Tag Archives: biological molecules

Biomining for rare earth elements with Alberta’s (Canada) Ingenuity Lab

Alberta’s Ingenuity Lab and its biomining efforts are being featured in a Feb. 3, 2014 Nanowerk Spotlight article which was supplied by Ingenuity Lab (Note: A link has been removed),

Scientists at Ingenuity Lab in Edmonton, Alberta are taking cues from nature, as they focus on nanotechnology gains in the area of biomining. Using microorganisms and biomolecules, the group is making significant advances in the recovery of rare earth and precious metals from industrial processes and the environment thanks to superior molecular recognition techniques.

In recent decades, the utility of protein/peptide molecules and their inorganic material recognition and binding abilities has come to light. Combinatorial biology tools have enabled researchers to select peptides for various materials such as ceramics, metal oxides, alloys and pure metals. Even though the binding mechanism of peptides hasn’t yet been fully resolved, studies are ongoing and these peptides continue to be used in many nanotechnology applications.

The Spotlight article further describes the approach being undertaken,

… researchers at Alberta’s first nanotechnology accelerator laboratory (Ingenuity Lab) are looking to take advantage of inorganic binding peptides for mining valuable and rare earth elements/metals that exist in nature or synthetic materials.

Rare earth elements (REE) are sought after materials that facilitate the production of electrical car batteries, high power magnets, lasers, fiber optic technology, MRI contrast agents, fluorescent lightening and much more. Despite increasing demand, mining and processing yields are not enough to satisfy the growing need. This is mainly due to the great loss during mining (25-50%) and beneficiation (10-30%).

Since REEs exist as a mixture in mineral ores, their beneficiation and separation into individual metals requires unique processes. Depending on the chemical form of the metal, different compounds are necessary during beneficiation steps to convert minerals into metal nitrates, oxides, chlorides and fluorides, which would be further extracted individually. Furthermore, this process must be followed with solvent separation to obtain individual metals. These excessive steps not only increase the production cost and energy consumption but also decrease the yield and generate environmental pollution due to the use of various chemicals and organic solvents.

…  Ingenuity Lab is working on generating smart biomaterials composed of inorganic binding peptides coated on the core of magnetic nanoparticles. These smart materials will expose two functions; first they will recognize and bind to a specific REE through the peptide region and they will migrate to magnetic field by the help of Iron Oxide core.

You can find more detail and illustrations in the Spotlight article.

There is biomining research being performed in at least one other lab (in China) as I noted in a Nov. 1, 2013 posting about some work to remove REEs from wastewater and where I noted that China had announced a cap on its exports of REEs.

Tim Harper’s Cientifica emerging technologies and business consultancy offers a white paper (free), Simply No Substitute? [2013?], which contextualizes and provides insight into the situation with REEs and other other critical materials. From Cientifica’s Simply No Substitute? webpage,

There is increasing concern that restricted supplies of certain metals and other critical minerals could hinder the deployment of future technologies. This new white paper by Cientifica and Material Value,  Simply No Substitute? takes a critical look at the current technology and policy landscape in this vital area, and in particular, the attempts to develop substitutes for critical materials.

A huge amount of research and development is currently taking place in academic and industrial research laboratories, with the aim of developing novel, innovative material substitutes or simply to ‘engineer-out’ critical materials with new designs.  As an example, our analysis shows the number of patents related to substitutes for rare earth elements has doubled in the last two years. However, the necessity and effectiveness of this research activity is still unclear and requires greater insight. Certainly, as this white paper details, there is no universal agreement between Governments and other stakeholders on what materials are at risk of future supply disruptions.

In an effort to ensure the interests of end-users are represented across this increasingly complex and rapidly developing issue, the publication proposes the creation of a new industry body. This will benefit not just end-users, but also primary and secondary producers  of critical materials, for who it is currently only feasible to have sporadic and inconsistent interaction with the diverse range of industries that use their materials.

You can download the white paper from here.

Getting back to Ingenuity Lab, there is no research paper mentioned in the Spotlight article. Their website does offer this on the Mining page,

The extraction of oil and gas is key to the economic prosperity of Alberta and Canada. We have the third largest oil reserves in the world behind Saudi Arabia and Venezuela. Not only is our oil and gas sector expected to generate $2.1 trillion in economic activity across Canada over the next 25 years, Canadian employment is expected to grow from 75,000 jobs in 2010 to 905,000 in 2035. However, it’s not without its impacts to the environment. This, we know. There are great strides being made in technology and innovation in this sector, but what if we could do more?

Then, there’s this from the site’s Biomining subpage,

Using a process called biomining, the research team at Ingenuity Lab is engineering new nano particles that have the capability to detect, extract or even bind to rare earth and precious metals that exist in nature or found in man-made materials.

Leveraging off of the incredible advances in targeted medical therapies, active nanoparticle and membrane technologies offer the opportunity to recover valuable resources from mining operations while leading to the remediation of environmentally contaminated soil and water.

