#amsen

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[sigrise]

The ‘Scary Dark’ of the Underground Mine (AMSEN)

by Alan Anderson

March 10, 2015

Silas Hango, a native of Namibia, joined RISE as an AMSEN PhD student with a strong interest in metallurgical engineering. Thanks to the tradition of collaboration among RISE institutions, he has been able to conduct his studies at the University of the Witwatersrand in Johannesburg (Wits), while focusing his research on a site in his home country.

With its strong program in metallurgy, Wits offers many opportunities to study the behavior of metal alloys, which are useful in countless industrial applications worldwide. One of these is mining, which challenges engineering researchers to come up with durable materials that can perform in extremely corrosive environments.

Corrosion engineering is a familiar subject area for him, because mining, especially diamond mining, is the largest contributor to Namibia’s economy. The mine that sought out his assistance in combating corrosion was not seeking diamonds, however, but copper, and it is only a short drive from Namibia’s capital city of Windhoek. This was the Otjihase Mine, operated by Ongopolo Mining and Processing Ltd. and, after some financial troubles, owned by Weatherly International of the United Kingdom. The mine is not only tiny, but it is virtually the only functioning copper mine in Namibia. With an output of about 5,000 tons of copper per year, the Otjihase Mine, and therefore the country of Namibia, are among the smallest copper producers in the world; it compares with production of 5 million tons by the copper mines of Chile, and, in Africa, with the much larger copper producers in Zambia and the Democratic Republic of Congo, each of which produces more than 600,000 tons per year.

Nonetheless, small-scale mining is not easy mining. It is the nature of underground mining that one must grapple with constant corrosion issues that threaten both safety and productivity every day of the year. Luckily for Silas, his location at Wits gives him access to industrial researchers who are well aware of these challenges, and modern equipment at nearby Mintek, a global-scale minerals research firm in Randburg. For a young student starting out, the presence of skilled mentors is essential. At Wits he benefits from the supervision of Prof. Lesley Cornish, and co-supervision of Drs. Josias van der Merwe and Lesley Chown, other faculty members who work at the Centre of Excellence in Strong Materials, and Prof. Frank Kavishe at the University of Namibia.

Silas emphasizes the huge difference between the peaceful environment of the labs in Johannesburg and the menacing darkness of the Otjihase Mine. “I’ve been down underground at the mine three times,” he said. “I always wear a powerful headlamp, like the miners, so the light is strong. But I still find it scary to be in the dark down there.”

Indeed, the more he learns about that dark workplace, the more there is to fear. One challenge is simply to clean the air so it is fit to breathe. Every underground mine depends on powerful systems of ventilation and air circulation to sustain a livable environment. The lives of the hundreds or even thousands of underground workers depend on these systems, which must run day and night to clear the toxic fumes created by blasting and the exhaust fumes of the diesel equipment.

A second major challenge is managing the damage done by groundwater as it moves into and through the mineral environment of the mine. As the water moves, it dissolves and absorbs many elements, such as chlorine, sulfur, nitrates, and other chemicals. Some of these form corrosive acids, especially sulfuric acid and hydrochloric acid, so that much of the water circulation machinery, especially the critical water pumps, are under near-constant assault by corrosion. The acids form pits in the metal surfaces, reducing pumping efficiency and eventually weakening the structures themselves.

“The pumps are very corroded,” said Silas, “and they fail all the time. The miners have to replace the shaft and sleeve of each pump every week because of corrosion and wear. I have seen whole areas of failed pumps.”

During his visits to the mine, he investigates the corrosion status of the water pumps, system, and pipes. Most of the pumps are located about 900m below the surface, and they are responsible for removing rainwater infiltration and small stream flow. The water system of the mine is so complex that he depends on the collaboration of the miners for much of the routine work. Company technicians pitch in every day, monitoring the quality of the water, tracking changes in its elemental composition, and reporting to him monthly on the fluctuations in flow through the pumping system.

The first job of the pumps is to move the water into deep mine sumps where it is stored. However, the water cannot remain in the sumps for long because it becomes progressively contaminated until it cannot be used in cooling systems or for any other purposes for which water is vital in mine operation. The miners must continually pump it from the underground sumps to a much larger outside sump, where it is cleaned (at considerable expense) and then returned for use in the mine.

