Nanotechnology Now

Our NanoNews Digest Sponsors

Heifer International

Wikipedia Affiliate Button


DHgate

Home > Press > The Chicken or the Egg?

Growing a good egg: Metadynamics simulations show that the eggshell protein ovocleidin-17 induces the formation of calcite crystals from amorphous calcium carbonate nanoparticles. Multiple spontaneous crystallization and amorphization events were simulated; these simulations suggest a catalytic cycle that explains the role of ovocleidin-17 in the first stages of eggshell formation (the picture shows one intermediate of this cycle). Credit: Angew. Chem. Int. Ed.
Growing a good egg: Metadynamics simulations show that the eggshell protein ovocleidin-17 induces the formation of calcite crystals from amorphous calcium carbonate nanoparticles. Multiple spontaneous crystallization and amorphization events were simulated; these simulations suggest a catalytic cycle that explains the role of ovocleidin-17 in the first stages of eggshell formation (the picture shows one intermediate of this cycle). Credit: Angew. Chem. Int. Ed.

Abstract:
The Numerical Algorithms Group (NAG) provides an essential ingredient to help researchers find the answer.

The Chicken or the Egg?

UK | Posted on December 2nd, 2010

When researchers at the University of Warwick and the University of Sheffield decided to use the UK's national academic supercomputer HECToR to study a problem in egg shell formation, they made use of NAG HPC software engineering expertise (www.nag.com/hpc/index.asp ). The results they obtained may also give a partial answer to the age old question "which came first - the chicken or the egg?"

The answer to the question seems to be ‘chicken' - at least for one particular protein.

Researchers knew that a chicken eggshell protein called ovocledidin-17 (OC-17) must play some role in egg shell formation. The protein is found only in the mineral region of the egg (the hard part of the shell) and laboratory results showed that it appeared to influence the transformation of calcium carbonate into calcite crystals. How this process could be used to form an actual eggshell remained unclear.

University of Warwick researchers Mark Rodger and David Quigley, in collaboration with colleagues at the University of Sheffield, used molecular dynamics simulation and the HECToR supercomputer (a 12,000 core Cray XT4), to solve the problem. The researchers created a model to show how the protein bound to a calcium carbonate surface. However the early performance of the simulation software on HECToR would have kept the validation of this model beyond reach.

Luckily, as well as the Cray supercomputers managed by the University of Edinburgh, the Research Councils' HECToR service includes a comprehensive Computational Science and Engineering (CSE) support service provided by NAG. One of NAG's HPC experts identified input and especially output (I/O) as the bottleneck for the simulation software, known as DL_POLY_3 - originating from Daresbury Laboratories. A solution was provided for this research and NAG has gone on to optimize all the I/O routines, to help other users of DL_POLY_3. This was done by reordering data to take advantage of modern file systems, and then further improved by performing the I/O in parallel. This 6 months of work resulted in the I/O for DL_POLY_3 being, on average, around 50 times faster.

With the performance improvement, use of the specific model to investigate the eggshell formation became tractable. Results of the simulation now show how the protein binds using two clusters of amino acid residues on two loops of the protein. This creates a chemical clamp to nano-sized particles of calcium carbonate which encourages calcite crystallites to form. Once the crystallites are large enough to grow on their own, the protein drops off. This frees up the OC-17 to promote yet more crystallization, facilitating the overnight creation of an eggshell - started, first, by this chicken protein.

Dr David Quigley from the Department of Physics and Centre for Scientific Computing, University of Warwick, said: "Prior to the I/O improvements, DL_POLY_3 was unable to make effective use of the parallel file system on HECToR, severely crippling the performance of our simulations. The new code has reduced the time taken to write a single snapshot from 3 minutes to less than half a second, resulting in an overall factor of 20 improvement in our net performance. Without this development, HECToR would have been effectively useless for our purposes."

The researchers believe that this insight into the elegant and highly efficient methods of promoting and controlling crystallization in nature will be of great benefit to anyone exploring how to promote and control artificial forms of crystallization.

For more details of the research please refer to: Freeman et al, "Structural Control of Crystal Nuclei by an Eggshell Protein" Angew. Chem. Int. Ed. 49 (30) pp 5135-5137 (2010)

####

About Numerical Algorithms Group
With origins in several UK universities, the Numerical Algorithms Group (NAG) has its headquarters in Oxford, and is a not-for-profit organization that collaborates with world-leading researchers and practitioners in academia and industry. NAG serves its customers from offices in Oxford, Manchester, Chicago, Tokyo and Taipei, through field sales staff in France and Germany, as well as via a global network of distributors. NAG provides high-quality computational software and high performance computing services to tens of thousands of users, from Global 500 companies, major learning academies, the world’s leading supercomputing sites, numerous independent software vendors and many others.

