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Untangling the Mysteries of Knots with Quantum Computers

What Quantum Advantage actually looks like

March 25, 2025

One of the greatest privileges of working directly with the world’s most powerful quantum computer at ҹɫֱ 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.

ҹɫֱ’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 ҹɫֱ 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 ҹɫֱ’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, ҹɫֱ’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.

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About ҹɫֱ

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

Blog
June 26, 2025
ҹɫֱ Overcomes Last Major Hurdle to Deliver Scalable Universal Fault-Tolerant Quantum Computers by 2029

Quantum computing companies are poised to exceed $1 billion in revenues by the close of 2025, to McKinsey & Company, underscoring how today’s quantum computers are already delivering customer value in their current phase of development.

This figure is projected to reach upwards of $37 billion by 2030, rising in parallel with escalating demand, as well as with the scale of the machines and the complexity of problem sets of which they will be able to address.  

Several systems on the market today are fault-tolerant by design, meaning they are capable of suppressing error-causing noise to yield reliable calculations. However, the full potential of quantum computing to tackle problems of true industrial relevance, in areas like medicine, energy, and finance, remains contingent on an architecture that supports a fully fault-tolerant universal gate set with repeatable error correction—a capability that, until now, has eluded the industry.  

ҹɫֱ is the first—and only—company to achieve this critical technical breakthrough, universally recognized as the essential precursor to scalable, industrial-scale quantum computing. This milestone provides us with the most de-risked development roadmap in the industry and positions us to fulfill our promise to deliver our universal, fully fault-tolerant quantum computer, Apollo, by 2029.

In this regard, ҹɫֱ is the first company to step from the so-called “NISQ” (noisy intermediate-scale quantum) era towards utility-scale quantum computers.

Unpacking our achievement: first, a ‘full’ primer

A quantum computer uses operations called gates to process information in ways that even today’s fastest supercomputers cannot. The industry typically refers to two types of gates for quantum computers:

  • Clifford gates, which can be easily simulated by classical computers, and are relatively easy to implement; and
  • Non-Clifford gates, which are usually harder to implement, but are required to enable true quantum computation (when combined with their siblings).

A system that can run both gates is classified as and has the machinery to tackle the widest range of problems. Without non-Clifford gates, a quantum computer is non-universal and restricted to smaller, easier sets of tasks - and it can always be simulated by classical computers. This is like painting with a full palette of primary colors, versus only having one or two to work with. Simply put, a quantum computer that cannot implement ‘non-Clifford’ gates is not really a quantum computer.

A fault-tolerant, or error-corrected, quantum computer detects and corrects its own errors (or faults) to produce reliable results. ҹɫֱ has the best and brightest scientists dedicated to keeping our systems’ error rates the lowest in the world.

For a quantum computer to be fully fault-tolerant, every operation must be error-resilient, across Clifford gates and non-Clifford gates, and thus, performing “a full gate set” with error correction. While some groups have performed fully fault-tolerant gate sets in academic settings, these demonstrations were done with only a few qubits and —too high for any practical use.

Today, we have published that establishes ҹɫֱ as the first company to develop a complete solution for a universal fully fault-tolerant quantum computer with repeatable error correction, and error rates low enough for real-world applications.

This is where the magic happens

The describes how scientists at ҹɫֱ used our System Model H1-1 to perfect magic state production, a crucial technique for achieving a fully fault-tolerant universal gate set. In doing so, they set a record magic state infidelity (7x10-5), 10x better than any .

Our simulations show that our system could reach a magic state infidelity of 10^-10, or about one error per 10 billion operations, on a larger-scale computer with our current physical error rate. We anticipate reaching 10^-14, or about one error per 100 trillion operations, as we continue to advance our hardware. This means that our roadmap is now derisked.

Setting a record magic state infidelity was just the beginning. The paper also presents the first break-even two-qubit non-Clifford gate, demonstrating a logical error rate below the physical one. In doing so, the team set another record for two-qubit non-Clifford gate infidelity (2x10-4, almost 10x better than our physical error rate). Putting everything together, the team ran the first circuit that used a fully fault-tolerant universal gate set, a critical moment for our industry.

Flipping the switch

In the , co-authored with researchers at the University of California at Davis, we demonstrated an important technique for universal fault-tolerance called “code switching”.

Code switching describes switching between different error correcting codes. The team then used the technique to demonstrate the key ingredients for universal computation, this time using a code where we’ve previously demonstrated full error correction and the other ingredients for universality.

In the process, the team set a new record for magic states in a distance-3 error correcting code, over 10x better than with error correction. Notably, this process only cost 28 qubits . This completes, for the first time, the ingredient list for a universal gate setin a system that also has real-time and repeatable QEC.

To perform "code switching", one can implement a logical gate between a 2D code and a 3D code, as pictured above. This type of advanced error correcting process requires ҹɫֱ's reconfigurable connectivity.
Fully equipped for fault-tolerance

Innovations like those described in these two papers can reduce estimates for qubit requirements by an order of magnitude, or more, bringing powerful quantum applications within reach far sooner.

With all of the required pieces now, finally, in place, we are ‘fully’ equipped to become the first company to perform universal fully fault-tolerant computing—just in time for the arrival of Helios, our next generation system launching this year, and what is very likely to remain as the most powerful quantum computer on the market until the launch of its successor, Sol, arriving in 2027.