The amount of sump water that must be pumped and cleaned varies with the amount of rainfall. Seasonal rains may bring a two to five percent increase in the moving groundwater — and more work for the pumps. Water quantity also increases as the mine deepens. These technical challenges demand virtually constant attention and equipment of the highest quality.

Silas’ principle challenge is to find more effective alloys than the traditional iron alloys. He began by testing two candidates that are commercial products, both made in the United States. Ultimet is a cobalt-based alloy, strengthened by chromium, nickel and molybdenum; compared to iron-based alloys, it is highly resistant to corrosion, galling (where two surfaces stick, then rip apart), and wear. Stellite 6B is also cobalt-based, and includes chromium, tungsten, nickel, and a small but important amount of carbon. It was invented in the early 1900s as a substitute for steel cutlery that stained.

These alloys, which are expensive, were initially donated by the MultyAlloy company of Midrand, South Africa. They had not been used in mines, but in other very harsh environments, including seawater and chloride solutions. “We tested them for hardness, corrosion, and wear resistance. With our special needs, we had to make them even stronger to increase corrosion and wear resistance. We wanted to add ruthenium first, but the problem with starting with cobalt alloys is that they are specialized and hard to get in small amounts we needed. The company offered me the powered form, but the minimum they would sell was 130 kilograms. I need about one kilogram! So I’m getting the melted version, which is more homogeneous. For lab testing, we plan to try a ruthenium content between 0.1 % and 0.5%, and after testing in the lab we’ll take it to the mine.”

Because Silas is dealing with rare metals, they are not easy to procure or handle. “Ruthenium has good properties for us,” he said, “but the challenge is how to get the materials, and how to test them. We need special testing equipment, and everyone has to queue up to use it.” At Wits, the fourth-year engineering students have priority when they are busy with their final year projects. I could do it at Mintek, but they use a different system.” He was finally able to use the equipment and software at Mintek, and the results, he said, were “awesome, convincing, and presentable.”

Given all the many difficulties of his work, Silas might be tempted to find an easier project — but he is gratified by his progress so far. Already he has given presentations at Wits and at the 2nd Annual Science Research Conference in Namibia, and published part of his work in the International Science and Technology Journal of Namibia (ISTJN), Volume 4. At Wits he won a Corrosion Prize at the School of Chemical and Metallurgical Engineering Poster Day. Given the complexity of forces creating corrosion, and the need to accommodate men, machinery, and ore handling systems safely and economically, he believes it is essential that these corrosion problems are effectively solved.

[sigrise]

Bacteria That Tweet (AMSEN)

by Alan Anderson

January 27, 2015

Just a few years ago, the idea of achieving international acclaim as a young scientist seemed like an impossible dream to Gloria Hlongwane. Today she is an accomplished and outgoing PhD student at the School of Chemical and Metallurgical Engineering at the University of the Witwatersrand (Wits) who has done just that, despite early difficulties that few of her peers had to endure. The story she tells is one of persistence, self-belief, and a stubborn faith in her abilities despite little help from anyone.

She was raised by a single mother, and her early years were a time of few resources and little hope. Her mother could provide scant guidance toward an education of any kind, let alone the advanced path she currently travels. Gloria’s mother was a Jehovah’s Witness, and she tried to convince her talented daughter to use her skills as a minister in that faith – a career far from science that did not interest Gloria. Yet even without the parental push that launched the careers of many RISE students, she has taken every advantage of teachers and mentors to achieve the challenge and excitement of PhD-level research in advanced science. Her conversation overflows with excitement and her hopes for continuing success as a leader and advisor in her own right.

Gloria grew up in the town of Carletonville, about an hour west of Wits’ location in Johannesburg. The town is relatively new, and sits near the western end of the enormous Witwatersrand reef of gold that underlies the nation’s largest metropolitan region. Gold was discovered around Carletonville and developed by various mining companies from 1937 onward; the dusty town itself grew slowly and was not officially incorporated until more than two decades later, in 1959. It was named after the mining director of Consolidated Gold Fields, Guy Carleton Jones, and is widely known for the huge depth of its sweltering mines. One of its three Western Deep Levels mines, called Mponeng (meaning “look at me” in the Tswana language), is said to be the deepest in the world. Mponeng’s tunnels now extend some 2.4 miles beneath the earth’s surface, where the rock temperature is about 140 degrees; slurries of ice must be pumped through the tunnels so that the miners can work there at a humid but more tolerable 86 degrees. The mines continue to be dangerous, with multiple deaths reported every year. Nonetheless, with few other employment opportunities in the area, more than 4,000 miners risk their lives every day in its 200-mile labyrinth of tunnels.