Biomining technology offers the opportunity to maximize the utility of our natural resources, establish a new path forward to restore the pristine land and water of our forefathers and redefine Canada’s legacy of societal environmental, and economic prosperity.

Finally, there’s this page (Ingenuity Attracts Attention with Biomining Advances)  which seems to have originated the Spotlight article and is the source of the images in the Spotlight article.  I am curious as to whose attention they’ve attracted although I can certainly understand why various groups and individuals might be,

… Ingenuity’s system will also be able to work in a continuous flow process. There will be a constant input of metal mixture, which could be mine acid drain, tailing ponds or polluted water sources, and smart biomaterial. Biomaterial will be recovered from the end point of the chamber together with the targeted metal. Since the interaction between the peptide and the metal of interest is not covalent bonding, metal will be removed from the material without the need for harsh chemicals. This means valuable materials, currently discarded as waste, will be accessible and the reuse of the smart biomaterial will be an option, lowering the purification cost even more.

These exciting discoveries are welcome news for the mining industry and the environment, but also for communities around the world and generations to come.  Thanks to ingenuity, we will soon be able to maximize the utility of our precious resources as we restore damaged lands and water.

In any event I hope to hear more about this promising work with more details (such as:  At what stage is this work?, Is it scalable?) and the other research being performed at Ingenuity Lab.

Similarities between biological molecules and synthetic nanocrystals extend beyond size

Researchers at the University of Illinois at Urbana-Champaign have determined that there are more similarities between biological molecules and synthetic nanocrystals than formerly believed, according to a Dec. 17, 2013 news item on Nanowerk (Note: A link has been removed),

Researchers have long thought that biological molecules and synthetic nanocrystals were similar only in size. Now, University of Illinois at Urbana-Champaign chemists have found that they can add reactivity to the list of shared traits. Atoms in a nanocrystal can cooperate with each other to facilitate binding or switching, a phenomenon widely found in biological molecules.

The finding could catalyze manufacturing of nanocrystals for smart sensors, solar cells, tiny transistors for optical computers, and medical imaging. Led by chemistry professor Prashant Jain, the team published its findings in the journal Nature Communications (“Co-operativity in a nanocrystalline solid-state transition”).

A Dec. 16, 2013 University of Illinois at Urbana-Champaign news release, which originated the news item, explains why the scientists are so interested and how they went about their investigation,

“In geological, industrial and domestic environments, the nanoscale grains of any material undergo chemical transitions when they are put under reactive conditions,” Jain said. “Iron rusting over time and diamond forming from carbon are examples of two commonly occurring transitions. Understanding how these transitions occur on the scale of the tiniest grains of the material is a major motivation of our work.”

Scientists can exploit such transitions to make nanocrystals that conform to a particular structure. They can make a nanocrystal of one material and transform it into another material, essentially using the original nanocrystal framework as a template for creating a nanocrystal of the new material with the same size and shape. This lets researchers create nanocrystals of new materials in shapes and structures they may not be able to otherwise.

In the new study, the researchers transformed tiny crystals of the material cadmium selenide to crystals of copper selenide. Copper selenide nanocrystals have a number of interesting properties that can be used for solar energy harvesting, optical computing and laser surgery. Transformation from cadmium selenide creates nanocrystals with a purity difficult to attain from other methods.

The researchers, including graduate student Sarah White, used advanced microscopy and spectroscopy techniques to determine the dynamics of the atoms within the crystals during the transformation and found that the transformation occurs not as a slow diffusion process, but as a rapid switching thanks to co-operativity.

The researchers saw that once the cadmium-selenide nanocrystal has taken up a few initial copper “seed” impurities, atoms in the rest of the lattice can cooperate to rapidly swap out the rest of the cadmium for copper. Jain compares the crystals to hemoglobin, the molecule in red blood cells that carries oxygen. Once one oxygen molecule has bound to hemoglobin, other binding sites within hemoglobin slightly change conformation to more easily pick up more oxygen. He posits that similarly, copper impurities might cause a structural change in the nanocrystal, making it easier for more copper ions to infiltrate the nanocrystal in a rapid cascade.

The researchers reproduced the experiment with silver, in addition to copper, and saw similar, though slightly less speedy, cooperative behavior.

Now, Jain’s team is using its advanced imaging to watch transitions happen in single nanocrystals, in real time.

“We have a sophisticated optical microscope in our lab, which has now allowed us to catch a single nanocrystal in the act of making a transition,” Jain said. “This is allowing us to learn hidden details about how the transition actually proceeds. We are also learning how one nanocrystal behaves differently from another.”

Next, the researchers plan to explore biomolecule-like cooperative phenomena in other solid-state materials and processes. For example, co-operativity in catalytic processes could have major implications for solar energy or manufacturing of expensive specialty chemicals.

“In the long term, we are interested in exploiting the co-operative behavior to design artificial smart materials that respond in a switch-like manner like hemoglobin in our body does,” Jain said.

