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  • Condensed Matter Physics
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Quanta Magazine recently spoke with Goldenfeld about collective phenomena, expanding the Modern Synthesis model of evolution, and using quantitative and theoretical tools from physics to gain insights into mysteries surrounding early life on Earth and the interactions between cyanobacteria and predatory viruses. A condensed and edited version of that conversation follows.

  • Research
  • Biological Physics
  • Computational Physics

It took two years on a supercomputer to simulate 1.2 microseconds in the life of the HIV capsid, a protein cage that shuttles the HIV virus to the nucleus of a human cell. The 64-million-atom simulation offers new insights into how the virus senses its environment and completes its infective cycle.

The findings are reported in the journal Nature Communications.

  • In the Media
  • Biological Physics

A common bacteria is furthering evidence that evolution is not entirely a blind process, subject to random changes in the genes, but that environmental stressors can also play a role. A NASA-funded team is the first group to design a method demonstrating how transposongs-DNA sequences that move positions within a genome-jump from place to place. The researchers saw that the jumping rate of these transposons, aptly-named "jumping genes" increases or decreases depending on factors in the environment, such as food supply.

  • Research
  • Biological Physics

“Jumping genes” are ubiquitous. Every domain of life hosts these sequences of DNA that can “jump” from one position to another along a chromosome; in fact, nearly half the human genome is made up of jumping genes. Depending on their specific excision and insertion points, jumping genes can interrupt or trigger gene expression, driving genetic mutation and contributing to cell diversification. Since their discovery in the 1940s, researchers have been able to study the behavior of these jumping genes, generally known as transposons or transposable elements (TE), primarily through indirect methods that infer individual activity from bulk results.  However, such techniques are not sensitive enough to determine precisely how or why the transposons jump, and what factors trigger their activity.

Reporting in the Proceedings of the National Academy of Sciences, scientists at the University of Illinois at Urbana-Champaign have observed jumping gene activity in real time within living cells. The study is the collaborative effort of physics professors Thomas Kuhlman and Nigel Goldenfeld, at the Center for the Physics of Living Cells, a National Science Foundation Physics Frontiers Center.

  • Research
  • Biological Physics

Researchers from the University of Illinois at Urbana-Champaign and the University of California-Davis (UC Davis) are combining in vivo experimentation with computation for highly accurate prediction of the genome-wide binding pattern of a key protein involved in brain disorders.

 “The MeCP2 gene is critical for proper brain development and expressed at near-histone levels in neurons, but the mechanism of its genomic localization remains poorly understood,” explained Jun Song, a professor of bioengineering and of physics at the University of Illinois at Urbana-Champaign. “Using high-resolution MeCP2 binding data, we show that DNA sequence features alone can predict binding with 88% accuracy.”

  • Research
  • Biological Physics

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.

  • Research
  • Biological Physics
  • Biophysics

A new study offers the first atomic-scale view of an interaction between the HIV capsid – the protein coat that shepherds HIV into the nucleus of human cells – and a host protein known as cyclophilin A. This interaction is key to HIV infection, researchers say.

A paper describing the research appears in the journal Nature Communications.

Cyclophilin A is found in most tissues of the human body, where it plays a role in the inflammatory response, immunity and the folding and trafficking of other proteins. When it fails to work properly or is overproduced in cells, cyclophilin A also can contribute to diseases such as rheumatoid arthritis, asthma, cancer and cardiovascular disease. It also facilitates some viral infections, including HIV.

  • Research
  • Biological Physics
  • Biophysics

Bacterial chemotaxis, the process by which a bacterium changes direction in response to environmental cues, involves a complex array of chemical receptors (red, elongated molecules) and other sensory proteins (blue and green molecules), which work together to process sensory information. A new study offers high-resolution details of the structure and function of the chemosensory array, researchers report. 

