Thursday, May 30th 2013

NVIDIA Tesla Powers HIV Research Breakthrough

Researchers at the University of Illinois at Urbana-Champaign (UIUC) have achieved a major breakthrough in the battle to fight the spread of the human immunodeficiency virus (HIV) using NVIDIA Tesla GPU accelerators, NVIDIA today announced.

Featured on the cover of the latest issue of Nature, the world's most-cited interdisciplinary science journal, a new paper details how UIUC researchers collaborating with researchers at the University of Pittsburgh School of Medicine have, for the first time, determined the precise chemical structure of the HIV "capsid," a protein shell that protects the virus's genetic material and is a key to its virulence. Understanding this structure may hold the key to the development of new and more effective antiretroviral drugs to combat a virus that has killed an estimated 25 million people and infected 34 million more.

UIUC researchers uncovered detail about the capsid structure by running the first all-atom simulation of HIV on the Blue Waters Supercomputer. Powered by 3,000 NVIDIA Tesla K20X GPU accelerators -- the highest performance, most efficient accelerators ever built -- the Cray XK7 supercomputer gave researchers the computational performance to run the largest simulation ever published, involving 64 million atoms.

"It would have been very difficult to run a simulation of this size without the power of GPU-accelerated supercomputing in the Blue Waters system," said Klaus Schulten, professor of physics at the University of Illinois. "We started using GPU accelerators more than five years ago, and GPUs have fundamentally accelerated the pace of our research."

Designed to accelerate a broad range of scientific and technical computing applications, NVIDIA Tesla GPU accelerators are enabling researchers worldwide to make dramatic new breakthroughs across a variety of scientific domains -- including alternative energy, astrophysics, drug development, and climate research, among others. They deliver significantly higher performance and better energy efficiency as compared with CPU-based systems.

"GPUs help researchers push the envelope of scientific discovery, enabling them to solve bigger problems and gain insight into larger and more complex systems," said Sumit Gupta, general manager of the Tesla Accelerated Computing Business Unit at NVIDIA. "Blue Waters and the Titan supercomputer, the world's No. 1 open science supercomputer at Oak Ridge National Labs, are just two of many GPU-equipped systems that are enabling the next wave of real-world scientific discovery."

Capsid May Be Key to More Effective Drugs
With the planned addition of more GPUs to the Blue Waters system, UIUC researchers expect to increase simulation times, providing additional insight into the structure and behavior of the HIV capsid.

The capsid has become an attractive target for the development of new antiretroviral drugs, largely due to the discovery that Rhesus monkeys have developed an immunity to HIV through a protein that disrupts capsid functioning.

The capsid is the protein cell of a virus, containing the virus's genetic material. It protects and "smuggles" the genetic material into the human host cell. Once inside, it uncoats the material and initiates the infection.

No existing HIV drug treatments are designed to target the capsid. However, by providing a better understanding of the structure of the HIV capsid, pharmacologists have a wealth of new information to develop new and potentially more effective antiviral HIV drugs.
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66 Comments on NVIDIA Tesla Powers HIV Research Breakthrough

#1
Bytales
Reply

by: W1zzard
simple answer is profit. if you find the cure to HIV/cancer, cold fusion, zero point energy or anything else you just patent it and price it as high as you want, make more money than god
Just to point out something here.
Zero point energy is allready a viable source of energy.

The second this technology was announced publicly USA-goverment made it illegal to use such energy inside USA.

Why ? Because they cannot own it, as said techlogy was invented by an iranian. If you want to know more, just look up with google, Keshe Foundation, or click here http://www.keshefoundation.org/.
The funny thing is, the iranian who invented said technology is ready to give it up for free so that we all may freely benefit for it.
Hes not trying to make more money than god, as some pointed out. Or as some would do in his place !

We have allready invented the technology that makes interstellar travel a reality, we have the technology to discard petrol all togther, to have free energy for the rest of our lives, but why havent you people heard of it allready ?

Let me answer to that ! Because such knowledge is being systematically supressed, as is the case with urine therapy as well.

Another info is also that if you do the right things you can live in your biological body that you have now forever.
So please spare me the '' super computer X was used to find a treatment for the super diseases Y" discussion.

