Untangling the Mysteries of Knots with Quantum Computers
What Quantum Advantage actually looks like
By Konstantinos Meichanetzidis
One of the greatest privileges of working directly with the world’s most powerful quantum computer at Quantinuum 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.
Quantinuum’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 Quantinuum 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 Quantinuum’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.
They all have the same Jones polynomial, as it is an invariant.
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.
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, Quantinuum’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.
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 Quantinuum
Quantinuum, the world’s largest integrated quantum company, pioneers powerful quantum computers and advanced software solutions. Quantinuum’s technology drives breakthroughs in materials discovery, cybersecurity, and next-gen quantum AI. With over 500 employees, including 370+ scientists and engineers, Quantinuum leads the quantum computing revolution across continents.
- Researchers from Quantinuum, Caltech, the University of Chicago, and Harvard created a rare topologically ordered state of matter on Quantinuum's System Model H2 and used it to perform protected universal quantum gates with non-Abelian anyons.
- The work explores an alternative approach to fault tolerance by using topological properties to protect quantum information. This could reduce the need for magic state distillation, which can (in some circumstances) be resource-intensive.
- Quantinuum continues to show leadership in fault tolerance, with successful demonstrations spanning world record error rates to exotic approaches like topological computing
Quantum computing is all about putting the exotic properties of physics to work. Qubits can exist in two states at once, like the famous cat that is both alive and dead. Qubits can also be entangled, where the state of one will instantaneously affect the state of another - even when they have no way to “talk” to each other. Qubits can even be teleported, moving a quantum state from one place to another without physically moving it through space.
These features give quantum computing its power. But the ‘spooky’ nature of quantum computing doesn’t stop there: our quantum computers are potent enough to make exotic states of matter out of our qubits, and to perform calculations that would warp the mind of more traditional thinkers.
A new approach
In a recent paper published in Nature, researchers at Quantinuum teamed up with Caltech, the University of Chicago, and Harvard to create a rare ‘topologically ordered’ state of matter from our qubits.
When the qubits become ‘topologically ordered’, they become more than individual particles, now ‘related’ to each other in a specific way. This is like how hydrogen and oxygen act as individual gas particles alone, but you can put them together in a certain way so that they become water, a liquid, and an entirely different creature.
When the qubits become topologically ordered, the quantum information that they carried individually gets spread out over the whole system, which acts as a sort of protection from noise. This is like how a net makes a stronger barrier than a bunch of un-knotted ropes.
Once the researchers had topologically ordered qubits, they used the exotic particles that resulted (called non-Abelian anyons) to compute, performing error-protected gates and measurements.
To perform gates, the researchers 'braided' the anyons, which is like changing the shape of the “net”. This is something like the children’s game ‘cats cradle’. Through a sequence of changes to the “net”, the quantum computer can perform full calculations, one day helping scientists to understand the secrets hidden in the world around us.
Why go to such trouble? Well, for the love of discovery of course - but the team had an additional, specific motivation. One of the biggest challenges in building practical quantum computers is protecting them from errors while still being able to perform every operation needed for computation (this is referred to as universality).
This work takes a fresh approach to this challenge. Unlike traditional quantum error correction, the special properties of topological matter enable a universal set of fault tolerant gates without relying on expensive magic state distillation.
Why this matters
Quantum error correction is essential for large-scale quantum computing. While it protects fragile quantum information from noise by turning delicate physical qubits into robust logical qubits, it also introduces a significant constraint: not every quantum gate can be performed directly on logical qubits.
For decades, the standard solution has been to supplement error-corrected operations with magic states. These specially prepared quantum resources enable universal computation but can come at a steep cost - in many estimates of future fault-tolerant quantum computers, magic state preparation dominates both the physical qubit count and the runtime of useful algorithms.
Reducing this overhead has therefore become an important goal in quantum computing. This new approach may significantly reduce the cost by enabling the ‘topological preparation’ of magic states, eliding expensive protocols like distillation. If universal computation can be performed without large-scale magic state distillation, quantum computers could require significantly fewer physical qubits and spend much less time generating computational resources before running useful algorithms.
