Monitoring the development of a tumour using the memory of bacteria

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Cryo-chip overcomes obstacle to large-scale quantum computers

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Health problems from air pollution often originate from distant emissions

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Variations in precipitation at the North Pole set to increase sharply

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TU Delft and the National Library of the Netherlands launch Future Libraries Lab

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TU Delft Stories

Reading time: 8 min

How not to waste energy on 5G

From an energy point of view, humanity’s insatiable hunger for mobile data is unsustainable, unless you’re willing to break a few long-held believes in the field of wireless communication. Professor Earl McCune is geared up to do just that. Many bits of energy make a big problem You may be jumping with joy when your mobile phone provider quadruples your data plan each year, for the next five years. A thousand times more data sounds great. ‘But there is always a cost,’ says Earl McCune, professor in the Electronic Circuits and Architectures group at TU Delft and specialized in sustainable wireless systems. ‘All of the systems needed to provide these services, available on demand, draw power. The digital network core, the electronic systems processing and building the signals, the switching and data centres and, most of all, the transmitters and receivers.’ Three percent of the global energy demand goes into wireless communication services. And with projections of the demand for mobile data to increase a hundred to ten thousand times over the next five to ten years, we are in trouble. ‘The problem is that the communication industry in general has pretty much focused on trying to maximize the number of bits that can be transmitted per second,’ McCune explains. ‘Very little attention has been paid to the energy efficiency that goes along with that. I want to fix this.’ 5G: a solution in the making Most of the hype in wireless communications focusses on 5G – the fifth-generation cellular network technology. ‘The eventual switch to 5G comes with two major improvements,’ McCune explains. ‘One is the intended use of millimetre-wave directed beams for communication, saving lots of energy. The second improvement allows for a major increase in the speed of communications. This will enable, for example, internet of things controllable factories.’ The official goal of the 5G communications standard is a ten thousand times increase in data traffic, at flat cost and flat energy use. ‘What they didn’t tell us, however, is how to exactly implement the standard and to achieve all this,’ McCune continues. ‘We know the math behind 5G, but it simply is not yet ready to be deployed on a massive scale. In order to reach the 5G energy efficiency goal, all links in the communication chain need to be overhauled.’ Presently rolled-out 5G networks are about as energy efficient as the old incandescent lightbulb. Power to the signal The present paradigm in wireless communications, laid down in 1915, is to first build a very low-power signal. It consists of the addition of many sinewaves, simultaneously carrying a few bytes of information. Next, this jumbled signal is amplified to a communications useful power level of several watts. ‘There is something called Ohm’s law,’ McCune explains. ‘It says that if you have certain signal properties, then you will not be efficient at amplifying these, particularly when you require linearity in your circuitry.’ Linearity means that the high-level output signal coming out of an amplifier is a faithful representation of the low-level input signal. To ensure linearity under all circumstances, the signal amplifiers will most of the time operate well below their maximum output level. As a consequence, the continuous effort to increase data rates has come with a continuous decrease in energy efficiency. Going from 2G to 4G, it has dropped from 60% to 20%. A twenty percent efficiency means that for every watt of useful signal, four watts of energy will just end up as heat. ‘For 5G, the efficiency will be only 10%, meaning that nine watts will be turned into heat,’ says McCune. ‘We're paying for the power, we're paying for the huge power supply, and we're paying to move that heat away into a giant block of aluminium serving as a heat sink.’ For presently rolled-out 5G using millimetre-waves, which still uses 4G hardware, the efficiency is at a mere one percent. ‘That’s even worse than the old-fashioned incandescent light bulb,’ McCune continues. ‘The old tradition of using the linear amplifier, trying to find a version that is efficient, has run its course. But, in our digital age, physics gives us another way to make an accurate signal. If you have a sampling-based system, using square signals, Ohm’s law then says you can be as efficient as you want it to be, bringing the efficiency of amplifiers up to 70%. That’s a huge improvement, just by letting go of linearity and changing the circuitry. And we don’t have to touch the signal standards themselves.’ Writing the textbook of next generation signal amplifiers There is a catch, though. ‘We need to build these square signals at communications-useful power, not in the microwatt range,’ McCune explains. ‘There is no textbook explaining how to build a sampling system at power. We’re going to be writing that.’ Being both a part-time professor at TU Delft and part-time consultant and entrepreneur in California, McCune is involved in two separate approaches to build these untraditional amplifiers. In Silicon Valley, he pursues the idea of building one big switch, adjusting the power that is made available to it. Here at TU Delft, his group and two more groups will work on a solution consisting of hundreds of smaller transistors, in varying sizes. ‘It’s like playing a very big organ, adding the power signals up to make the desired output,’ McCune explains. ‘To have both a high accuracy and high efficiency, the transistors must switch on and off at a much faster speed than the carrier signal that is being sampled.’ Such power switches are already available for the lower range of 5G frequencies, below 6 GHz. But most of the unused 5G bandwidth is the millimetre wave bands, having frequencies above 24 GHz. ‘This requires the power supply to switch at speeds of at least 600 GHz,’ McCune says. ‘We don’t yet have transistors with this capability and need to improve them by another threefold or more.’ In order to reach the 5G energy efficiency goal, all links in the communication chain need to be overhauled. No time to idle It’s not just the power supply for amplifying the wireless signals that has to be revisited. ‘On average, when switched on, your desktop computer is not performing any useful tasks for 96% of the time,’ says McCune. ‘Likewise, the components making up the digital core of the communications network – the switching and data centres – are idle about 72% of the time. The logic components in the computer switch about a million times faster than the power supplies presently used. To have immediate performance when needed, we just leave the power on.’ His proposed solution is quite like the modern cars that turn off and back on when waiting at a traffic light. It takes so little time that it doesn’t interrupt your driving experience. ‘We can already build the power supplies that respond in less than one microsecond,’ McCune continues. ‘The problem is that the computing chip community has interleaved their computer logic circuitry with some of the memory. Switch your computer off, and you’ll erase a part of its memory too. We have to slightly rearchitect the chips, separating memory from logic. Then, we can reduce computing power consumption by a factor of four, saving millions of euros.’ Line of sight communications Probably the most hyped promise of 5G telecommunications is the use of directional beams for communication, transmitting power only where you need it. The present 4G network relies on antenna’s that put out their radio signal across vast areas. As you move around campus, you’ll always find the same signal everywhere. ‘From a transmitter point of view, that is silly,’ says McCune. ‘This way, almost all radiated power is just going to warm up the grass. Using directed power, the antenna will create small beams, sending radio waves of the same strength only to where you are. When you move around, it will follow you like a theatre spotlight.’ It works a bit like the satellite dishes used for satellite communications. But instead of parabolic antennas, it takes the coordination of hundreds of small antennas to create a beam covering only a very small segment of the sky. ‘It is solved, but only in computer simulations,’ says McCune. ‘It will take some years for it to work in real-time in the real world, especially for 5G in the millimetre wave bands. The signal will be interrupted by bouncing off spinning windmills, cars driving by, the buildings people enter and exit. Even you yourself are a reflector, as millimetre-waves cannot penetrate the human skin.’ The love for building things One evening, when McCune was twelve, his now late father explained a few months’ worth of network theory of electrical circuits to him. ‘He was a good explainer, and it just made sense,’ says McCune. He now has more than 45 years of experience in technology development in the field of radiofrequency and wireless design, most of which he spent in industry. ‘I just love to build things,’ he says, ‘and I have seen a lot of what works, and what doesn’t work.’ Enjoying an early retirement in California, but still wanting to help solve societies problems, he accepted a professorship at TU Delft. ‘When pressured, industry will change its technology only incrementally, just enough to keep making money. I thought we were missing something, there’s so much room for big improvements.’ The Fly’s Eye project ‘Now here’s a challenge,’ McCune says. ‘Imagine the world cup soccer final with eighty thousand spectators who all, simultaneously, want to post their own high-resolution video of the winning goal. Can we do that?’ This is what the Fly’s Eye project is about, one of the ongoing TU Delft projects McCune is now involved in. ‘It is very multi-disciplinary, with Nuria Llombart-Juan from the Terahertz Sensing group as the lead researcher,’ he says. ‘Instead of having spots moving around the stadium, the idea of the Fly’s Eye is to “just make a lot of spots”, covering the entire stadium. We simply hand the signal off to the next spot, should a user move around too much.’ One of these passport-photo-sized spots is already being tested in the lab. It consists of a bunch of transmitters covered by a clear plastic lens that is able to focus radio waves in the millimetre-wave spectrum. The eventual structure will have 1500 of these spots, their beams partially overlapping. At just over a meter in diameter, it will hang in the middle of the stadium. To handle the massive amount of wireless data, a bundle of optical fibres will connect the Fly’s Eye to the internet, much like your optic nerves are the communication highway between your eyes and your brain. ‘I just love the eye metaphor,’ McCune says. Only a few minutes to dump satellite memory McCune is also intrigued by the communications problem posed by cubesats. These tiny satellites, consisting of up to a few ten-centimetre cubes, are cheap to build and to bring into earth orbit. They are often equipped with one or more camera’s for earth observation, collecting huge amounts of data. At their altitude of 500 kilometres they move so fast that direct line of sight communication with a ground station is severely limited. ‘We have only a few minutes to transmit gigabytes of data, and there are some very limiting constraints,’ McCune explains. ‘There isn’t much energy available in a ten-centimetre cube. The antenna can’t be very big either, limiting us to high radio frequencies. Then, there’s the oxygen in earth’s atmosphere, which is very efficient at absorbing millimetre wave radiation.’ His voice sounds more and more enthusiastic with every added challenge he mentions. ‘It’s a 5G type of problem,’ he says. ‘It involves energy, antennas, all kinds of things. To boost efficiency from two percent to fifty percent, we have to overhaul everything.’ There is no textbook explaining how to build a sampling system at power. We’re going to be writing that. Back to all stories Energy Transition Climate Action Urbanisation & Mobility Health & Care Digital Society Earl McCune +31 15 27 83826 E.W.McCuneJR@tudelft.nl This is a story from Electrical Engineering, Mathematics and Computer Science Many bits of energy make a big problem You may be jumping with joy when your mobile phone provider quadruples your data plan each year, for the next five years. A thousand times more data sounds great. ‘But there is always a cost,’ says Earl McCune, professor in the Electronic Circuits and Architectures group at TU Delft and specialized in sustainable wireless systems. ‘All of the systems needed to provide these services, available on demand, draw power. The digital network core, the electronic systems processing and building the signals, the switching and data centres and, most of all, the transmitters and receivers.’ Three percent of the global energy demand goes into wireless communication services. And with projections of the demand for mobile data to increase a hundred to ten thousand times over the next five to ten years, we are in trouble. ‘The problem is that the communication industry in general has pretty much focused on trying to maximize the number of bits that can be transmitted per second,’ McCune explains. ‘Very little attention has been paid to the energy efficiency that goes along with that. I want to fix this.’ 5G: a solution in the making Most of the hype in wireless communications focusses on 5G – the fifth-generation cellular network technology. ‘The eventual switch to 5G comes with two major improvements,’ McCune explains. ‘One is the intended use of millimetre-wave directed beams for communication, saving lots of energy. The second improvement allows for a major increase in the speed of communications. This will enable, for example, internet of things controllable factories.’ The official goal of the 5G communications standard is a ten thousand times increase in data traffic, at flat cost and flat energy use. ‘What they didn’t tell us, however, is how to exactly implement the standard and to achieve all this,’ McCune continues. ‘We know the math behind 5G, but it simply is not yet ready to be deployed on a massive scale. In order to reach the 5G energy efficiency goal, all links in the communication chain need to be overhauled.’ Presently rolled-out 5G networks are about as energy efficient as the old incandescent lightbulb. Power to the signal The present paradigm in wireless communications, laid down in 1915, is to first build a very low-power signal. It consists of the addition of many sinewaves, simultaneously carrying a few bytes of information. Next, this jumbled signal is amplified to a communications useful power level of several watts. ‘There is something called Ohm’s law,’ McCune explains. ‘It says that if you have certain signal properties, then you will not be efficient at amplifying these, particularly when you require linearity in your circuitry.’ Linearity means that the high-level output signal coming out of an amplifier is a faithful representation of the low-level input signal. To ensure linearity under all circumstances, the signal amplifiers will most of the time operate well below their maximum output level. As a consequence, the continuous effort to increase data rates has come with a continuous decrease in energy efficiency. Going from 2G to 4G, it has dropped from 60% to 20%. A twenty percent efficiency means that for every watt of useful signal, four watts of energy will just end up as heat. ‘For 5G, the efficiency will be only 10%, meaning that nine watts will be turned into heat,’ says McCune. ‘We're paying for the power, we're paying for the huge power supply, and we're paying to move that heat away into a giant block of aluminium serving as a heat sink.’ For presently rolled-out 5G using millimetre-waves, which still uses 4G hardware, the efficiency is at a mere one percent. ‘That’s even worse than the old-fashioned incandescent light bulb,’ McCune continues. ‘The old tradition of using the linear amplifier, trying to find a version that is efficient, has run its course. But, in our digital age, physics gives us another way to make an accurate signal. If you have a sampling-based system, using square signals, Ohm’s law then says you can be as efficient as you want it to be, bringing the efficiency of amplifiers up to 70%. That’s a huge improvement, just by letting go of linearity and changing the circuitry. And we don’t have to touch the signal standards themselves.’ Writing the textbook of next generation signal amplifiers There is a catch, though. ‘We need to build these square signals at communications-useful power, not in the microwatt range,’ McCune explains. ‘There is no textbook explaining how to build a sampling system at power. We’re going to be writing that.’ Being both a part-time professor at TU Delft and part-time consultant and entrepreneur in California, McCune is involved in two separate approaches to build these untraditional amplifiers. In Silicon Valley, he pursues the idea of building one big switch, adjusting the power that is made available to it. Here at TU Delft, his group and two more groups will work on a solution consisting of hundreds of smaller transistors, in varying sizes. ‘It’s like playing a very big organ, adding the power signals up to make the desired output,’ McCune explains. ‘To have both a high accuracy and high efficiency, the transistors must switch on and off at a much faster speed than the carrier signal that is being sampled.’ Such power switches are already available for the lower range of 5G frequencies, below 6 GHz. But most of the unused 5G bandwidth is the millimetre wave bands, having frequencies above 24 GHz. ‘This requires the power supply to switch at speeds of at least 600 GHz,’ McCune says. ‘We don’t yet have transistors with this capability and need to improve them by another threefold or more.’ In order to reach the 5G energy efficiency goal, all links in the communication chain need to be overhauled. No time to idle It’s not just the power supply for amplifying the wireless signals that has to be revisited. ‘On average, when switched on, your desktop computer is not performing any useful tasks for 96% of the time,’ says McCune. ‘Likewise, the components making up the digital core of the communications network – the switching and data centres – are idle about 72% of the time. The logic components in the computer switch about a million times faster than the power supplies presently used. To have immediate performance when needed, we just leave the power on.’ His proposed solution is quite like the modern cars that turn off and back on when waiting at a traffic light. It takes so little time that it doesn’t interrupt your driving experience. ‘We can already build the power supplies that respond in less than one microsecond,’ McCune continues. ‘The problem is that the computing chip community has interleaved their computer logic circuitry with some of the memory. Switch your computer off, and you’ll erase a part of its memory too. We have to slightly rearchitect the chips, separating memory from logic. Then, we can reduce computing power consumption by a factor of four, saving millions of euros.’ Line of sight communications Probably the most hyped promise of 5G telecommunications is the use of directional beams for communication, transmitting power only where you need it. The present 4G network relies on antenna’s that put out their radio signal across vast areas. As you move around campus, you’ll always find the same signal everywhere. ‘From a transmitter point of view, that is silly,’ says McCune. ‘This way, almost all radiated power is just going to warm up the grass. Using directed power, the antenna will create small beams, sending radio waves of the same strength only to where you are. When you move around, it will follow you like a theatre spotlight.’ It works a bit like the satellite dishes used for satellite communications. But instead of parabolic antennas, it takes the coordination of hundreds of small antennas to create a beam covering only a very small segment of the sky. ‘It is solved, but only in computer simulations,’ says McCune. ‘It will take some years for it to work in real-time in the real world, especially for 5G in the millimetre wave bands. The signal will be interrupted by bouncing off spinning windmills, cars driving by, the buildings people enter and exit. Even you yourself are a reflector, as millimetre-waves cannot penetrate the human skin.’ The love for building things One evening, when McCune was twelve, his now late father explained a few months’ worth of network theory of electrical circuits to him. ‘He was a good explainer, and it just made sense,’ says McCune. He now has more than 45 years of experience in technology development in the field of radiofrequency and wireless design, most of which he spent in industry. ‘I just love to build things,’ he says, ‘and I have seen a lot of what works, and what doesn’t work.’ Enjoying an early retirement in California, but still wanting to help solve societies problems, he accepted a professorship at TU Delft. ‘When pressured, industry will change its technology only incrementally, just enough to keep making money. I thought we were missing something, there’s so much room for big improvements.’ The Fly’s Eye project ‘Now here’s a challenge,’ McCune says. ‘Imagine the world cup soccer final with eighty thousand spectators who all, simultaneously, want to post their own high-resolution video of the winning goal. Can we do that?’ This is what the Fly’s Eye project is about, one of the ongoing TU Delft projects McCune is now involved in. ‘It is very multi-disciplinary, with Nuria Llombart-Juan from the Terahertz Sensing group as the lead researcher,’ he says. ‘Instead of having spots moving around the stadium, the idea of the Fly’s Eye is to “just make a lot of spots”, covering the entire stadium. We simply hand the signal off to the next spot, should a user move around too much.’ One of these passport-photo-sized spots is already being tested in the lab. It consists of a bunch of transmitters covered by a clear plastic lens that is able to focus radio waves in the millimetre-wave spectrum. The eventual structure will have 1500 of these spots, their beams partially overlapping. At just over a meter in diameter, it will hang in the middle of the stadium. To handle the massive amount of wireless data, a bundle of optical fibres will connect the Fly’s Eye to the internet, much like your optic nerves are the communication highway between your eyes and your brain. ‘I just love the eye metaphor,’ McCune says. Only a few minutes to dump satellite memory McCune is also intrigued by the communications problem posed by cubesats. These tiny satellites, consisting of up to a few ten-centimetre cubes, are cheap to build and to bring into earth orbit. They are often equipped with one or more camera’s for earth observation, collecting huge amounts of data. At their altitude of 500 kilometres they move so fast that direct line of sight communication with a ground station is severely limited. ‘We have only a few minutes to transmit gigabytes of data, and there are some very limiting constraints,’ McCune explains. ‘There isn’t much energy available in a ten-centimetre cube. The antenna can’t be very big either, limiting us to high radio frequencies. Then, there’s the oxygen in earth’s atmosphere, which is very efficient at absorbing millimetre wave radiation.’ His voice sounds more and more enthusiastic with every added challenge he mentions. ‘It’s a 5G type of problem,’ he says. ‘It involves energy, antennas, all kinds of things. To boost efficiency from two percent to fifty percent, we have to overhaul everything.’ There is no textbook explaining how to build a sampling system at power. We’re going to be writing that. Earl McCune +31 15 27 83826 E.W.McCuneJR@tudelft.nl This is a story from Electrical Engineering, Mathematics and Computer Science Back to all stories Energy Transition Climate Action Urbanisation & Mobility Health & Care Digital Society Related stories The impact of algorithms Control theory in a selfish world The responsibility gap with self driving cars Related stories