Having grown up in a town where daily conversations were filled with news about injuries and injustice, Gloria could not as a young child see a path to a better life for herself. She had great ability but few allies, and her early school years brought her no sense of achievement or models to work toward.

“In primary school,” she said, “I was smart, and all the teachers liked me. But this meant that none of the kids liked me. Also, I was tiny. When I went to Tswasongu High School, the kids were all bigger than I was. I cried every day. When I got there, the girls had nice hair and the boys knew how to smoke.  I thought, why am I the only one who doesn’t have anything? So I decided to keep quiet. In crowds I did not speak. I would just walk between the tall people, and eat my lunch by myself, sitting in my seat in the classroom.”

The school work continued to come easily to her, however, and gradually she began to see that it might lead to a better place. “I got it,” she remembers. “If I couldn’t be like the other kids, I’d be able to show the older people. Ok, if I’m not gonna grow, or have hair like the other girls, at least I can make sure the teachers like me, because I was smart enough to do that. My older sister was in the same school, but she wouldn’t acknowledge me, so I had to figure life out for myself. I cried the entire grade eight. ”

She realized that her way out of this life, and the township she lived in, was to become a star student. When her mother married, and had even less time to help her, she set her sights on a goal that seemed impossible: entrance to a university. And not just any university, but one of the best – the University of the Witwatersrand, one of the most prestigious universities in South Africa. It was a bold step for a girl without connections or friends in high places.

“When my mom got married, it was hard. The only thing I could think of was to get a bursary on my own. But the first year I tried, in 2007, I didn’t get one. I didn’t know the ropes, and my application was late. I wrote letters to companies and to government. My mother paid me five rand for washing the stoop to our building, and I spent all that money on envelopes and stamps. I didn’t get any answers. I tried the telephone; I would call and call.”

In January 2008 – on a Friday, she remembers – she again faced disappointment. Monday was registration day at Wits for students with bursaries; those without funds would have to wait another year. She checked the newspaper, as she did every day, for notices about bursaries, and found nothing. In frustration, she decided to check the old newspaper ads she had used to apply for bursaries. The first one she picked up was to the Department of Agriculture, and she saw that she had not only met their requirements, but surpassed them. Her indignation surged and she decided to act.

“They hadn’t let me know anything,” she remembered. “Why hadn’t they contacted me? So I called the phone number. A guy answered and actually spoke to me. He said that their bursary probably went to someone with more pull than I had. He also said that my last name, Hlongwane, was almost the same as the last name of the person in charge of the bursaries, so that might have caused some confusion. He called the people for me, and found that I was in fact offered the bursary. The acceptance was faxed to the nearest library. Hooray! I was hopping up and down I was so happy. It turned out that the bursary paid for her entire course of undergraduate studies.

She decided to focus on science, she said, because “I had an instinctive appreciation for the integrative nature of modern scientific research, especially in developing tools that solve problems within various industries, and can in turn benefit humanity.” During her first year, she chose among some of science’s hottest fields, majoring in microbiology and molecular biology, with chemistry as a second major. After graduating in 2010, she felt she knew enough to continue with an honors program in 2011 in microbiology and biotechnology, and she became more and more interested in what might be done by combining the skills of biology and engineering. A major step was to join a small team of students that was organized to compete in the iGEM (international Genetically Engineered Machines) competition, organized in 2004 by students and faculty at MIT in the U.S. A Wits group had done well in 2010, and the competitive Gloria was sure her new group, aided by several faculty advisors from both Wits and the Council for Scientific and Industrial Research (CSIR), could do even better in 2011.

“My friends and I were working in bio-engineering,” she said. “That’s using genes, but like robots. It is a way of using DNA as tools that will be useful.” The group was supported by faculty from Wits, where her two advisors were Karl Rumbold of the  School of Molecular and Cell Biology and Marco Weinberg of the Department of Molecular Medicine in the medical school, and by synthetic biology researchers at CSIR in Pretoria. The team voted to explore the concept of social networking among very small organisms.