For more information, please click here

Contacts:
For editorial inquiries, please contact:
Amy Munice
ALM Communications

+1-773-862-6800
(skype) ALMCommunications

Or

Katie O’Hare
NAG Marketing Communications Manager

+44 (0)1865 511245

Or

Hiro Chiba
Chief Operating Officer – Nihon NAG

+81 3 5542 6311

Or

Edward Chou
NAG Greater China General Manager

Tel: +886-2-25093288

Or

NAG, Booth 3131, SC10
Ernest N. Moriale Convention Center
New Orleans

Copyright © Numerical Algorithms Group

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 News Press

News and information

'Lasers rewired': Scientists find a new way to make nanowire lasers: Berkeley Lab, UC Berkeley scientists adapt next-gen solar cell materials for a different purpose February 12th, 2016

Breaking cell barriers with retractable protein nanoneedles: Adapting a bacterial structure, Wyss Institute researchers develop protein actuators that can mechanically puncture cells February 12th, 2016

Replacement of Toxic Antibacterial Agents Possible by Biocompatible Polymeric Nanocomposites February 12th, 2016

Properties of Polymeric Nanofibers Optimized to Treat Damaged Body Tissues February 12th, 2016

Software

Researchers from the California NanoSystems Institute at UCLA have created a new technique that greatly enhances digital microscopy images January 27th, 2016

Digital Surf launches revolutionary SEM image colorization January 26th, 2016

Materials scientists at FAU reconstruct turbine material atom by atom in computer simulations January 19th, 2016

NanoOK: Quality Control for portable, rapid, low-cost DNA sequencing December 21st, 2015

Academic/Education

SUNY Poly and GLOBALFOUNDRIES Announce New $500M R&D Program in Albany To Accelerate Next Generation Chip Technology: Arrival of Second Cutting Edge EUV Lithography Tool Launches New Patterning Center That Will Generate Over 100 New High Tech Jobs at SUNY Poly February 9th, 2016

COD Grad Begins Postdoctoral Fellow at Harvard University: Marsela Jorgolli's Passion for Physics Has Led to a Decade of Academic Research That Continues at Harvard University as a Postdoctoral Fellow February 2nd, 2016

Heriot-Watt's Institute of Photonics & Quantum Sciences uses the Deben Microtest 2 kN tensile stage to characterise ceramics and engineering plastics January 21st, 2016

Multiple uses for the JPK NanoWizard AFM system in the Smart Interfaces in Environmental Nanotechnology Group at the University of Illinois at Urbana-Champaign January 20th, 2016

Announcements

Graphene leans on glass to advance electronics: Scientists' use of common glass to optimize graphene's electronic properties could improve technologies from flat screens to solar cells February 12th, 2016

Breaking cell barriers with retractable protein nanoneedles: Adapting a bacterial structure, Wyss Institute researchers develop protein actuators that can mechanically puncture cells February 12th, 2016

Replacement of Toxic Antibacterial Agents Possible by Biocompatible Polymeric Nanocomposites February 12th, 2016

Properties of Polymeric Nanofibers Optimized to Treat Damaged Body Tissues February 12th, 2016

Research partnerships

'Lasers rewired': Scientists find a new way to make nanowire lasers: Berkeley Lab, UC Berkeley scientists adapt next-gen solar cell materials for a different purpose February 12th, 2016

Breaking cell barriers with retractable protein nanoneedles: Adapting a bacterial structure, Wyss Institute researchers develop protein actuators that can mechanically puncture cells February 12th, 2016

Research reveals carbon films can give microchips energy storage capability: International team from Drexel University and Paul Sabatier University reveals versatility of carbon films February 11th, 2016

SLAC X-ray laser turns crystal imperfections into better images of important biomolecules: New method could remove major obstacles to studying structures of complex biological machines February 11th, 2016

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





  Premium Products
NanoNews-Custom
Only the news you want to read!
 Learn More
NanoTech-Transfer
University Technology Transfer & Patents
 Learn More
NanoStrategies
Full-service, expert consulting
 Learn More











ASP
Nanotechnology Now Featured Books




NNN

The Hunger Project







Car Brands
Buy website traffic