The good part of it all, is that such knowledge is starting to emerge, and more and more people will learn what the truth really is.
Posted on Reply
#2
btarunr
Editor & Senior Moderator
by: arterius2
no, HIV is a long term goal, it will gradually become more effective over time. or generations. HIV has a R-Knot of about 2-5, and is un-curable, the R-knot is especially effective when a given disease is un-curable. if you wonder what that is, I suggest you do some reading.
A pandemic with that R° would consume a 7-billion population over hundreds of years, and that's keeping the population constant. AIDS is consuming our population slower than our population growth. So you can't see it as a population control measure. It's a popularized pandemic, but one that doesn't necessarily control population. It failed to retard population growth. You can't "fuck around," but you can produce any practical number of children with other healthy people.

If I really wanted to control population, I'd create something more devastating, and surreptitiously distribute its cure to people that I want to save.
Posted on Reply
#3
Prima.Vera
by: W1zzard
simple answer is profit. if you find the cure to HIV/cancer, cold fusion, zero point energy or anything else you just patent it and price it as high as you want, make more money than god
Perfectly agree. This is what I am telling also to the cobnuts obsessed with conspiracies..
Posted on Reply
#4
arterius2
by: btarunr
A pandemic with that R° would consume a 7-billion population over hundreds of years, and that's keeping the population constant. AIDS is consuming our population slower than our population growth. So you can't see it as a population control measure. It's a popularized pandemic, but one that doesn't necessarily control population. It failed to retard population growth. You can't "fuck around," but you can produce any practical number of children with other healthy people.

If I really wanted to control population, I'd create something more devastating, and surreptitiously distribute its cure to people that I want to save.
you cannot see everything in black and white, AIDS can be seen as a population DETERRENT, is not the ONLY method of population control we have, the introduction of AIDS promotes the practice of safe sex (condoms and abstinence) which is also a method of birth control. and it will be passed on to your offsprings, THEORETICALLY the way you can see this as: if AIDS remain incurable, as T approaches infinity, mortality rate also approaches 100%
Posted on Reply
#5
Easy Rhino
Linux Advocate
only on the internet do people get pissed off at scientific research breakthroughs.
Posted on Reply
#6
Fourstaff
by: arterius2
you cannot see everything in black and white, AIDS can be seen as a population DETERRENT, is not the ONLY method of population control we have, the introduction of AIDS promotes the practice of safe sex (condoms and abstinence) which is also a method of birth control. and it will be passed on to your offsprings, THEORETICALLY the way you can see this as: if AIDS remain incurable, as T approaches infinity, mortality rate also approaches 100%
Find a cure for AIDS and send it the way smallpox went. Do you have a problem with that, or are you in favour of population control through AIDS?
Posted on Reply
#7
m1dg3t
Smallpox is still around. I think... :o

Edit: I think i was wrong, no surprise there LoL
Posted on Reply
#8
theonedub
habe fidem
by: arterius2
the objective of the disease is to create a near "painless" death for most carriers, and allows them to "almost" live their entire life normally, ironically, the trick in the disease is that its able to be spread by the most desirable activity of mankind - sex. However it does help stabilize population growth to a degree.
The diseases you end up dying from after HIV progresses to AIDS are not painless at all. That is one of the most ignorant statements I have seen- and after reading this thread, that's quite the accomplishment.

by: m1dg3t
You could combine every single PC used for distributed computing and it still would not equate to a single super computer.
As much as I dislike Bitcoin, it is a form of distributed computing.

Posted on Reply
#9
m1dg3t
by: theonedub
As much as I dislike Bitcoin, it is a form of distributed computing.

http://img.techpowerup.org/130530/orly.jpg
Ok. I was wrong. You need 3 or 4 "SuperComputers" :rolleyes: :laugh: :rolleyes:

CNN is a joke, i'm to lazy to check any other sources so i'll take it as is.

Distributed computing makes no sense to me. Maybe if i was using a combination of renewable energy sources such as wind/solar i would be in to it, but as it is now it seems like just a waste of resources. :o

I don't even pay for my electric as i'm currently in an apartment... If i could, i'd have a couple small turbines hangin' off my balcony but we aren't allowed to affix anythin other than a Satelite :( At least we can have a BBQ! :D:pimp::D
Posted on Reply
#10
arterius2
by: theonedub
The diseases you end up dying from after HIV progresses to AIDS are not painless at all. That is one of the most ignorant statements I have seen- and after reading this thread, that's quite the accomplishment.



As much as I dislike Bitcoin, it is a form of distributed computing.

http://img.techpowerup.org/130530/orly.jpg
and you sir are one of the most ignorant person I have ever seen, quite the accomplishment also
Posted on Reply
#11
theonedub
habe fidem
by: m1dg3t
Ok. I was wrong. You need 3 or 4 "SuperComputers" :rolleyes: :laugh: :rolleyes:

CNN is a joke, i'm to lazy to check any other sources so i'll take it as is.

