A quantum Rosetta Client? D-Wave offering free use of their Quantum Computer for anyone working on Covid19

Message boards : Rosetta@home Science : A quantum Rosetta Client? D-Wave offering free use of their Quantum Computer for anyone working on Covid19

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Message 93816 - Posted: 8 Apr 2020, 5:26:20 UTC
Last modified: 8 Apr 2020, 5:31:39 UTC

The title pretty much says what I am wondering.

Today I read this: https://techcrunch.com/2020/03/31/d-wave-gives-anyone-working-on-responses-to-the-covid-19-free-access-to-its-quantum-computer/
and
https://www.dwavesys.com/press-releases/d-wave-provides-free-quantum-cloud-access-global-response-covid-19

for those who dont want to follow the link, here is what d-wave said in their release:
BURNABY, BC – (March 31, 2020) — D-Wave Systems Inc., the leader in quantum computing systems, software, and services, today announced the immediate availability of free access to its quantum systems via the Leap quantum cloud service for anyone working on responses to the COVID-19 crisis. Joining the effort are partners and customers including CINECA, DENSO, Forschungszentrum Jülich, Kyocera Corporation, KYOCERA Communication Systems, MDR/Cliffhanger, Menten AI, NEC Solution Innovators Ltd., OTI Lumionics, QAR Lab at LMU Munich, Sigma-i, Tohoku University, and Volkswagen, who will provide access to engineering teams with expertise on how to use the quantum computer and formulate problems, as well as help in developing solutions.

This initiative comes in response to a request from the Canadian government for solutions to the pandemic across industries. Unfettered, free access to D-Wave’s quantum computers via Leap is available immediately to anyone working on COVID-19 response in the 35 countries across North America, Europe, and Asia where access is available to the Leap quantum cloud service.

Effectively responding to COVID-19 requires a collaborative and global effort across diverse organizations, including both private and public institutions. By providing free access to Leap’s quantum processing resources and quantum expertise, D-Wave and its partners hope to contribute to finding solutions to the COVID-19 crisis. Through this new initiative, anyone developing responses to the pandemic can immediately get unlimited, commercial contract-level access to the recently launched Leap 2.

Leap 2 includes the hybrid solver service designed to bring both classical and quantum resources to quickly and precisely solve highly complex problems with up to 10,000 fully connected variables.

“We’re living through an unprecedented crisis affecting nearly every industry and population. Deftly responding to this pandemic requires creativity and new approaches to solving problems. We believe that by combining our customers’ and partners’ expertise with hybrid quantum computing, we can together bring a potentially powerful resource to the individuals, organizations, and governments around the world building solutions nimbly and collaboratively,” said Alan Baratz, CEO of D-Wave. “D-Wave and its partners and customers have significant quantum computing expertise. Together, we hope we can aid the solutions to problems using hybrid quantum-classical solutions. We want to expand the computational capabilities available to experts across disciplines, verticals, and geographies and bring the community’s deep quantum knowledge to bear on the complex and dynamic COVID-19 situation.”

Hybrid quantum classical computing could be well-suited for solving a range of complex problems of this nature. Potential areas of focus for COVID-19 include a diverse range of hybrid quantum applications, such as analyzing new methods of diagnosis, modeling the spread of the virus, optimizing hospital logistics, supply distribution, pharmaceutical combinations, and beyond.

“Computing technology has long contributed to the development of science and industry. Quantum computing now has the potential to further this development, and we were one of the first to start research in this field in the auto industry,” said Koji Arima, President & CEO of DENSO. “We are honored to join the project, which will leverage this experience, mobilize our global expertise, and activate our spirit of collaboration. We believe we can overcome this crisis through the collaboration of humankind.”

"It is promising to accelerate the solution of complex problems in pharmacology and epidemiology, such as those that have arisen in the unprecedented COVID-19 crisis, by means of hybrid workflows from quantum-classical computer simulations," said Prof. Dr. Kristel Michielsen from the Jülich Supercomputing Centre. "To make efficient use of D-Wave's optimization and AI capabilities, we are integrating the system into our modular HPC environment.”