“We started with an idea,” said Gloria. “We though it would be so cool if we could understand how bacteria communicate with each other. We decided to call it bio-tweeting. We wanted to understand how the bacteria might communicate and how that makes them move around.” For their work, she and her colleagues used the common E. coli bacteria partly because they are highly mobile, well understood, and easily available in the laboratory. “We decided to test whether they might be able to move in a controlled manner, from one place to another and only to that place, as opposed to just wandering here and there.”

One member of their team was an engineer, who built an experimental model for the group. In the laboratory, the team prompted the bacteria to move by introducing a pollutant into the environment – in this case a common anti-asthma drug called theophylline. Each bacterium can move by means of a tiny vibrating flagellum, and they saw that the cells would move faster with higher concentrations of the stimulant.

To understand what caused the bacteria to move, Gloria’s team had to delve deeply into its genetic code of DNA, the messenger RNA (mRNA) that copies the DNA, and the ribosomes that act as complex molecular “factories” linking amino acids into new strands of DNA in the order specified by the mRNA molecules. The DNA of E. coli is arranged in a circle, and the team chose a sequence of the DNA which has a “riboswitch,” or segment of mRNA that switches on and off certain genes. For example, they knew that this tiny switch may be able to sense small amounts of potentially harmful molecules, such as the drug theophylline.

Her group found that the riboswitch indeed responded to the theophylline. “We thought it would be so cool if we could make the bacteria communicate like people do on Twitter. We thought, We know it moves, how can we make it move toward something. We found that it was the riboswitch that caused it to go toward the theophylline. It was going to check what was there.”

In its entirety, the bio-tweet concept as a whole is even more ambitious, testing whether there is a bacterial communication network that emulates social networking to facilitate speedy assimilation and exchange of information. Working out the complexities of this concept is likely to keep researchers busy for a long time.

Their project was so successful they were accepted in the iGEM competition. Because there is no African section, they were invited to Amsterdam to compete in the European section. One aim of the iGEM is to encourage a new generation of scientists who think differently about biology, including cross-disciplinary collaboration. It focuses on creation of biological “machines” designed by engineering principles but made from biological components, such as DNA and proteins. Hundreds of teams compete, including those of top institutions world-wide.

In 2011, most teams had 10 people or more; the Wits team had four. But they were generously supported by both Wits and CSIR, and several faculty mentors, and the quality of their work was high. For their presentation in Amsterdam they were ranked second in the European regionals (Imperial College London was first) and awarded two of 10 special prizes. They were selected as one of the three teams from the European regionals to win a trip to MIT to compete in the finals. At that point, Gloria was quoted as saying: “We have faith in our ability to do South Africa proud. We will give it everything we have and show the world what South Africa has to offer.” At MIT they were picked as one of the “Sweet Sixteen,” along with the likes of Harvard, Yale, UC Davis, Paris Bettencourt, and Tokyo Tech, and went home feeling like champions.

Still, once the celebrations subsided, Gloria was ready to move on from bio-tweets and bio-Twitter. “During my honors year we did the fun part of the project,” she said. “We did the basic research, and stopped there. I didn’t want to spend my MSc time continuing to do the same thing.”

In 2013, she was working toward her master’s degree, which was in the process of being upgraded to a PhD, when she was recruited to join the Wits node of AMSEN. She saw that RISE would allow her to devote her post-graduate years to studies that might “make a contribution to knowledge.” She found a challenging project that seemed to have great potential value, an effort to make a biosensor using DNA and graphene. Graphene, first produced in the laboratory in 2004, consists of very strong sheets of carbon only one atom thick. Among other remarkable – though largely unexploited – properties is its strong affinity for DNA. Working with Prof. Sunny Iyuke of Wits’ School of Chemical and Metallurgical Engineering and Dr. Daniel Wamwangi of Wits’ School of Physics, she is exploring this ability in more detail. “We have many things that are being bioengineered,” she said. “One line of investigation is forensic research” – using graphene’s ability to detect DNA to solve crimes. “We want to be able to identify a person’s DNA with great accuracy,” she said. “And we’re hoping graphene will help us do that.”