Reading time: 4 minutes

Building the foundations of a quantum computer

When you set foot in the lab, you instantly feel that something special is happening here. The room houses a long desk with monitors showing graphs, but most of the space is taken up by two complicated-looking machines, surrounded by fences that keep guests at a safe distance.

reading time: 4 min

The creepy crawlies that can save lives

Doris van Halem’s aim is to make drinking water safe and accessible to all. Not by adding expensive chemicals but by putting to work the tiny creatures already present in it. She is tackling the two health risks associated with contaminated drinking water which have been hardest to eradicate: arsenic poisoning and infectious diseases caused by viruses. ‘Our colleagues stared in disbelief when they heard about our approach,’ Van Halem says. ‘How can you remove arsenic from water using something that is present in that same water? Traditionally research into drinking water is focused on physico-chemical processes, which means either destroying the pollutants or filtering them out.’ There’s life in drinking water Micro-organisms did not figure high on Van Halem’s list either when she started looking at alternative water treatment methods. ‘The life forms that naturally occur in water are usually regarded as yukky creepy crawlies. If they end up in a drinking water filter – a process called biofouling – we usually throw a lot of chemicals at them so they die.’ In waste water treatment micro-organisms play a very important role but their use in the treatment of drinking water has met with little recognition. ‘Drinking water is seen as water that has very few nutrients for micro-organisms to feed on. And yet this nutrient-poor water has active micro-organisms. The question is how to use this activity for the aim we have in mind.’ A village in Bangladesh In order to design more effective water treatment methods Van Halem needed to gain a better understanding of the processes taking place in the water itself. ‘Many researchers will go for new, expensive materials with, for instance, nanoparticles. Those could definitely work but for me the question is: do we need them? A country like Bangladesh cannot afford them and Dutch companies will also prefer a cheaper option.’ Van Halem developed her method while exploring two main problems affecting drinking water worldwide diseases caused by viruses and bacteria, and arsenic poisoning. Removing viruses with ceramic pot filters Van Halem first recognised the importance of the role of micro-organisms in water by accident. It was during a research project which took her to Ghana, Cambodia and Nicaragua where she was testing a ceramic pot filter with tiny holes which filtered out harmful bacteria and protozoa. The pots are made in factories the world over using local materials. But what they cannot do is filter out the viruses responsible for such water-related diseases as, for instance, hepatitis. ‘These ceramic pots always contain a little silver solution which is often used in many other products as well because it is seen as a disinfectant. But we didn’t know if it is of any use to combat viruses. Van Halem looked at pots both with and without silver solution and found that over time biofilms developed in the filters that contained no silver solution. Trapped on the inside of the filter the organic material and the bacteria continued to grow. ‘People want clean drinking water so their first instinct was to clean the filter and get rid of the slimy sludge. But after a couple of months we found that the biofilm filters were much better at removing viruses.’ Arsenic poisoning Years later Van Halem and her team achieved another important breakthrough. They found that it was possible to remove arsenic from groundwater by means of the iron that naturally occurs alongside of it. Arsenic naturally occurs in groundwater and is highly toxic. Elevated concentrations of arsenic can cause skin diseases and cancer. ‘A country like Bangladesh has had problems related to arsenic poisoning for decades. Because of the pollution of the surface water people were digging shallow wells everywhere. But the water they were pumping up turned out to be contaminated with arsenic.’ Arsenic oxidation is a very slow process and the received wisdom among drinking water treatment experts is that the process can only be speeded up with the help of a chemical, i.e. an oxidant. Iron which is also present in the water also oxidises and during that process it absorbs the arsenic. But the quicker the oxidation the less arsenic is removed. ‘We thought, what if we can reverse the process? How can we slow down the oxidation process of the iron in the drinking water and remove the arsenic all the quicker? Then Van Halem and her team hit on new idea: delayed iron oxidation. ‘By slowing down the oxidation of the iron immediately after the water is pumped up, it will remove more arsenic from the water. To put is simply, it makes a difference if instead of putting the water in a bucket it is put in a bottle closed off with a top. What if the same principle can be applied to a central purification system?’ Impact Van Halem wants her work to be relevant. ‘In areas which are experiencing huge problems your work can make a big difference.’ But although her work is aimed at solving problems she wants to do more. ‘I also want to find out how things really work and use that knowledge to devise better solutions. There are many researchers who are focused more on figuring out challenging scientific puzzles than solving problems. In the field of drinking water treatment it’s the practical problem solvers who are in the majority. We bridge the gap between the two.’ Published: February 2020 Back to all stories Climate Action Urbanisation & Mobility Health & Care Energy Transition Digital Society Doris van Halem +31 15 2785838 D.vanHalem@TUDelft.nl This is a story from CEG Read more about the Global Drinking Water Programme Co-workers: Md Annaduzzaman Kajol, Jink Gude, Mona Soliman, Gertjan Medema Partners: Ceramic filters will be produced at local factories (Nicaragua) ‘Our colleagues stared in disbelief when they heard about our approach,’ Van Halem says. ‘How can you remove arsenic from water using something that is present in that same water? Traditionally research into drinking water is focused on physico-chemical processes, which means either destroying the pollutants or filtering them out.’ There’s life in drinking water Micro-organisms did not figure high on Van Halem’s list either when she started looking at alternative water treatment methods. ‘The life forms that naturally occur in water are usually regarded as yukky creepy crawlies. If they end up in a drinking water filter – a process called biofouling – we usually throw a lot of chemicals at them so they die.’ In waste water treatment micro-organisms play a very important role but their use in the treatment of drinking water has met with little recognition. ‘Drinking water is seen as water that has very few nutrients for micro-organisms to feed on. And yet this nutrient-poor water has active micro-organisms. The question is how to use this activity for the aim we have in mind.’ A village in Bangladesh In order to design more effective water treatment methods Van Halem needed to gain a better understanding of the processes taking place in the water itself. ‘Many researchers will go for new, expensive materials with, for instance, nanoparticles. Those could definitely work but for me the question is: do we need them? A country like Bangladesh cannot afford them and Dutch companies will also prefer a cheaper option.’ Van Halem developed her method while exploring two main problems affecting drinking water worldwide diseases caused by viruses and bacteria, and arsenic poisoning. Removing viruses with ceramic pot filters Van Halem first recognised the importance of the role of micro-organisms in water by accident. It was during a research project which took her to Ghana, Cambodia and Nicaragua where she was testing a ceramic pot filter with tiny holes which filtered out harmful bacteria and protozoa. The pots are made in factories the world over using local materials. But what they cannot do is filter out the viruses responsible for such water-related diseases as, for instance, hepatitis. ‘These ceramic pots always contain a little silver solution which is often used in many other products as well because it is seen as a disinfectant. But we didn’t know if it is of any use to combat viruses. Van Halem looked at pots both with and without silver solution and found that over time biofilms developed in the filters that contained no silver solution. Trapped on the inside of the filter the organic material and the bacteria continued to grow. ‘People want clean drinking water so their first instinct was to clean the filter and get rid of the slimy sludge. But after a couple of months we found that the biofilm filters were much better at removing viruses.’ Arsenic naturally occurs in groundwater and is highly toxic. Elevated concentrations of arsenic can cause skin diseases and cancer. ‘A country like Bangladesh has had problems related to arsenic poisoning for decades. Because of the pollution of the surface water people were digging shallow wells everywhere. But the water they were pumping up turned out to be contaminated with arsenic.’ Arsenic oxidation is a very slow process and the received wisdom among drinking water treatment experts is that the process can only be speeded up with the help of a chemical, i.e. an oxidant. Iron which is also present in the water also oxidises and during that process it absorbs the arsenic. But the quicker the oxidation the less arsenic is removed. ‘We thought, what if we can reverse the process? How can we slow down the oxidation process of the iron in the drinking water and remove the arsenic all the quicker? Then Van Halem and her team hit on new idea: delayed iron oxidation. ‘By slowing down the oxidation of the iron immediately after the water is pumped up, it will remove more arsenic from the water. To put is simply, it makes a difference if instead of putting the water in a bucket it is put in a bottle closed off with a top. What if the same principle can be applied to a central purification system?’ Doris van Halem +31 15 2785838 D.vanHalem@TUDelft.nl This is a story from CEG Read more about the Global Drinking Water Programme Back to all stories Climate Action Urbanisation & Mobility Health & Care Energy Transition Digital Society Related stories Water treatment in India: a matter for the local community 20.000 weather stations in Africa measuring water quality with a smartphone in myanmar