Here’s an image of the various forms of cadmium selenide used in research,

Nanocrystals of cadmium selenide, known for their brilliant luminescence, display intriguing chemical behavior resulting from positive cooperation between atoms, a behavior akin to that found in biomolecules.  Photo courtesy Prashant Jain

Nanocrystals of cadmium selenide, known for their brilliant luminescence, display intriguing chemical behavior resulting from positive cooperation between atoms, a behavior akin to that found in biomolecules. Photo courtesy
Prashant Jain

For the curious, here’s a link to and a citation for the paper,

Co-operativity in a nanocrystalline solid-state transition by Sarah L. White, Jeremy G. Smith, Mayank Behl, & Prashant K. Jain Nature Communications 4, Article number: 2933 doi:10.1038/ncomms3933 Published 12 December 2013

This article is behind a paywall.

Computer simulation errors and corrections

In addition to being a news release, this is a really good piece of science writing by Paul Preuss for the Lawrence Berkeley National Laboratory (Berkeley Lab), from the Jan. 3, 2013 Berkeley Lab news release,

Because modern computers have to depict the real world with digital representations of numbers instead of physical analogues, to simulate the continuous passage of time they have to digitize time into small slices. This kind of simulation is essential in disciplines from medical and biological research, to new materials, to fundamental considerations of quantum mechanics, and the fact that it inevitably introduces errors is an ongoing problem for scientists.

Scientists at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have now identified and characterized the source of tenacious errors and come up with a way to separate the realistic aspects of a simulation from the artifacts of the computer method. …

Here’s more detail about the problem and solution,

How biological molecules move is hardly the only field where computer simulations of molecular-scale motion are essential. The need to use computers to test theories and model experiments that can’t be done on a lab bench is ubiquitous, and the problems that Sivak and his colleagues encountered weren’t new.

“A simulation of a physical process on a computer cannot use the exact, continuous equations of motion; the calculations must use approximations over discrete intervals of time,” says Sivak. “It’s well known that standard algorithms that use discrete time steps don’t conserve energy exactly in these calculations.”

One workhorse method for modeling molecular systems is Langevin dynamics, based on equations first developed by the French physicist Paul Langevin over a century ago to model Brownian motion. Brownian motion is the random movement of particles in a fluid (originally pollen grains on water) as they collide with the fluid’s molecules – particle paths resembling a “drunkard’s walk,” which Albert Einstein had used just a few years earlier to establish the reality of atoms and molecules. Instead of impractical-to-calculate velocity, momentum, and acceleration for every molecule in the fluid, Langevin’s method substituted an effective friction to damp the motion of the particle, plus a series of random jolts.

When Sivak and his colleagues used Langevin dynamics to model the behavior of molecular machines, they saw significant differences between what their exact theories predicted and what their simulations produced. They tried to come up with a physical picture of what it would take to produce these wrong answers.

“It was as if extra work were being done to push our molecules around,” Sivak says. “In the real world, this would be a driven physical process, but it existed only in the simulation, so we called it ‘shadow work.’ It took exactly the form of a nonequilibrium driving force.”

They first tested this insight with “toy” models having only a single degree of freedom, and found that when they ignored the shadow work, the calculations were systematically biased. But when they accounted for the shadow work, accurate calculations could be recovered.

“Next we looked at systems with hundreds or thousands of simple molecules,” says Sivak. Using models of water molecules in a box, they simulated the state of the system over time, starting from a given thermal energy but with no “pushing” from outside. “We wanted to know how far the water simulation would be pushed by the shadow work alone.”

The result confirmed that even in the absence of an explicit driving force, the finite-time-step Langevin dynamics simulation acted by itself as a driving nonequilibrium process. Systematic errors resulted from failing to separate this shadow work from the actual “protocol work” that they explicitly modeled in their simulations. For the first time, Sivak and his colleagues were able to quantify the magnitude of the deviations in various test systems.

Such simulation errors can be reduced in several ways, for example by dividing the evolution of the system into ever-finer time steps, because the shadow work is larger when the discrete time steps are larger. But doing so increases the computational expense.

The better approach is to use a correction factor that isolates the shadow work from the physically meaningful work, says Sivak. “We can apply results from our calculation in a meaningful way to characterize the error and correct for it, separating the physically realistic aspects of the simulation from the artifacts of the computer method.”

You can find out more in the Berkeley Lab news release, or (H/T)  in the Jan. 3, 2013 news item on Nanowerk, or you can read the paper,

“Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics simulations,” by David A. Sivak, John D. Chodera, and Gavin E. Crooks, will appear in Physical Review X (http://prx.aps.org/) and is now available as an arXiv preprint at http://arxiv.org/abs/1107.2967.

This casts a new light on the SPAUN (Semantic Pointer Architecture Unified Network) project, from Chris Eliasmith’s team at the University of Waterloo, which announced the most  successful attempt (my Nov. 29, 2012 posting) yet to simulate a brain using virtual neurons. Given the probability that Eliasmith’s team was not aware of this work from the Berkeley Lab, one imagines that once it has been integrated that SPAUN will be capable of even more extraordinary feats.