Marconi invented radio in 1898. Today he is working on Gravitational Waves

Marconi invented radio in 1898. Today he is working on Gravitational Waves

1.3 billion years ago. Two blackholes which had being dancing, spiraling inexorably, for millions of years, finally merged in a distant region of the universe, rippling space-time .

December 10th, 1909. Around 1000 guests are reunited at the Stockholm City Hall including a 35 years old italian and the King of Sweden. A couple of hours earlier, this Italian scientist, Guglielmo Marconi, had stepped forward to receive the Nobel Prize of Physics. He and many other scientists had been working on an invention that changed our world: radio. As many other scientific breakthroughs, it proved its value during World War I. Armies did not need wagons pulled by horses to carry cables along enormous distances to communicate any more: we had entered the wireless era.

Guglielmo Marconi. Source: Library of Congress, US. Deposited in the US Copyright Office before 1924.

September 14th, 2015. Echoes from the merging of that two old black holes were detected at LIGO Observatory. It was the first time that we, humans, came to detect gravitational waves -disturbances in space-time curvature. This discovery not only confirmed one of the most fascinating predictions of Einstein’s gravitational theory but also opened a completely new window to the study of the universe. Many have said that, until yesterday, we were just seeing the universe while today we are also capable of hearing it.

Today, Italian scientists are studying gravitational waves and MARCONI is involved this research. How so? We have realized in the recent years that, to perform this and many other experiments -such as the Higgs Boson discovery-, huge computational resources are needed. US and China are the leading the race of supercomputers but several European countries have partnered to work together on building competitive supercomputers and created the PRACE partnership. One of these countries, Italy, is naming his supercomputers after eminent scientists and the biggest one of them, #21 in the world, is called MARCONI.

Two technicians working at MARCONI. Source: CINECA Flickr account. Permission granted by author.

Under the umbrella of such an amazing institution, 25 European late degree and master’s students are developing 25 different projects in 12 European supercomputers. First stop, Bologna -home of MARCONI supercomputer-. For one week, we learnt how to use key technologies to work with supercomputers such as OpenMP, MPI or CUDA. All of this in situ, testing our codes at MARCONI’s younger brother, GALILEO. After this training, we departed to our destination cities. In my case, Athens.

Group picture of Summer of HPC participants and coordinators. Source: CINECA. Permission granted by author.

And that is how, on July 6th, I arrived in Greece: more than 2000 islands, excellent food, astonishing history and one great supercomputing institution: GRNET. There and for the next 8 weeks I will be working together with a team from BRFAA on finding more effective drugs. For a drug to be active, its molecules must bind tightly and selectively to a target molecule in our bodies. Once they are bound, they generate the desired effect in our health. Consequently, to find effective drugs, we evaluate how strongly a drug molecule binds to its therapeutic target.

In fact, we are evaluating the binding strength of many drugs and select the one that binds more strongly. This one has a stronger effect on our health and, consequently, taking a fewer amount of it the same therapeutic results are obtained.

To find out the binding strength, we use computer simulations. These simulations take the structure of the drug (how the atoms are located) and its target. Then, using fundamental physics laws such as Newton’s equations of motion, they calculate how good a linkage is. Since thousands of these simulations are needed, supercomputers are needed (nop, sorry, your Acer laptop is too weak for this).

The most accurate technique to simulate and compare several bindings is called Free Energy Perturbations. In FEP, the key magnitude is the amount of energy that can be extracted from the system (without irreversibly changing it). This magnitude is called Gibbs Free Energy. And what we call “a system” is the combination of a drug, a protein and water around them. Thus, we compare how this energy changes when we modify the drug of the system. The bigger this change, the better the new drug is. Hence, my project compares many modifications of a drug used in cancer metastasis treatments and finds the one which binds better to the target. That one could be more effective, reducing the dose needed. The final goal is to compare simulation to experimental results to prove FEP is a valid technique to create better drugs.

Hemoglobin structure. Source: own.

Keep an eye on my posts (tag “Antonio Miranda”) to share this journey with me!

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