Distributed computing makes no sense to me. Maybe if i was using a combination of renewable energy sources such as wind/solar i would be in to it, but as it is now it seems like just a waste of resources. :o

I don't even pay for my electric as i'm currently in an apartment... If i could, i'd have a couple small turbines hangin' off my balcony but we aren't allowed to affix anythin other than a Satelite :( At least we can have a BBQ! :D:pimp::D
The Top500 Supercomputers combined don't match the combined power of the BTC mining network. Your math needs work.
Posted on Reply
#12
m1dg3t
by: theonedub
The Top500 Supercomputers combined don't match the combined power of the BTC mining network. Your math needs work.
According to CNN :roll:
Posted on Reply
#13
Vinska
The supercomputer which did these calculations:
"Powered by 3,000 NVIDIA Tesla K20X GPU accelerators"

Okay, how many [tens of] millions Nvidia GPUs have shipped since the 8000 series? (The first series capable of GPGPU). Now, add all the [tens of] millions of AMD GPU capable of GPGPU. Then add all the CPUs.

Unless You have a Titan supercomputer army numbering in ten thousand strong, You won't even dent the computing power of ALL available "consumer computers".
Posted on Reply
#14
theoneandonlymrk
by: Random Murderer
Screw the fact that NV powered this breakthrough, shouldn't the news just be that there has been a major advancement in HIV research?
If you ask me, that's much more important than some bullshit PR. People matter more.
That was my point in reply 1.
And that no scientists are named , shame on you nvidia PR dpt you enabled this no more then charles Babbage.
And where did all the looneys come from , ive seen all the same conspiracy docs they have yet reasoning hasn't left me, and that iranian idiot who's solved zero point energy also sorted flying discs (anti gravity style) and is willing to share all he knows with all nations, my ford pumas still got wheels and planes are awfully popular still and it's a year in now.

I AM A CONSPIRACY NUT fair enough but im not an idiot , theres a conspiracy for every occasion.
Posted on Reply
#15
Prima.Vera
by: theoneandonlymrk

And where did all the looneys come from , ive seen all the same conspiracy docs they have yet reasoning hasn't left me, and that iranian idiot who's solved zero point energy also sorted flying discs (anti gravity style) and is willing to share all he knows with all nations, my ford pumas still got wheels and planes are awfully popular still and it's a year in now.
He also has a Coca Cola reactor:
http://www.keshefoundation.org/new-horizons/dynamic-reactors.html

:D
Posted on Reply
#17
theoneandonlymrk
by: Prima.Vera
He also has a Coca Cola reactor:
http://www.keshefoundation.org/new-horizons/dynamic-reactors.html

:D
:D seen that too dude and whilst it is all relatively interesting its as balls as snooker.:).
Im a mere engineer and I can see all kinds of bull in this guys science, ,,, I like the mega sized links to his 40 euro books too , funny guy but he's probably already rich from book sales off idiots who should have stayed in education longer.
Posted on Reply
#18
m1dg3t
by: Vinska
The supercomputer which did these calculations:
"Powered by 3,000 NVIDIA Tesla K20X GPU accelerators"

Okay, how many [tens of] millions Nvidia GPUs have shipped since the 8000 series? (The first series capable of GPGPU). Now, add all the [tens of] millions of AMD GPU capable of GPGPU. Then add all the CPUs.

Unless You have a Titan supercomputer army numbering in ten thousand strong, You won't even dent the computing power of ALL available "consumer computers".
Ok. And how do you factor in the resources required to power all these into the grand scheme of things? To me it just seems like a poor return on a persons "investment". Just my $0.02 :o
Posted on Reply
#19
Vinska
by: m1dg3t
Ok. And how do you factor in the resources required to power all these into the grand scheme of things? To me it just seems like a poor return on a persons "investment". Just my $0.02 :o
Power usage is a completely different topic. It doesn't change the fact that the computation power of all those devices dwarfs that of hundreds of supercomputers. Which was the idea we discussed. NOT the power usage.

(If You really need to know - in distributed computing the volunteers power their own machines. Simple.)
Posted on Reply
#20
m1dg3t
by: Vinska
Power usage is a completely different topic. It doesn't change the fact that the computation power of all those devices dwarfs that of hundreds of supercomputers. Which was the idea we discussed. NOT the power usage.
My point is; Is it really an efficient use of resources?

What have we cured with all of this distributed computing? Does power in = results out? What are the effects of consuming all of these extra resources for a POTENTIAL result?

