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Dissecting the mechanism of protein unfolding by SDS

Researchers at the University of Illinois at Urbana-Champaign have used molecular dynamics simulations to understand how sodium dodecyl sulfate causes protein unfolding. SDS is commonly used in labs to separate proteins and determine their molecular weights.

• https://www.eurekalert.org/pub_releases/2020-04/bifa-dtm041720.php
• https://www.azonano.com/news.aspx?newsID=37240

Nanopores can identify the amino acids in proteins, the first step to sequencing

A new study demonstrates that nanopores can be used to identify all 20 amino acids in proteins, a major step toward protein sequencing. Researchers at the University of Illinois at Urbana-Champaign, Cergy-Pontoise University in France and the University of Freiburg in Germany published the findings in the journal Nature Biotechnology.

• https://eurekalert.org/pub_releases/2019-12/uoia-nci121819.php

Simulation reveals how bacterial organelle converts sunlight to chemical energy

Researchers used supercomputers to construct a 136 million-atom model of the chromatophore, a primitive light-harvesting structure in purple bacteria. The simulated organelle behaved just as it does in nature, the team reports.

• https://news.illinois.edu/view/6367/804431
• https://www.sciencedaily.com/releases/2019/11/191114115845.htm

Imperfections in Nanopore Membranes Could Improve Biomolecule Transport

While watching the production of porous membranes used for DNA sorting and sequencing, University of Illinois researchers wondered how tiny steplike defects formed during fabrication could be used to improve molecule transport. They found that the defects - formed by overlapping layers of membrane - make a big difference in how molecules move along a membrane surface. Instead of trying to fix these flaws, the team set out to use them to help direct molecules into the membrane pores.

• https://www.sciencecodex.com/researchers-embrace-imperfection-improve-biomolecule-transport-631012
• https://www.nanowerk.com/nanotechnology-news2/newsid=53321.php
• https://www.eurekalert.org/pub_releases/2019-08/uoia-rei080219.php
• https://phys.org/news/2019-08-embrace-imperfection-biomolecule.html
• https://news.illinois.edu/view/6367/801710
• https://www.graphene-info.com/university-illinois-team-finds-defects-graphene-membranes-may-improve
• https://www.azonano.com/news.aspx?newsID=36919
• https://www.miragenews.com/researchers-embrace-imperfection-to-improve-biomolecule-transport/
• https://www.genengnews.com/news/dna-circling-the-nanopore-drain-may-improve-sequencing-flow/

Supercomputer Simulations Show New Phenomenon with Nanopore Data Sequencing

Using supercomputers, scientists found a surprising amount of water compression at the nanoscale. These findings could help advance medical diagnostics through creation of nanoscale systems that detect, identify, and sort biomolecules.

• https://www.hpcwire.com/off-the-wire/supercomputer-simulations-show-new-phenomenon-with-nanopore-data-sequencing/
• https://phys.org/news/2018-10-simulations-phenomenon-nanopore-dna-sequencing.html
• https://www.nanowerk.com/nanotechnology-news2/newsid=51174.php
• https://www.rdmag.com/news/2018/10/research-uncovers-new-phenomenon-nanopore-dna-sequencing

DNA enzyme shuffles cell membranes a thousand times faster than its natural counterpart

Researchers at University of Illinois at Urbana-Champaign and the University of Cambridge say their lipid-scrambling DNA enzyme is the first in its class to outperform naturally occurring enzymes – and does so by three orders of magnitude. They published their findings in the journal Nature Communications.

