where today’s systems are useful, and to see how fault-tolerant approaches are progressing. Ultimately, algorithm-level benchmarking like this is one of the most useful ways to understand not just where we are, but where we are going.

A Transformative Approach

Primitives like Fourier Transform are so widespread because they simplify problems by transforming them into something that is easier to deal with. At ԹϺ, not only are they crucial for industrial applications but they can also simplify algorithms, making them possible to run now instead of later. This ‘transformational’ approach extends beyond the QFT - other transforms exist, and we have even invented our own quantum-native transforms.

Using our Helios quantum computer and Guppy language, the joint team explored running the QFT on both physical qubits and on logical qubits, showing that fault tolerance is progressing quickly.  Running the QFT on 98 physical qubits; the paper shows a clear progression from previous results.

Then, using the Steane code, one of the best-studied quantum error correcting codes, the team used Helios’ 98 physical qubits to form 12 logical qubits, successfully running the QFT with the mechanisms of quantum error correction interwoven into the algorithm. This marks a crucial step forward for the field.

Foundational Progress

Taken together, these results provide a more concrete lens through which to view progress in quantum computing: not as abstract projections, but as measurable advances in the execution of foundational algorithms at increasing scale. By benchmarking the Quantum Fourier Transform on both physical and logical qubits, Mitsui & Co. and Mitsubishi Electric are helping to clarify what today’s hardware can already achieve, and where fault-tolerant approaches begin to extend those limits.

More broadly, the organizations best positioned to benefit from quantum computing will be those that focus on these foundational capabilities early, and use them to build a clear, evidence-based understanding of how the technology fits into their business goals.

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