Seems to me like the only winners are the utility companies.

by: Vinska
(If You really need to know - in distributed computing the volunteers power their own machines. Simple.)
Thank you captain obvious! I really thought someone else would pay someone elses power bill :laugh: :rolleyes:

You, or anyone for that matter, are free to do as they please. :pimp:

For myself, i just don't see the point. As we continue to live in a world with diminishing resources, consuming the resources we have for an unknown result is, IMHO, non sensical :o
Posted on Reply
#21
theoneandonlymrk
by: m1dg3t
My point is; Is it really an efficient use of resources?

What have we cured with all of this distributed computing? Does power in = results out? What are the effects of consuming all of these extra resources for a POTENTIAL result?

Seems to me like the only winners are the utility companies.



Thank you captain obvious! I really thought someone else would pay someone elses power bill :laugh: :rolleyes:

You, or anyone for that matter, are free to do as they please. :pimp:

For myself, i just don't see the point. As we continue to live in a world with diminishing resources, consuming the resources we have for an unknown result is, IMHO, non sensical :o
I like that everyone has his own most important cause , for you its clearly the green scene whereas folders love topgear and care more about the possibility of cureing illness and folding for example will continue until protein behaviour is fully understood but benefits almost all branches of medicine as all diseases can , are or do affect proteins or our use of them.
Posted on Reply
#22
Frick
Fishfaced Nincompoop
by: Bytales
Just to point out something here.
Zero point energy is allready a viable source of energy.

The second this technology was announced publicly USA-goverment made it illegal to use such energy inside USA.

Why ? Because they cannot own it, as said techlogy was invented by an iranian. If you want to know more, just look up with google, Keshe Foundation, or click here http://www.keshefoundation.org/.
The funny thing is, the iranian who invented said technology is ready to give it up for free so that we all may freely benefit for it.
Hes not trying to make more money than god, as some pointed out. Or as some would do in his place !

We have allready invented the technology that makes interstellar travel a reality, we have the technology to discard petrol all togther, to have free energy for the rest of our lives, but why havent you people heard of it allready ?

Let me answer to that ! Because such knowledge is being systematically supressed, as is the case with urine therapy as well.

Another info is also that if you do the right things you can live in your biological body that you have now forever.
So please spare me the '' super computer X was used to find a treatment for the super diseases Y" discussion.

The good part of it all, is that such knowledge is starting to emerge, and more and more people will learn what the truth really is.
I ... I have found my soulmate. I want you inside me.

by: theoneandonlymrk
I like that everyone has his own most important cause , for you its clearly the green scene whereas folders love topgear and care more about the possibility of cureing illness and folding for example will continue until protein behaviour is fully understood but benefits almost all branches of medicine as all diseases can , are or do affect proteins or our use of them.
He's into anarchy and pot, don't take him seriously. :laugh:
Posted on Reply
#23
Vinska
still, completely irrelevant when comparing only the computational power the two sides provides and NOTHING ELSE.

Example: if You'd say You Bugatti Veyron outperforms a random VW Golf from the street, I will have no objections. If I started rambling how much B.V. costs and how much gas it eats, that would have absolutely no impact on the fact it runs much faster and Your original statement would still hold.

Okay, if You really need to know - a large portion of the people who participate in distributed computing are very conscious about efficiency. After all - it's them who have to pay for all that. I do see that people who participate more seriously tend to keep the efficiency up.
I myself, for example, could add 5 more boxen to crunch on WCG. But 2 of those boxen are fairly outdated (~6 y.o.) while the remaining three are nearly 10 years old. The power bill is already hard to manage, thus those five additional would be a nightmare in that regard, while producing very limited gains. I can bring them to my university and leech the power off them for free. But I only plan on doing that with one of the boxen (the newest one) as I see the the gains of the other boxen's computations to be outweighed by the negative impact of power usage.
Also, that CNN's thing on bitcoin miners - that is probably true. Using an array of 7970s is a norm there. There are many distributed computing networks. Many I haven't come across yet. But summing up all those I know && had statistics checked of, it was obvious the computational power is extreme and way out of supercomputer league.
Posted on Reply
#24
Fourstaff
by: m1dg3t
My point is; Is it really an efficient use of resources?
Unless we find another method of understanding and modelling how protein folds, there is nothing to compare it to.
Posted on Reply
#25
theoneandonlymrk
by: Frick
I ... I have found my soulmate. I want you inside me.



He's into anarchy and pot, don't take him seriously. :laugh:
Pot's better than crack :p as for anarchy thats so 80's nowadays id call the feck it I can't be arsed generation but I can't be bothered:D.
Posted on Reply
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