We will never stop exploring
While there is still considerable work ahead to understand the practical implementation and scalability of these ideas, this result expands the landscape of what's possible in quantum fault tolerance.
Of course, this impressive demonstration describes just one approach we are taking to fault tolerance at scale. We will continue to push forward with topological computing alongside more traditional approaches to quantum error correction, as well as exploring everything we can imagine in between. We are looking at a number of ways to reduce the resource cost of magic states in particular, and are making strides in multiple dimensions. With machines that are both flexible and accurate enough to do it all, who can resist?
- Quantinuum continues its progress toward fault-tolerant quantum computing, with a series of peer-reviewed breakthroughs in fault-tolerant operations.
- Our progress is not only scientific; it is commercial. By improving logical-qubit reliability and encoding efficiency, Quantinuum is reducing the resource overhead required to scale its quantum computers toward commercially useful workloads.
- These results were achieved on commercial Quantinuum hardware, reinforcing that our architecture is not just setting new standards, but building a practical foundation for customers, partners, and researchers preparing for the fault-tolerant era.
Fault-tolerant quantum computing is the threshold the industry must cross before quantum computers can solve the hardest, highest-value problems with confidence. To be commercially useful at scale, the question is not simply who can build more qubits. It is who can build reliable, efficient, scalable systems that reduce technical risk and accelerate the path to commercial usefulness.
Quantinuum is progressing on that path.
Last year, in partnership with Microsoft, we published a breakthrough in logical computing, demonstrating logical qubits that outperformed their physical counterparts by a factor of 800. We are proud to announce that this work is now being published in Nature, one of the most highly regarded scientific journals in the world.
This work highlights our leading fidelities, as shown in Table 1:
Since then, we’ve accelerated our efforts to reach large-scale fault tolerance and advanced what we believe to be the core building blocks of fault-tolerant quantum computing, from logical-qubit teleportation and multiple error-correction breakthroughs to one of the first meaningful computations using logical qubits. Importantly, these results were achieved on commercial Quantinuum hardware, demonstrating not just scientific progress, but a practical and efficient path toward scalable, customer-ready fault tolerance.
A Recap of Our Recent Technical Progress
Since the work with Microsoft, we achieved a milestone years ahead of schedule, demonstrating high-fidelity teleportation of a logical qubit, which was published in Science, one of the world’s most prestigious journals. Later, we beat our own record in this crucial fault tolerance milestone, thanks to continued improvements to our System Model H2’s fidelity.
Then, a series of results demonstrating more error-correcting milestones (and codes):
- Better than physical results in a high-rate non-local code,
- First-ever demonstration of a single-shot error correcting code (which significantly reduces resource requirements) in 4 dimensions
- Extending qubit lifetimes by 10x with a concatenated code
- Observed fault-tolerance thresholds with concatenated codes
- High fidelity magic states and a fully fault tolerant universal gate set in two different papers
Recently, we topped ourselves yet again by performing one of the first meaningful computations with logical qubits – exploring key questions in materials and magnetism, using logical qubits with better error rates than their physical counterparts. This result also includes a leading “encoding rate” squeezing 48 logical qubits out of just 98 physical qubits, emphasizing how our architecture helps to support large scale fault tolerance without enormous resource costs.
It is worth noting that all these results were achieved on our commercial hardware, not on one-off laboratory test-stands – reflecting the performance that we are able to deliver to our customers.
We also did crucial theoretical work, exploring new options for error correction that can reduce resource requirements, time to solution, and shorten the timeline to large scale fault tolerance.
Commercial Implications and the Road Ahead
We believe the commercial implication is clear: Quantinuum is reducing the uncertainty around the path to fault-tolerant quantum computing. Our architecture, hardware fidelity, full-stack control, and error-correction progress are converging into a practical roadmap for systems that can support valuable scientific and commercial workloads.
For those evaluating when quantum computing will become strategically relevant, we believe the signal is also increasingly clear: the fault-tolerant era is no longer a distant concept. It is becoming an engineering reality, and Quantinuum is leading the way.
