Research on the Supercomputers - Morad Alawneh

Research on the Supercomputers

Today, BYU offers a great resource to all faculty and students, supercomputing. Research today would be crippled without the aid of computers. Despite the improvements in personal computers, some research is too complex for even the most powerful desktop computer to handle. Most people know that the supercomputers are used for 3d animation used in the BYU Animation Department's award winning short movies. Even though 3d rendering for movies requires more power than a desktop computer can provide, the BYU Animation Department only reflects a small percent of computing capacity of all the supercomputers on BYU campus. In fact, it reflects probably less than 1%. What about that other 99%?

Around 140 users, both faculty and students (including undergraduate students) use the supercomputers for their research. Morad Alawneh, one of those users, takes advantage of the supercomputing resources to accomplish several things. Morad's research will help model and study how the influenza A virus interacts with the surrounding substances. He also studies how changing the dielectric constant of a double layer affects their properties. Additionally, Morad's research studies the properties of colloidal systems. Currently, Morad's research on the subject has lead to 8 papers which have already been published or sent for publication.

About Morad Alawneh

Morad Alawneh studies here at BYU and is working towards receiving a PhD in Theoretical and Computational Chemistry. He is originally from Palestine, and has a BS in Chemistry with a minor in Computer Science and an MS in Physical Chemistry from Yarmouk University in Jordan. He chose BYU based on the Chemistry Department's reputation. He studies and carries out research with Prof. Douglas Henderson and Prof. David Busath. As of today, Morad Alawneh has been working on his latest project for approximately 2 years. During that time, he utilized BYU's most powerful supercomputer, marylou4. To understand why someone would need so much computing power, you need to understand the research that Morad is working on.

Morad Alawneh's Research

The influenza A virus is coated by a cell membrane containing several copies of a receptor-cleavage protein (neuraminidase), a fusion protein (hemagglutinin), and most relevant to Morad's research, proton channels known as M2 channels. The full structure of the M2 channel is not known, but scientists do know that the channel plays a key role in the viral activation. After the virus is taken up by a host cell through endocytosis, the pH of the virus's immediate surroundings drops to become acidic.

The M2 channel allows protons (H⁺) to pass through the cell membrane from the acidic surroundings to the matrix of the virus. The acidity frees the ribonuclear proteins and RNA into the host's cytoplasm in order to initiate transcription, the basis of viral replication. Back to the beginning of the process, if the M2 channel is blocked, the protons can never reach the matrix of the virus, and the virus will never release its genetic material. Without the release of RNA and ribonucleic proteins, the virus will remain dormant. A drug called amantadine blocks the M2 channel and can cause the influenza A virus to be dormant. Like many drugs, though, how exactly amantadine works is still unknown.

It is known that the M2 channels consist of proteins which are made up by 97 amino acids, but scientists focus only on 25 fairly well-understood amino acids found in the lipid membrane. Using what is known about the 25 amino acids in the M2 channel, Morad Alawneh, with the aid of the supercomputers, simulates the transmembrane domain of the M2 channel. As a result, the simulations will help check the accuracy of the current model of the transmembrane domain of the M2 channel. Moreover, Morad expects it to give a better understanding of how the M2 channel actually works. Such simulations could also help identify and analyze the properties of the other unknown amino acids. Simulations that would shed light on the M2 channel might also help researchers to learn more about how amantadine blocks the channel, which in turn helps identify or design new and better drugs to block the M2 channel.

How do Morad's simulations work?

Morad Alawneh simulates molecular and atomic interactions over a period of time using what is known as molecular dynamic simulations. At each timestep, for every individual atom, there are two approximations for Newton's Law of motion calculated for each of the three spacial dimensions. Morad's experiments contain anywhere between 6,000 to 86,000 atoms. As the number of atoms in the computer simulation increase, the closer the results will reflect the real world situations. Morad's experiments typically cover about 1 nanosecond (1.0x10^-9 seconds). A simulation of 33,000 atoms over that 1 nanosecond period will take one computer processor about 8 days to complete. The relationship between the number of atoms and the time needed to complete the simulation is largely geometric. A simulation with 86,000 atoms that runs for 10 nanoseconds takes 128 high performance processors about 8 days. As a rough comparison, it would probably take a performance tuned desktop computer close to 3 years to run the same simulation. A good molecular dynamic simulation becomes very complex very quickly. As computers have become more powerful, simulations, like the ones that Morad carries out, become not only possible, but feasible.