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Blog
June 10, 2025
Our Hardware is Now Running Quantum Transformers!

If we are to create ‘next-gen’ AI that takes full advantage of the power of quantum computers, we need to start with quantum native transformers. Today we announce yet again that ҹɫֱ continues to lead by demonstrating concrete progress — advancing from theoretical models to real quantum deployment.

The future of AI won't be built on yesterday’s tech. If we're serious about creating next-generation AI that unlocks the full promise of quantum computing, then we must build quantum-native models—designed for quantum, from the ground up.

Around this time last year, we introduced Quixer, a state-of-the-art quantum-native transformer. Today, we’re thrilled to announce a major milestone: one year on, Quixer is now running natively on quantum hardware.

Why this matters: Quantum AI, born native

This marks a turning point for the industry: realizing quantum-native AI opens a world of possibilities.

Classical transformers revolutionized AI. They power everything from ChatGPT to real-time translation, computer vision, drug discovery, and algorithmic trading. Now, Quixer sets the stage for a similar leap — but for quantum-native computation. Because quantum computers differ fundamentally from classical computers, we expect a whole new host of valuable applications to emerge.  

Achieving that future requires models that are efficient, scalable, and actually run on today’s quantum hardware.

That’s what we’ve built.

What makes Quixer different?

Until Quixer, quantum transformers were the result of a brute force “copy-paste” approach: taking the math from a classical model and putting it onto a quantum circuit. However, this approach does not account for the considerable differences between quantum and classical architectures, leading to substantial resource requirements.

Quixer is different: it’s not a translation – it's an innovation.

With Quixer, our team introduced an explicitly quantum transformer, built from the ground up using quantum algorithmic primitives. Because Quixer is tailored for quantum circuits, it's more resource efficient than most competing approaches.

As quantum computing advances toward fault tolerance, Quixer is built to scale with it.

What’s next for Quixer?

We’ve already deployed Quixer on real-world data: genomic sequence analysis, a high-impact classification task in biotech. We're happy to report that its performance is already approaching that of classical models, even in this first implementation.

This is just the beginning.

Looking ahead, we’ll explore using Quixer anywhere classical transformers have proven to be useful; such as language modeling, image classification, quantum chemistry, and beyond. More excitingly, we expect use cases to emerge that are quantum-specific, impossible on classical hardware.

This milestone isn’t just about one model. It’s a signal that the quantum AI era has begun, and that ҹɫֱ is leading the charge with real results, not empty hype.

Stay tuned. The revolution is only getting started.

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Blog
June 9, 2025
Join us at ISC25

Our team is participating in (ISC 2025) from June 10-13 in Hamburg, Germany!

As quantum computing accelerates, so does the urgency to integrate its capabilities into today’s high-performance computing (HPC) and AI environments. At ISC 2025, meet the ҹɫֱ team to learn how the highest performing quantum systems on the market, combined with advanced software and powerful collaborations, are helping organizations take the next step in their compute strategy.

ҹɫֱ is leading the industry across every major vector: performance, hybrid integration, scientific innovation, global collaboration and ease of access.

  • Our industry-leading quantum computer holds the record for performance with a Quantum Volume of 2²³ = 8,388,608 and the highest fidelity on a commercially available QPU available to our users every time they access our systems.
  • Our systems have been validated by a #1 ranking against competitors in a recent benchmarking study by Jülich Research Centre.
  • We’ve laid out a clear roadmap to reach universal, fully fault-tolerant quantum computing by the end of the decade and will launch our next-generation system, Helios, later this year.
  • We are advancing real-world hybrid compute with partners such as RIKEN, NVIDIA, SoftBank, STFC Hartree Center and are pioneering applications such as our own GenQAI framework.
Exhibit Hall

From June 10–13, in Hamburg, Germany, visit us at Booth B40 in the Exhibition Hall or attend one of our technical talks to explore how our quantum technologies are pushing the boundaries of what’s possible across HPC.

Presentations & Demos

Throughout ISC, our team will present on the most important topics in HPC and quantum computing integration—from near-term hybrid use cases to hardware innovations and future roadmaps.

Multicore World Networking Event

  • Monday, June 9 | 7:00pm – 9:00 PM at Hofbräu Wirtshaus Esplanade
    In partnership with Multicore World, join us for a ҹɫֱ-sponsored Happy Hour to explore the present and future of quantum computing with ҹɫֱ CCO, Dr. Nash Palaniswamy, and network with our team.

H1 x CUDA-Q Demonstration

  • All Week at Booth B40
    We’re showcasing a live demonstration of NVIDIA’s CUDA-Q platform running on ҹɫֱ’s industry-leading quantum hardware. This new integration paves the way for hybrid compute solutions in optimization, AI, and chemistry.
    Register for a demo

HPC Solutions Forum

  • Wednesday, June 11 | 2:20 – 2:40 PM
    “Enabling Scientific Discovery with Generative Quantum AI” – Presented by Maud Einhorn, Technical Account Executive at ҹɫֱ, discover how hybrid quantum-classical workflows are powering novel use cases in scientific discovery.
See You There!

Whether you're exploring hybrid solutions today or planning for large-scale quantum deployment tomorrow, ISC 2025 is the place to begin the conversation.

We look forward to seeing you in Hamburg!

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