  • Research
  • Condensed Matter Physics
  • Biological Physics

University of Illinois Swanlund Professor of Physics Nigel Goldenfeld, graduate student Farshid Jafarpour, and postdoctoral researcher Tommaso Biancalani have made a breakthrough in one of the most central chemical quirks of life as we know it: homochirality, the uniform “handedness” of biological molecules. Their new model addressing the emergence of this feature, published in Physical Review Letters (doi: 10.1103/PhysRevLett.115.158101) and highlighted by Physics suggests that homochirality can be used as a universal signature of life.

  • Research
  • Biological Physics
  • Biophysics

Researchers, led by a team from the Beckman Institute, combined the power of two computational programs to determine the atomic structure of the abiological molecule cyanostar. This breakthrough will allow researchers to investigate the structure of more abiological molecules, which are relatively unknown.

  • Research
  • Biological Physics
  • Biophysics

More than 500,000 people in the United States die each year of cancer-related causes. Now, emerging research has identified the mechanism behind one of the most common mutations that helps cancer cells to replicate limitlessly. The team’s findings, published in the May 14 issue of Science, have exciting implications for new, more precise and personalized cancer treatments with fewer side effects compared with current treatments.

  • Accolades
  • Biological Physics
  • Biophysics

The National Academy of Sciences has elected to membership Taekjip Ha, the Edward William and Jane Marr Gutgsell Professor of Physics at the University of Illinois at Urbana-Champaign.

 

Head of Department and Professor Dale Van Harlingen said, “Taekjip is a deserving and welcome addition to the academy membership. His innovative work has stretched the boundaries of biological physics, and he is a true visionary in his field. Through his many fruitful collaborations, Taekjip has substantially contributed to the agenda of several strategic campus research initiatives. And he has done much to position Illinois as a world leader in biological physics."

  • Accolades
  • Biological Physics
  • Biophysics
  • Condensed Matter Physics

Associate Professor Aleksei Aksimentiev and Assistant Professor Shinsei Ryu have each received the 2015 Dean's Award for Excellence in Research from the College of Engineering at the University of Illinois at Urbana Champaign. The two were recognized for their trailblazing research that represents significant contributions to their respective fields. They each received their awards at a College of Engineering faculty awards banquet on Monday, April 27, 2015.

  • Accolades
  • Biological Physics
  • Biophysics

Three University of Illinois professors have been elected to the American Academy of Arts and Sciences, one of the longest-standing honorary societies in the nation. Physics professor Taekjip Ha will join psychology professors J. Kathryn Bock and Gary S. Dell and other new members in an induction ceremony in October in Cambridge, Massachusetts.

Ha is the Edward William and Jane Marr Gutgsell Endowed Professor, a Howard Hughes Medical Institute Investigator, a professor in the Beckman Institute and the Cellular Decision Making in Cancer theme leader in the Carl R. Woese Institute for Genomic Biology at Illinois. He also is co-director of the National Science Foundation-funded Center for the Physics of Living Cells at the U. of I.
 

  • Research
  • Biological Physics
  • Biophysics

By combining two highly innovative experimental techniques, scientists at the University of Illinois at Urbana-Champaign have for the first time simultaneously observed the structure and the correlated function of specific proteins critical in the repair of DNA, providing definitive answers to some highly debated questions, and opening up new avenues of inquiry and exciting new possibilities for biological engineering.

Illinois biological physicists Taekjip Ha and Yann Chemla have combined two cutting-edge laboratory techniques that together directly get at the structure-function relationship in proteins. Ha is well recognized for his innovative single molecule fluorescence microscopy and spectroscopy techniques. Professor Yann Chemla is a top expert in optical trapping techniques. Their combined method—simultaneous fluorescence microscopy and optical trapping—yields far more definitive answers to questions relating structure to function than either technique could independently.

 

  • Research
  • Biological Physics
  • Biophysics

“We discovered this interesting physics of DNA that its sequence determines the flexibility and thus the stability of the DNA package inside the cell,” said Gutgsell Professor of Physics Taekjip Ha, who is a member of the Carl R. Woese Institute for Genomic Biology. “This is actually very elementary DNA physics. Many people thought we should have known this many decades ago, but there are still surprises in the physics of DNA.”