Nanotechnology Now

Our NanoNews Digest Sponsors
Heifer International

Wikipedia Affiliate Button

Home > Press > Team brings subatomic resolution to 'computational microscope'

Researchers can simulate atomic and subatomic dynamics in large molecular systems. Here is a visualization of the process by which the amino acid glutamate (Glu) is attached to a specific region of its transfer RNA (tRNA). An energy-rich molecule, ATP, drives this reaction and is converted to AMP in the process. The red and blue bubbles represent the probability of finding electrons in particular regions. Green dotted lines delineate the atoms that bond in this chemical reaction.
CREDIT
Graphic by Rafael Bernardi, Zan Luthey-Schulten and Marcelo Melo
Researchers can simulate atomic and subatomic dynamics in large molecular systems. Here is a visualization of the process by which the amino acid glutamate (Glu) is attached to a specific region of its transfer RNA (tRNA). An energy-rich molecule, ATP, drives this reaction and is converted to AMP in the process. The red and blue bubbles represent the probability of finding electrons in particular regions. Green dotted lines delineate the atoms that bond in this chemical reaction. CREDIT Graphic by Rafael Bernardi, Zan Luthey-Schulten and Marcelo Melo

Abstract:
Scientists have built a "computational microscope" that can simulate the atomic and subatomic forces that drive molecular interactions. This tool will streamline efforts to understand the chemistry of life, model large molecular systems and develop new pharmaceutical and industrial agents, the researchers say.

Team brings subatomic resolution to 'computational microscope'

Champaign, IL | Posted on March 27th, 2018

They report their findings in the journal Nature Methods.

The scientists combined two computational approaches used to simulate molecular interactions. The first, a nanoscale molecular-dynamics program known as NAMD, uses classical-mechanics methods to model the structure and simulate the behavior of hundreds of millions of individual atoms. The second program zooms in on the subatomic realm, simulating the interactions of protons, neutrons and electrons. Modeling at this quantum-mechanical scale demands a lot of computational power, so the researchers implemented a method for partitioning large molecules into classical- and quantum-mechanics regions. This allows them to focus their computational resources on small regions involved in critical interactions, such as the making or breaking of chemical bonds.

Both molecular mechanics and quantum mechanics programs have been available for years, and other teams have worked to combine them, said University of Illinois chemistry professor Zaida (Zan) Luthey-Schulten, who led the new research with her husband, U. of I. physics professor Klaus Schulten. But the new effort streamlines the process of setting up, performing and analyzing the simulations.

"We set it up so that researchers can easily choose how they will partition their own systems," Luthey-Schulten said. "My own students are trying it out, and most of them are able to do it without much difficulty."

Schulten developed NAMD at Illinois in 1995, combining it with a visualization software, VMD, which enables researchers to watch large-scale molecular interactions unfold. Schulten, who died in 2016, equated this approach to "building a computational microscope."

The computational microscope is ideal for modeling structural traits and motions of large complexes. For example, in 2013, Schulten and his colleagues used NAMD to model the HIV capsid, which is made up of more than 1,300 identical proteins that assemble into a cagelike structure that protects the virus until it enters a host cell. That simulation accounted for the interactions of more than 64 million atoms and required the use of the Blue Waters supercomputer at the National Center for Supercomputing Applications at the U. of I. The new study also made use of Blue Waters, this time to improve the resolution of the computational microscope.

The NAMD software is designed to describe the behavior of individual atoms. But individual atoms involved in specific chemical interactions and reactions don't always behave like their counterparts elsewhere. Understanding how they vary requires a closer look at the subatomic forces at play. This is particularly important in the dynamic regions of molecules - for example, those places where chemical bonds are made or broken, the researchers said.

In the new study, the research team at Illinois teamed up with QM experts Frank Neese, of the Max Planck Institute for Coal Research in Mulheim an der Ruhr, Germany; and Gerd B. Rocha, of the Federal University of Paraiba, in Joao Pessoa, Brazil.

As a demonstration of the new approach, the researchers simulated the chemical behavior of transfer RNAs, molecules that play a key role in translating genetic information into proteins. Using NAMD, they modeled the overall molecular structure of tRNA at the moment that a special protein loads an amino acid to the tRNA. They partitioned two sites of the complex into regions requiring the more focused quantum mechanical approach. (Watch a movie of the simulation.)

The subatomic simulations of the interactions of the two regions allowed the team to run simulations of four different scenarios that would allow the tRNA to function as it does in the cell. Their simulations revealed that one of the four potential chemical pathways was more energetically favorable than the others and thus more likely to occur.

The researchers also used various methods to partition the tRNA complex between the MM and QM regions and reported on each approach.

"We didn't pick just one way; we picked as many as possible. We give the user freedom. How you structure it really depends on the particular system you're studying," said U. of I. postdoctoral researcher Rafael Bernardi, a co-lead author on the study with graduate student Marcelo Melo.

"We don't do the whole system quantum mechanically because that would take forever to calculate," Melo said.

"NAMD was designed - and this was my husband's vision - to treat really large systems," Luthey-Schulten said. "Now we can add the subatomic scale to that, opening up vast new possibilities for research."

###

The molecular dynamics tools developed at the U. of I. are freely available to the public. This research was conducted in part at the National Institutes of Health Center for Macromolecular Modeling and Bioinformatics at the Beckman Institute for Advanced Science and Technology and the National Science Foundation Center for the Physics of Living Cells at the U. of I.

The National Science Foundation, the National Institutes of Health and the Keck Foundation support this research.

####

For more information, please click here

Contacts:
Diana Yates

217-333-5802

Zan Luthey-Schulten
217-333-3518;


Rafael C. Bernard


Marcelo C. R. Melo

Copyright © University of Illinois at Urbana-Champaign

If you have a comment, please Contact us.

Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.

Bookmark:
Delicious Digg Newsvine Google Yahoo Reddit Magnoliacom Furl Facebook

Related Links

The paper "NAMD goes quantum: An integrative suite for hybrid simulations" :

Related News Press

News and information

The lightest shielding material in the world: Protection against electromagnetic interference July 3rd, 2020

Spintronics: Faster data processing through ultrashort electric pulses July 3rd, 2020

A path to new nanofluidic devices applying spintronics technology: Substantial increase in the energy conversion efficiency of hydrodynamic power generation via spin currents July 3rd, 2020

Towards lasers powerful enough to investigate a new kind of physics: An international team of researchers has demonstrated an innovative technique for increasing the intensity of lasers July 3rd, 2020

Imaging

Developing new techniques to improve atomic force microscopy June 26th, 2020

Single-spin electron paramagnetic resonance spectrum with kilohertz spectral resolution June 19th, 2020

Oxford Instruments Asylum Research Jupiter XR Large-Sample AFM Now Includes New Ergo Software Interface for Even Greater Productivity June 18th, 2020

Oxford Instruments Asylum Research Announces New “Relate” Software for Correlative Imaging with Atomic Force Microscopy and Electron Microscopy June 12th, 2020

Govt.-Legislation/Regulation/Funding/Policy

Towards lasers powerful enough to investigate a new kind of physics: An international team of researchers has demonstrated an innovative technique for increasing the intensity of lasers July 3rd, 2020

Carbon-loving materials designed to reduce industrial emissions July 3rd, 2020

Charcoal a weapon to fight superoxide-induced disease, injury: Nanomaterials soak up radicals, could aid treatment of COVID-19 July 2nd, 2020

The nature of nuclear forces imprinted in photons June 30th, 2020

Possible Futures

Spintronics: Faster data processing through ultrashort electric pulses July 3rd, 2020

A path to new nanofluidic devices applying spintronics technology: Substantial increase in the energy conversion efficiency of hydrodynamic power generation via spin currents July 3rd, 2020

Towards lasers powerful enough to investigate a new kind of physics: An international team of researchers has demonstrated an innovative technique for increasing the intensity of lasers July 3rd, 2020

Crystal structure discovered almost 200 years ago could hold key to solar cell revolution July 3rd, 2020

Discoveries

The lightest shielding material in the world: Protection against electromagnetic interference July 3rd, 2020

Spintronics: Faster data processing through ultrashort electric pulses July 3rd, 2020

A path to new nanofluidic devices applying spintronics technology: Substantial increase in the energy conversion efficiency of hydrodynamic power generation via spin currents July 3rd, 2020

Towards lasers powerful enough to investigate a new kind of physics: An international team of researchers has demonstrated an innovative technique for increasing the intensity of lasers July 3rd, 2020

Announcements

Towards lasers powerful enough to investigate a new kind of physics: An international team of researchers has demonstrated an innovative technique for increasing the intensity of lasers July 3rd, 2020

Crystal structure discovered almost 200 years ago could hold key to solar cell revolution July 3rd, 2020

Flexible material shows potential for use in fabrics to heat, cool July 3rd, 2020

Carbon-loving materials designed to reduce industrial emissions July 3rd, 2020

Interviews/Book Reviews/Essays/Reports/Podcasts/Journals/White papers/Posters

A path to new nanofluidic devices applying spintronics technology: Substantial increase in the energy conversion efficiency of hydrodynamic power generation via spin currents July 3rd, 2020

Towards lasers powerful enough to investigate a new kind of physics: An international team of researchers has demonstrated an innovative technique for increasing the intensity of lasers July 3rd, 2020

Crystal structure discovered almost 200 years ago could hold key to solar cell revolution July 3rd, 2020

Flexible material shows potential for use in fabrics to heat, cool July 3rd, 2020

Tools

Developing new techniques to improve atomic force microscopy June 26th, 2020

Extremely low thermal conductivity in 1D soft chain structure BiSeX (X = Br, I) June 19th, 2020

Oxford Instruments Asylum Research Jupiter XR Large-Sample AFM Now Includes New Ergo Software Interface for Even Greater Productivity June 18th, 2020

Oxford Instruments Asylum Research Announces New “Relate” Software for Correlative Imaging with Atomic Force Microscopy and Electron Microscopy June 12th, 2020

Grants/Sponsored Research/Awards/Scholarships/Gifts/Contests/Honors/Records

Towards lasers powerful enough to investigate a new kind of physics: An international team of researchers has demonstrated an innovative technique for increasing the intensity of lasers July 3rd, 2020

Charcoal a weapon to fight superoxide-induced disease, injury: Nanomaterials soak up radicals, could aid treatment of COVID-19 July 2nd, 2020

The nature of nuclear forces imprinted in photons June 30th, 2020

A Tremendous Recognition’ Engineer Jonathan Klamkin earns prestigious award from DARPA June 23rd, 2020

Quantum nanoscience

Macroscopic quantum interference in an ultra-pure metal June 26th, 2020

Process for 'two-faced' nanomaterials may aid energy, information tech June 26th, 2020

An EPiQS Pursuit: Physicist Andrea Young is chosen to receive an Experimental Investigator award from the Moore Foundation May 28th, 2020

Scientists break the link between a quantum material's spin and orbital states: The advance opens a path toward a new generation of logic and memory devices based on orbitronics that could be 10,000 times faster than today's May 15th, 2020

NanoNews-Digest
The latest news from around the world, FREE




  Premium Products
NanoNews-Custom
Only the news you want to read!
 Learn More
NanoStrategies
Full-service, expert consulting
 Learn More











ASP
Nanotechnology Now Featured Books




NNN

The Hunger Project