Meanwhile, her friends and colleagues continue to regard with awe Gloria’s energy and curiosity, having little doubt that she will succeed in her career. As one friend was quoted after the team’s success in the iGEM competition, “Gloria is a super crazy stickler for perfection, with a broad sense of humor. She likes organizing all her thoughts and ideas that occur throughout the busy day on paper towels or napkins. She talks non-stop, that is, all the time, all day, and every day.” Having spent several hours with her, I have to agree – and to wish her the best.

[sigrise]

October 27, 2014

[amsen]

DAS ME

[sigrise]

by Evelyn Lirri

September 3, 2012

An initiative to train science lecturers and boost collaboration among researchers at African universities is likely to be renewed and expanded next year.

The final installment of a US$5 million grant for the period 2011–2013 for the Regional Initiative in Science and Education (RISE), launched in 2008, will be provided by the Carnegie Corporation of New York, United States, in March next year.

But a third phase, from 2014 to 2016 — to focus on building partnerships for expansion and increasing the visibility of academic networks and their activities — is now likely to take place.

RISE plans an expansion into Francophone Africa, and possibly North Africa, according to Lori Mulcare, a RISE administrator based at the Science Initiative Group, the US science institute coordinating the initiative alongside African partners.

"The original competition [for RISE grants] in 2007 was open to universities in research institutions in Sub-Saharan Africa but, because of the linguistic limitations of our small secretariat, only English-language proposals were accepted and, as a result, very few proposals came from non-Anglophone countries," she told SciDev.Net.

RISE is yet to secure funding for the expansion, but it has formed a partnership with the African University of Science and Technology in Nigeria to host an African-based co-secretariat and add multilingual capacity as needed.

RISE works with PhD and MSc-level scientists and engineers in Sub-Saharan Africa, through university-based research and training networks, in disciplines such as biochemistry, environmental science and pharmacology. Its main purpose is to train new faculty members to teach in African universities, and to upgrade current faculty qualifications.

Five academic networks, including the African Materials Science and Engineering Network (AMSEN) and the Western Indian Ocean Regional Initiative, each received US$800,000 for the 2011–2013 phase.

Mulcare told SciDev.Net that the grant money mainly covers fees, bursaries, travel between network sites, student conferences and purchasing educational equipment.

"RISE’s primary goal is to use the network structure to provide comprehensive research and training for master’s and PhD students in science and engineering disciplines," said Mulcare. "RISE graduates are well prepared to contribute to and strengthen universities in their home countries or regions, as teachers, mentors and researchers," she added.

Mulcare said RISE is currently supporting 63 master’s and 67 doctoral students, of whom around a third are women.

Patrick Okori, Dean of the School of Agricultural Sciences at Makerere University in Kampala, Uganda, said the initiative could boost the number of African scientists working on the continent.

"Most of our scientists have gone to work outside the continent so we need a replacement for them," Okori said. "We will need students with analytical capacities and high level skills to drive new innovations and research, which can lead to the development of our continent."

[sigrise]

by Julie Frederikse

September 11, 2011

If postgraduate students at the Pan-African School of Materials (PASMAT) are asked what they’re studying this month, they aren’t being flippant if their answer is “stuff”. That’s because the field of materials science is often referred to as “the science of stuff”.

Calling it “stuff”, however, doesn’t mean it’s easily - or briefly - defined. An educational kid’s site - StrangeMatter puts it this way: “Understanding how [everything you use every day] is put together, how it can be used, how it can be changed and made better to do more amazing things - even creating completely new kinds of stuff: that’s what materials science is all about.”

Nearly two dozen masters and doctoral students in science and engineering are attending the PASMAT course at the African University of Science and Technology (AUST) in Abuja, Nigeria, through mid-September.

Aerospace engineer Wole Soboyejo, who teaches at Princeton University in the United States, is an AUST advisor and this week’s course lecturer. The topic: structural fatigue and fracture - or, in lay terms, what happens to matter when stressed.

To a non-scientist, it might sound esoteric, or even boring. But think of it like this; if you’re in an airplane that hits an air pocket, you’d want the engineers who built the fuselage to have paid attention in that part of the course! “The tools that postgraduates acquire at PASMAT will prepare them for materials research, as well as future efforts to develop new materials,” Soboyejo told Research Africa, a professional body for African government and institutional policymakers, researchers and research managers.