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Monitoring the development of a tumour using the memory of bacteria

Researchers at Delft University of Technology have discovered how certain proteins keep a bacterium's memory up to date. This is essential for bacteria, since their memory protects them from attacks by bacteriophages, their natural enemies. It is also interesting for us humans, since the system can be converted into a 'DNA recorder': a kind of biological logbook that keeps track of what happens in a cell. Such a DNA recorder could, for instance, be used to monitor how a tumour develops over time. The first DNA recorders have already been built, but they are inefficient and do not work in human cells. The new fundamental knowledge of bacterial memory formation gained by the Delft researchers can be used to develop the next generation of DNA recorders. The findings have been published in Nature . Despite the fact that researchers all over the world are using CRISPR-Cas9 for gene editing, there are still many open questions about the precise functioning of CRISPR systems and the proteins involved. This is because CRISRP-Cas9 is not a man-made molecular tool, but a biological defence mechanism that protects bacteria against their arch-enemies: bacteriophages, the viruses of bacteria. Race against time When bacteriophages encounter a bacterium in nature, they cling to it and inject their DNA into the cell. Then, a race against time begins. If a bacterium does not recognize and destroy the hostile DNA in time, the bacteriophage hijacks the cell and uses it to make copies of itself, finally causing the bacterium to explode. The newly released bacteriophages then start looking for their next victim. In order to recognise hostile DNA before it’s too late, a bacterium relies on its memory. Certain Cas proteins are tasked with storing pieces of hostile DNA in the bacterial genome. "This is done in a place called the 'CRISPR array'," says group leader Chirlmin Joo of Delft University of Technology. The CRISPR array is a kind of logbook that describes which enemy attacked the bacterium, in the form of fragments of hostile DNA separated by a recurring string of nucleotides. If a bacterium’s memory contains a fragment of the DNA of a bacteriophage, it has the ability to quickly recognise and render harmless any hostile DNA in the event the same bacteriophage mounts another attack. Bypass "The problem for bacteria is that bacteriophages constantly evolve, thus trying to bypass the bacterial immune system," says Joo. "Therefore, it is essential for bacteria to keep their memory up to date." Two cooperating proteins are involved in this process: Cas1 and Cas2. These proteins trim pieces of hostile DNA, which makes it possible for the genetic information to be stored in the memory of the bacterium - the CRISPR array. The Delft researchers have now discovered how Cas 1 and 2 proteins do this. It appears that more is required than just the two Cas proteins. Among other things, the researchers have discovered that an enzyme that also play an important role in other cellular processes is involved. This enzyme is called ‘DNA-polymerase III’ and it is known for its role in DNA replication, the copying of DNA. "DNA polymerase has a sort of backspace function for when it makes an error while copying DNA," Joo explains. "We've discovered that it also uses this function to trim fragments of hostile DNA in such a way that they can be incorporated into the CRISPR array." In addition to discovering that DNA polymerase plays a key role in memory formation in bacteria, the researchers also discovered what properties the fragments of hostile DNA need to have in order to allow the Cas proteins to do their work. They also found out how the proteins actually incorporate these DNA fragments into the bacterial memory. Biological logbook This new fundamental knowledge about memory formation in bacteria is important for the further development of a new technique called 'DNA recording'. "In recent years, several research groups have shown that it is possible to build a kind of biological logbook based on these systems," says research leader Sungchul Kim. The idea is that, with such a system, information about cellular processes can automatically be stored in the DNA of that cell. Since Cas1 and Cas2 store information in chronological order, one could determine exactly how, for instance, a tumour has developed by removing some cells from the tumour and consulting their biological logbook. Doctors could then use this valuable diagnostic data to make a tailor-made treatment plan. At the moment, DNA recording is still in its infancy. "Simple systems have already been developed, but they are not efficient and cannot, for example, follow multiple processes at the same time," says Kim. Moreover, they do not yet function in human cells. "But knowing how Cas1 and Cas2 work now gives us the information we need to understand where things went wrong with the first DNA recorders," Kim continues. "This allows us to design more efficient recorders that also work in human cells." Watch a scientific animation explaining the findings here. Selective loading and processing of prespacers for precise CRISPR adaptation, Sungchul Kim, Luuk Loeff, Sabina Colombo, Slobodan Jergic, Stan J. J. Brouns & Chirlmin Joo, Nature DOI: 10.1038/s41586-020-2018-1. Dr. Chirlmin Joo +31 15 27 83220 C.Joo@tudelft.nl Joo Lab Read more: CRISPR-Cas9

Cryo-chip overcomes obstacle to large-scale quantum computers

QuTech has resolved a major issue on the road towards a working large-scale quantum computer. QuTech (a collaboration of TU Delft and TNO), together with Intel, has designed and fabricated an integrated circuit that can operate at extremely low temperatures when controlling qubits, the essential building blocks of a quantum computer.

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