- University of Southern Denmark (SDU) to use Quantinuum Helios, supported by the Danish e-Infrastructure Consortium (DeiC)
- Access to Helios enables SDU to test and refine fault-tolerant algorithms and error-correction codes under realistic hardware conditions
- The collaboration supports at a scale of 48 logical qubits, positioning Denmark at the forefront of scalable, practical quantum computing
- Researchers exploring the scientific foundations for future development of applications in fields including pharmaceuticals, finance, and defense
Progress in quantum computing is measured by hardware advances plus the algorithms and quantum error-correction codes that turn quantum systems into useful computational tools.
Thanks to recent hardware advances, researchers are increasingly sharpening their tools to probe the performance of quantum algorithms and understand how they behave in realistic conditions – where stability, system architecture and algorithm design all shape performance.
A new Denmark-based collaboration between the University of Southern Denmark (SDU), Quantinuum, and the Danish e-Infrastructure Consortium (DeiC) will utilize Quantinuum Helios. Researchers at the SDU’s Centre for Quantum Mathematics, led by Jørgen Ellegaard Andersen, will use Helios to pursue research into topological quantum computing.
Their work could help explain how and why successful quantum algorithms perform as they do, informing the development of high-performance algorithms suited to emerging quantum systems. They’re exploring the scientific foundations that support future quantum applications across areas including pharmaceuticals, finance, and defense.
“We are thrilled to gain access to Quantinuum’s high-fidelity Helios system. This collaboration gives us a unique opportunity to test the limits of our algorithms and evaluate system performance, while advancing fundamental research and laying the foundation for future applications.”
— Professor Jørgen Ellegaard Andersen, Director of the Centre for Quantum Mathematics at University of Southern Denmark
Why topological methods matter
Topological quantum computing is an area of research that connects quantum computation with deep mathematical structures. It includes the study of error correcting codes known as surface codes that encode quantum information in the global properties of systems of logical qubits.
The research team will explore how these codes behave, and how they may support the development of fault-tolerant quantum algorithms in practical implementations under realistic conditions.
This distinction between theory and practical implementation matters. In theory, topological approaches offer a rich framework for designing algorithms and error-correcting codes. In practice, researchers need to understand how those ideas perform when implemented on real systems, where questions of noise, stability, overhead, and scaling become central. The collaboration will allow the SDU team to investigate these questions directly.
New ways to benchmark quantum processors
Beyond individual algorithms and codes, the research will also develop tools for benchmarking quantum processors. The goal is to develop new ways to characterize fidelity and stability in regimes that can be difficult to access.
The team will also explore hybrid quantum–classical approaches, including machine-learning techniques assisted by quantum hardware, to study the mathematical structures at the heart of topological quantum computing. This work reflects a broader field of research in which quantum and classical methods are used together, each contributing to parts of a computational problem.
Strengthening Denmark’s quantum ecosystem
The collaboration reflects the growing role of national quantum infrastructure in supporting research and talent development. Denmark has a long tradition of scientific innovation, and this collaboration is intended to support the country’s continued development in quantum technology.
The initiative is supported by DeiC, which played a central role in securing funding and enabling access to Quantinuum’s systems. DeiC has been assigned a particular role in developing and coordinating quantum infrastructure initiatives for the benefit of universities and industry, operating without its own commercial, sectoral, or geographical interests. This includes securing dedicated access to quantum computers, producing advisory services and supporting the development of new talent in the Danish quantum sector.
“DeiC’s special effort to secure funding and access for this research initiative is rooted in our organization’s role in relation to the Danish Government’s strategy for quantum technology.”
— Henrik Navntoft Sønderskov, Head of Quantum at Danish e-Infrastructure Consortium
This collaboration promises to accelerate the development of practical algorithms. It is grounded in fundamental science – but its focus is practical: discovering and testing mathematical approaches to topological quantum computing that can be implemented, evaluated, and improved on real quantum hardware.
That work requires both theoretical insight and access to a system such as Helios capable of supporting meaningful scientific work.