• https://news.illinois.edu/view/6367/663659
• https://www.nature.com/articles/s41467-018-04821-5
• http://www.tunisiesoir.com/health/study-dna-enzyme-shuffles-cell-membranes-a-thousand-times-faster-than-its-natural-counterpart-details-3700-2018/
• https://www.sciencedaily.com/releases/2018/06/180621112001.htm
• https://www.nanowerk.com/news2/biotech/newsid=50500.php
• https://eurekalert.org/pub_releases/2018-06/uoia-des062118.php
• https://phys.org/news/2018-06-dna-enzyme-shuffles-cell-membranes.html
• https://www.technologynetworks.com/proteomics/news/synthetic-dna-shuffling-enzyme-outpaces-natural-counterpart-305279
• https://www.news-medical.net/news/20180622/Lipid-scrambling-DNA-enzyme-outperforms-naturally-occurring-counterpart-say-researchers.aspx
• https://www.cambridgenetwork.co.uk/news/dna-enzyme-shuffles-cell-membranes-faster/
• https://www.businessweekly.co.uk/news/academia-research/synthetic-dna-discovery-set-boost-personal-drug-development

NCSA Grants $2.6M in Blue Waters Awards to Illinois Researchers

The National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign has awarded 3,697,000 node hours (NH) of time on the Blue Waters supercomputer to Illinois researchers from Spring 2017 proposal submissions. The combined value of these awards is over $2.6 million dollars, and through the life of the Blue Waters program, NCSA has awarded over 43 million node hours to UI researchers—a value of nearly $27 million. Some of the time allocated for Blue Waters will go to projects that focus on HIV research, Laser Interferometer Gravitational-Wave Observatory (LIGO) simulations, genomics and global warming research.

• https://www.hpcwire.com/off-the-wire/ncsa-grants-2-6m-blue-waters-awards-illinois-researchers/

Researchers use supercomputers to design and test new tools for cancer detection

An important factor in fighting cancer is the speed at which the disease can be identified, diagnosed and treated. The current standard involves a patient feeling ill or a physician seeing signs of a tumor. These indicators lead to more precise diagnoses via blood tests, x-rays or MRI imaging. But once the disease is far enough along to be noticeable, the cancer has often spread. In the future, though, it may be possible to diagnose cancer much earlier using more sensitive body scans, new types of biomarker tests, and even nano-sensors working in the bloodstream

Blue Waters Simulates Largest Membrane Channel Made of DNA Origami

What do you get when you cross an art form with something found in all living organisms? It may sound unusual, but DNA origami is something that has been explored in the scientific community for the last 10 years. DNA is a string of four nucleotide bases (A, T, G and C), each of which pairs only with one other base (A with T and G with C). In DNA origami, researchers take a long single strand of DNA (picture a ladder sawed in half vertically), and fold it into a shape using staple strands that have the corresponding bases. Everything from smiley faces to robots has been made using this method. While those are 2D, 3D shapes can also be made. Aleksei Aksimentiev’s group at the University of Illinois at Urbana-Champaign has been using this method to simulate membrane channels using the Blue Waters supercomputer at the National Center for Supercomputing Applications (NCSA) on the University of Illinois campus.

• https://www.hpcwire.com/off-the-wire/blue-waters-simulates-largest-membrane-channel-made-dna-origami-2/
• http://www.ncsa.illinois.edu/news/story/blue_waters_simulates_largest_membrane_channel_made_of_dna_origami

DNA molecules directly interact with each other based on sequence

Proteins play a large role in DNA regulation, but a new study finds that DNA molecules directly interact with one another in a way that's dependent on the sequence of the DNA and epigenetic factors. This could have implications for how DNA is organized in the cell and even how genes are regulated in different cell types, the researchers say. Led by Aleksei Aksimentiev, a professor of physics at the University of Illinois, and Taekjip Ha, a professor of biophysics and biophysical chemistry at Johns Hopkins University and an adjunct at the University of Illinois Center for the Physics of Living Cells along with Aksimentiev, the researchers published their work in the journal Nature Communications.

• https://phys.org/news/2016-03-dna-molecules-interact-based-sequence.html
• https://www.sciencedaily.com/releases/2016/03/160323115927.htm
• https://www.eurekalert.org/pub_releases/2016-03/uoia-dmd032216.php
• https://news.illinois.edu/blog/view/6367/341997

17 campus teams to accelerate their research with Blue Waters

Seventeen U of I research teams from a wide range of disciplines have been awarded computational and data resources on the sustained-petascale Blue Waters supercomputer at NCSA. “These diverse projects highlight the breadth of computational research at the University of Illinois,” said Athol Kemball, associate professor of Astronomy and chair of the Illinois allocation review committee. “Illinois has a tremendous pool of talented researchers in fields from political science to chemistry to engineering who can harness the power of Blue Waters to discover and innovate.”