“Unity and cooperation are key to overcoming the COVID-19 crisis,” said Hans Menlo, CEO, Menten AI. “We are excited to join forces with D-Wave and its partners and offer our expertise and resources in any way we can.”

"We are excited to join this initiative. In fact, we have already gotten started by building an optimization formulation for planning which hospital to allocate critically ill patients so as to prevent medical collapse,” said Dr. Masayuki Ohzeki, Tohoku University and CEO of Sigma-i Co. Ltd. “It is almost completed, and its assessment is underway.”

For more information on how to get immediate access to free quantum computing resources and programming assistance for COVID-19 response, please visit www.dwavesys.com.


I am absolutely not a biologist nor do I understand anything about biology more than knowing that "the mitochondria is the powerhouse of the cell" from high school, but I do know a bit about computers.

I did a google search to see if anyone has ever done any protein folding with quantum computers and I found this: https://arxiv.org/pdf/1908.02163.pdf , titled: Resource-Efficient Quantum Algorithm for Protein Folding

and authored by: Anton Robert,1, 2 Panagiotis Kl. Barkoutsos,1 Stefan Woerner,1 and Ivano Tavernelli1, ∗
1
IBM Research GmbH, Zurich Research Laboratory, Säumerstrasse 4, 8803 Rüschlikon, Switzerland
2PASTEUR, Département de chimie, École Normale Supérieure,
PSL University, Sorbonne Université, CNRS, 75005 Paris, France

(Dated: August 7, 2019)


For those who want the cliffs notes on the paper Here is the first paragraph of the paper:

Predicting the three-dimensional (3D) structure
of a protein from its primary sequence of amino
acids is known as the protein folding (PF) problem. Due to the central role of proteins’ 3D structures in chemistry, biology and medicine applications (e.g., in drug discovery) this subject has been
intensively studied for over half a century.1–7 Although classical algorithms provide practical solutions, sampling the conformation space of small
proteins, they cannot tackle the intrinsic NP-hard
complexity of the problem,8 even reduced to its
simplest Hydrophobic-Polar model.9 While faulttolerant quantum computers are still beyond reach
for state-of-the-art quantum technologies, there is
evidence that quantum algorithms can be successfully used on Noisy Intermediate-Scale Quantum
(NISQ) computers10,11 to accelerate energy optimization in frustrated systems.12–15 In this work,
we present a model Hamiltonian with O(N4
) scaling and a corresponding quantum variational algorithm for the folding of a polymer chain with N
monomers on a tetrahedral lattice. The model reflects many physico-chemical properties of the protein, reducing the gap between coarse-grained representations and mere lattice models. We use a robust and versatile optimisation scheme, bringing together variational quantum algorithms specifically
adapted to classical cost functions and evolutionary strategies (genetic algorithms), to simulate the
folding of the 10 amino acid Angiotensin peptide
on 22 qubits. The same method is also successfully
applied to the study of the folding of a 7 amino acid
neuropeptide using 9 qubits on an IBM Q 20-qubit
quantum computer. Bringing together recent advances in building gate-based quantum computers
with noise-tolerant hybrid quantum-classical algorithms, this work paves the way towards accessible
and relevant scientific experiments on real quantum
processors.


and here is the last paragraph of the paper:

Discussion and conclusions. In this work, we introduced a quantum algorithm for the solution of the PF
problem on a regular tetrahedral lattice. The model Hamiltonain describes a primary coarse-grained protein sequence
where each beads represents an amino acid. Side chains can
also be modeled by means of an additional bead linked to
the main chain. The interaction between the amino acids
(backbone and side chains) can be extended to l-NN (with
l > 1) along the lattice edges. This enables the modeling of sophisticated coarse-grained models accounting for
Lennard-Jones and Coulombic like interactions. We show
how the model can correctly reproduce secondary structure
elements through the simple adaptation of the imputed
contact map. The number of qubits scales quadratically
with the number of amino acids , while the number of elements in the Hamltonian scales in O(N4
). This implies the
use of an unconventional treatment of the overlaps, which
are avoided through the addition of penalty terms. Even
though the PF problem is a classical optimization problem, the variational quantum algorithm used, CVaR-VQE,
drastically reduces the number of measurements required to
minimize the classical cost function (instead of the quantum
mechanical average) and may lead to quantum advantage
through the use of entanglement. The construction of specific mixing ansatz can drastically speed-up the search in
the configuration space even when the ground state is not
entangled but classical.26,32 The direct connection between
qubits and physical properties (configuration and contacts
or interactions) allows a rationalisation of initialisation of
the qubit states and their entanglement, beyond the simple
scheme adopted in this preliminary investigation.
The locality of the Hamiltonian combined with the
favourable scaling of the qubit resources and the circuit
depth with the number of monomers, make our model the
candidate of choice for the solution of the PF problem on
NISQ devices and other quantum technologies. In this work
we performed the simulation of the folding of the 10 amino
acids protein Angiotensin using a realistic model for the
noise of the one and two qubit gate operations. Furthermore we used a 20 qubit IBM Q processor to compute the
folding of a 7 amino acid peptide on 9 qubits, which is to
our knowledge the largest folding calculation on a NISQ
device using a variational algorithm. The success of this
calculation demonstrates the potential of our folding algorithm and opens up new interesting avenues for the use
of quantum computers in the optimization of classical cost
functions using the CVaR-VQE approach combined with a
genetic algorithm for the selection of the best fitting variational parameters.


The paper finishes off with a few more pages of "ACKNOWLEDGEMENTS and MATERIALS AND METHODS" and then finally several more pages of "SUPPORTING INFORMATION FOR “RESOURCE-EFFICIENT QUANTUM ALGORITHM FOR PROTEIN FOLDING”

Trying to follow the paper made me dizzy, but from reading the parts that I understand (please correct me if I am wrong) they are saying that there is potential in folding proteins as they had success with their work when using IBMs 20 qubit computer.

Would it be possible to create a client that would work on D-Waves Quantum Hybrid computer system? As I understand it, their latest generation system is a 5000 qubit true quantum computer thats also backed by classical HPC servers to create a hybrid 'cloud' system that anyone can try out for free for small amounts of time on the cloud. You can gain more free time by doing various things like making your project open source on github and other similar things.

They are currently opening up their system to anyone who is working on the covid19 virus as the articles above show.

Some of the companies that are already customers of d-wave are using their computing time to research covid19 in their own ways. None of those companies have biological backgrounds as far as I understand - they are running problems like how to run a hospital more efficiently with covid19 as a variable, and how to keep infrastructure, government and supply chains running smoothly while keeping infections minimal.

I dont think any of them are looking directly at the virus itself with their computing time.

I am a big fan of boinc/F@H/decentralized computing etc and I have visited d-waves headquarters in Burnaby (I live in East Van) and they are quite serious about what they do, but they are still a very young company and yet they are very well funded and have created quite a buzz around the world with their accomplishments.

Folding@home Projects are known world wide for their development and popularization of distributed computing and also for their contribution to various scientific fields. When I found out that there was a distributed computing project that helped research COVID19 I looked into it as soon as I heard about it and I was donating my CPU and GPU within hours of landing on Rosettas website.

I am not a healthcare worker nor a scientist so other than staying educated on COVID19, being a responsible citizen by isolating to keep myself healthy and just as importantly, to not unknowingly or not spread it to anyone else - the only other major contribution I can think of doing is contributing to distributed computing that helps researchers understand this virus.

If Rosetta@home created a client that would work on d-wave systems Leap hybrid system, not only would Rosetta get free time on one of the only true quantum computers on the planet - but it would also create a lot of chatter. People would be talking about it.