The second week of training is being presented by Professor Lesley Cornish, assistant dean of - get ready for this - Research of the Faculty of Engineering and the Built Environment at South Africa’s University of the Witwatersrand (Wits), who will cover basic materials concepts required for the calculation of phase diagrams in materials science and engineering. If you’re not a scientist and want to be even further confused, take a look at this YouTube video.

On the other hand, you could just think of the airplane again. You really do want the builders to be able to calculate how complex mixtures of metals will respond under varying conditions. And wouldn’t it be nice if African scientists come up with innovative uses of materials to solve old or emerging problems of contemporary life?

When she’s not fully occupied with being dean of a university department whose name you can’t remember, Cornish is also the director of one of the PASMAT partner groups, the African Materials Science and Engineering Network (AMSEN), which aims to improve skills in materials science and engineering. One of the potential results of that work is to add value to Africa’s extensive mineral deposits. And that matters - a lot - to Africa’s future.

Oxford economist Paul Collier, in his recent book ‘The Plundered Planet’, writes that “the failure to harness natural capital is the single-most important missed opportunity in economic development”. In an interview with AllAfrica, Collier added that the “resource discoveries which are now happening in Africa are the biggest opportunity for good that Africa has ever had and is likely to have in our lifetimes”. If AMSEN-related faculty and students help increase the utility of the continent’s natural resources - retaining more of the value - the investment in science education would be enormous.

AMSEN has branches at the Universities of Botswana, Namibia and Nairobi, as well as Nigeria’s Federal University of Technology in Akure (FUTA) and at Cornish’s university, Wits in Johannesburg. AMSENis one of five networks in sub-Saharan Africa funded by the Carnegie-IAS Regional Initiative in Science and Education (RISE). The goal is to strengthen higher education in sub-Saharan Africa by preparing new faculty to teach in African universities and upgrading the qualifications of current faculty.

Professor Cornish is pleased that three of her students from the AMSEN network will be taking part in the PASMAT course, which is a collaboration between AUST-Abuja and RISE-AMSEN. Cornish’s students are Nigerian Adenike Olaseinde, winner of the TATA Africa Scholarship for Women Scientists, who was a lecturer at FUTA before coming to Wits; another Nigerian materials scientist, Apata Ayodeji, who taught at the Department of Metallurgical & Materials Engineering at the Federal Polytechnic of Idah in Nigeria’s Kogi State; and Kenyan Bernard Odera, who lectured at the University of Nairobi. All the AMSEN postgraduate students will return to their home institutions when they have completed their PhDs.

The rationale for the workshop is to provide training that will allow students to undertake research, with topics chosen so as to be applicable for many research topics, such as alloy development, corrosion, materials development and beneficiation - or enhancing the value - of local resources, said Cornish. She said the research is important not only as the basis for local industries, but also to make existing products last longer.

"Some places in southern Africa, which by tradition have simply exported raw minerals with no value added, are finally developing truly advanced technologies and applications for these minerals," said Alan H. Anderson, a consultant for the Science Initiative Group based at the Institute for Advanced Study in Princeton, New Jersey, which implements the RISE program. "The AMSEN program at Wits is one of the best examples of this."

Professor Cornish says she encouraged her students to use the opportunity of attending the PASMAT course to discuss their research problems with other materials scientists. “I’m developing alloys that have high strength in aggressive environments,” Cornish said. “I’ve got students working on steels and cermets (materials used for machining tools) on research which will contribute to the mining sector and other areas where high temperature alloys are used, like in turbine engines, and also in the petrochemical industry.”

She says an alloy she and her students are working on can withstand high temperatures more effectively than materials currently used, e.g. those that are nickel-based. What’s more, she says that because less fuel will be needed, the result is not only cost savings but less pollution.

Professor Cornish is also director of the Centre of Excellence in Strong Materials, funded by the South African government’s Department of Science and Technology and the National Research Foundation. But for all her scientific cred, while listening to the “scientists of stuff” as they chat about their mentor, they can be overheard referring to her in a more typically African tribute to a strong woman - as “Mama Cornish”. Tami Hultman contributed to this article.

[amsen]

I haven't produced or released anything in a while, so here's something..