• http://www.ncsa.illinois.edu/news/story/17_campus_teams_to_accelerate_their_research_with_blue_waters

2015 Blue Waters Symposium highlights successes, looks to the future of supercomputing

The 2015 Blue Waters Symposium, held May 10-13 at Oregon's beautiful Sunriver Resort, brought together leaders in petascale computational science and engineering to share successes and methods. Around 130 attendees, many of whom were Blue Waters users and the NCSA staff who support their work, enjoyed presentations on computational advances in a range of research areas—including sub-atomic physics, weather, biology, astronomy, and many others—as well as keynotes from innovative thinkers and leaders in high-performance computing. Over the three days of the symposium, 58 science teams from across the country presented on their work on Blue Waters.

• http://www.ncsa.illinois.edu/news/story/2015_blue_waters_symposium_highlights_successes_looks_to_the_future_of_supe

14 Illinois researchers selected for NCSA Fellowships

Fourteen faculty members at the University of Illinois at Urbana-Champaign have been selected to receive one-year fellowships that will enable their research teams to pursue collaborative projects with the National Center for Supercomputing Applications. NCSA's fellowship program aims to catalyze and develop long-term collaborations between the center and campus researchers, particularly in the center's six thematic areas of research: Bioinformatics and Health Sciences, Computing and Data Sciences, Culture and Society, Earth and Environment, Materials and Manufacturing, and Physics and Astronomy.

• http://www.ncsa.illinois.edu/news/story/14_illinois_researchers_selected_for_ncsa_faculty_fellowships

Charged graphene gives DNA a stage to perform molecular gymnastics

When Illinois researchers set out to investigate a method to control how DNA moves through a tiny sequencing device, they did not know they were about to witness a display of molecular gymnastics. Fast, accurate and affordable DNA sequencing is the first step toward personalized medicine. Threading a DNA molecule through a tiny hole, called a nanopore, in a sheet of graphene allows researchers to read the DNA sequence; however, they have limited control over how fast the DNA moves through the pore. In a new study published in the journal Nature Communications, University of Illinois physics professor Aleksei Aksimentiev and graduate student Manish Shankla applied an electric charge to the graphene sheet, hoping that the DNA would react to the charge in a way that would let them control its movement down to each individual link, or nucleotide, in the DNA chain.

12 Illinois faculty awarded prestigious Blue Waters Professorships

Twelve University of Illinois faculty members from a range of fields have been selected as Blue Waters Professors, an honor that comes with substantial computing and data resources on the Blue Waters supercomputer at the university’s National Center for Supercomputing Applications (NCSA).

• http://www.ncsa.illinois.edu/news/story/12_illinois_faculty_awarded_prestigious_blue_waters_professorships

22 Illinois projects receive time on Blue Waters

The University of Illinois at Urbana-Champaign has awarded access to the Blue Waters supercomputer—which is capable of performing quadrillions of calculations every second and of working with quadrillions of bytes of data—to 22 campus research teams from a wide range of disciplines. The computing and data capabilities of Blue Waters, which is operated by the National Center for Supercomputing Applications (NCSA), will assist researchers in their work on understanding DNA, developing biofuels, simulating climate, and more.

• http://www.ncsa.illinois.edu/news/story/22_illinois_projects_receive_time_on_blue_waters_supercomputer

• Molecular Dynamics of DNA Origami Nanostructures (2017-bluewaters-professor-report.pdf)
• Molecular Dynamics of DNA Origami Nanostructures (2016) (2016_report_Aksimentiev.pdf)
• Molecular Dynamics of DNA Origami Nanostructures (2015) (2014-bluewaters-professor-report (1).pdf)
• Molecular Dynamics Simulations of DNA Nanosystems (2019-bluewaters-professor-report.pdf)
• Molecular Mechanism of Transport Selectivity Across the Nuclear Pore Complex (2016-bluewaters-report.pdf)