Nanotechnology Now





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

Stanford breakthrough heralds super-efficient light-based computers: Light can transmit more data while consuming far less power than electricity, and an engineering feat brings optical data transport closer to replacing wires May 29th, 2015

Donuts, math, and superdense teleportation of quantum information May 29th, 2015

OSU researchers prove magnetism can control heat, sound: Team leverages OSC services to help confirm, interpret experimental findings May 29th, 2015

Two UCSB Professors Receive Early Career Research Awards: The Department of Energy’s award for young scientists acknowledges UC Santa Barbara’s standing as a top tier research institution May 29th, 2015

Software

New JEOL E-Beam Lithography System to Enhance Quantum NanoFab Capabilities May 6th, 2015

Time Dependant Spectroscopy of Microscopic Samples: CRAIC TimePro™ software is used with CRAIC Technologies microspectrometers to measure the kinetic UV-visible-NIR, Raman and fluorescence spectra of microscopic sample areas May 2nd, 2015

Lifeboat Foundation launches Interactive Friendly AI April 6th, 2015

State-of-the-art online system unveiled to pinpoint metrology software accuracy March 27th, 2015

Academic/Education

SUNY Poly CNSE and NIOSH Launch Federal Nano Health and Safety Consortium: May 20th, 2015

New JEOL E-Beam Lithography System to Enhance Quantum NanoFab Capabilities May 6th, 2015

FEI Partners With the George Washington University to Equip New Science & Engineering Hall: Suite of new high-performance microscopes will be used for cutting-edge experiments at GW’s new research facility April 29th, 2015

Renishaw Raman systems used to study 2D materials at Boston University, Massachusetts, USA. April 28th, 2015

Announcements

Stanford breakthrough heralds super-efficient light-based computers: Light can transmit more data while consuming far less power than electricity, and an engineering feat brings optical data transport closer to replacing wires May 29th, 2015

Donuts, math, and superdense teleportation of quantum information May 29th, 2015

OSU researchers prove magnetism can control heat, sound: Team leverages OSC services to help confirm, interpret experimental findings May 29th, 2015

Two UCSB Professors Receive Early Career Research Awards: The Department of Energy’s award for young scientists acknowledges UC Santa Barbara’s standing as a top tier research institution May 29th, 2015

Research partnerships

Linking superconductivity and structure May 28th, 2015

How spacetime is built by quantum entanglement: New insight into unification of general relativity and quantum mechanics May 28th, 2015

Collaboration could lead to biodegradable computer chips May 28th, 2015

Supercomputer unlocks secrets of plant cells to pave the way for more resilient crops: IBM partners with University of Melbourne and UQ May 21st, 2015

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