It would be good for d-wave, more people will hear about their small Canadian company with a unique service. Them working with a distributed folding at home project, ROSETTA, that is one of SETIs sister projects (not sure if thats exactly how you would say SETI and rosetta are related), would make them look very legitimate. They would get a lot of respect from many who previously were skeptical about their far-fetched sounding system if they were to run any well established distributed computing problem to help find solutions, especially rosetta, especially with covid19 influencing the whole planet right now.

Whats even more important tho, I think, is that even if their cloud system doesnt help rosetta very much, I think that it would give a lot of press for both d-wave company, and rosetta folding at home, and I dont exactly know what discovery we will make about covid19 if the processing power keeps increasing due to more and more people joining the project, but I bet only good can come of it.

Can someone explain to me what the best case scenario would be if a very well written quantum Rosetta client was written for d-waves leap cloud system and d-wave continued to run it for free as it was showing it was working very efficiently and possibly even factor in more classical folding at home rosetta clients due to the positive publicity of the two working together?

These were just some ideas i was thinking about. Whatever happens I hope we find something that helps, and soon! Being isolated I decided to finally get a computer up and running that I was previously going to use for mining or a node of some sort, but ill likely donate its power to rosetta.

Not going to lie - im in my 30s, am healthy, dont smoke but I am still scared to catch covid19, but I am more worried about my loved ones whom are thousands of miles away. I just want to not have to worry about them or getting sick myself, or even worse, making others sick. I really just want to go back to work.

Take care everyone!
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Profile robertmiles

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Message 95438 - Posted: 27 Apr 2020, 18:49:01 UTC

The quantum computer specifications I have seen so far include far less memory than the Rosetta client requires.

Therefore, any application for quantum computers would have to very different from the current Rosetta client.
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Kennywor

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Message 95999 - Posted: 4 May 2020, 9:57:02 UTC

Sounds like a PhD for someone.
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UniKnight

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Message 99539 - Posted: 3 Nov 2020, 7:32:29 UTC
Last modified: 3 Nov 2020, 7:44:29 UTC

Greetings fellow humanoid,

Looks like it's already in development:
A Peptide Designed using the Rosetta Software Suite and the D-Wave 2000Q

https://www.dwavesys.com/sites/default/files/Dwave_Menten%20AI_Case_Study_V7_1_0.pdf
https://www.dwavesys.com/sites/default/files/8_new_Menten.pdf
https://support.dwavesys.com/hc/en-us/community/posts/360042701053-Covid-19-genome


Looks like they're a couple of resources available.

Quantum Programming 101: Solving a Problem From End to End | D-Wave Webinar
https://www.youtube.com/watch?v=Q4FE4jou5CA

Free Quantum Cloud Access for Global Response to COVID-19
https://support.dwavesys.com/hc/en-us/articles/360045177574

Connect on COVID-19 Development
https://support.dwavesys.com/hc/en-us/community/topics/360001751313-Connect-on-COVID-19-Development


My Personal favorite's:

Quantum Computing Onboarding
https://support.dwavesys.com/hc/en-us/community/posts/360044286753-Quantum-Computing-Onboarding

The Leap IDE | D-Wave Leap
https://www.youtube.com/watch?v=62gDQ14pjwM

GitHub
https://github.com/dwave-examples

Best wishes!
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Profile [VENETO] boboviz

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Message 99545 - Posted: 3 Nov 2020, 15:24:57 UTC - in response to Message 99539.  

Looks like it's already in development:
A Peptide Designed using the Rosetta Software Suite and the D-Wave 2000Q

https://www.dwavesys.com/sites/default/files/Dwave_Menten%20AI_Case_Study_V7_1_0.pdf


VERY interesting!!!
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Message boards : Rosetta@home Science : A quantum Rosetta Client? D-Wave offering free use of their Quantum Computer for anyone working on Covid19



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