Professor Yuichi Kitamoto is an assistant professor in the Department of Bioengineering, Graduate School of Engineering, Tohoku University.
He is working on the development of new functional materials containing boron in the field of applied organic synthetic chemistry. We asked him in detail about how he decided to introduce a custom PC from Tegsys for quantum chemistry calculations, which are essential for his research, and the effects it has had.
Q1.
First, please tell us about your research.
Professor Kitamoto:My lab specializes in bioengineering, but my field is applied organic synthetic chemistry. Our fundamental goal is to create functional materials based on organic synthesis, and we are researching materials that are derived from biotechnology or that can be applied to biotechnology.
My current main research focus is on boron, with the aim of creating new functional materials that contain boron.
The element boron has the property of emitting light when bonded to a benzene ring. However, it has the problem of easily reacting with water and decomposing, so in the past, boron was typically used by protecting it three-dimensionally. However, this method limits the freedom of material design.
Therefore, we thought about developing a compound that can be stably handled even when boron is exposed. If we could achieve this, we should be able to create materials with unprecedented functions.
Specifically, we aimed to make decomposition less likely by increasing the barrier to decomposition, and by using heteroelements to create three bonds to boron instead of one, we achieved a structure that is less likely to break.
This is expected to lead to a variety of applications as a new light-emitting material, such as the realization of higher-resolution, more efficient organic electroluminescence displays.
Q2.
How are you using the Tegsys Custom PC in your research?
Professor Kitamoto:When developing new compounds, it is not possible to conduct efficient research and development by simply creating compounds randomly. Therefore, it is important to make predictions using computational chemistry before actually synthesizing them.
We mainly use quantum chemistry calculation software called Gaussian to optimize molecular structures, check stability, and predict luminescence properties.
Previously purchased Tegsys PC
Q3.
Please tell us how you first encountered Tegara and why you chose it.
Professor Kitamoto:When I was appointed as an assistant professor and was looking for a PC for calculations, I first considered using the university's supercomputer. However, there was an issue that it was too difficult for students in particular, so I decided to introduce my own computer with a Windows environment that would be easy for students to use in my lab.
At that time, we investigated several companies, but when we asked specific questions of other companies, many of them responded with "We are unable to respond to individual requests."
However, Tegara has a page on their website that allows you to select the appropriate machine for your needs, and I got the impression that it was very easy to consult with them.
What was particularly impressive was that even in the sub-100 million yen price range, they were willing to consult in detail about the CPU and memory configurations. They gave us specific advice such as, "When calculating with Gaussian, the CPU performance is basically the most important, and the impact of the GPU is limited, but if you don't have enough memory, the calculation speed will decrease."
This kind of careful support even before we made the purchase was the deciding factor. They didn't just sell us a product, but also worked with us to determine the specifications necessary for our research, which made us feel they could be trusted.
On the Tegsys website, we introduce examples of PC configurations proposed to suit customer requirements, as well as key points to consider when configuring a PC to suit your needs.
Q4.
You mentioned that you updated your custom PC this time. What was the reason for this and what were your impressions after updating it?
Professor Kitamoto: As our research progressed, the range of calculations we wanted to make expanded. We are currently considering expanding into bio-applications, battery applications, and even reaction development, which requires more intensive calculations.
So when we were thinking about adding more PCs, we looked at other companies, but in the end we decided to go with Tegara. There are a few reasons for this.
First of all, the price is advantageous. In order to perform heavy calculations, a water cooling system, power supply, memory, etc. are necessary, but if you ask other companies for the same price, there are many cases where the specifications are extremely low in some areas, which makes you feel that it will affect the performance. In that respect, Tegara's products were well-balanced overall and were priced affordable.
Another attractive feature was that they offer AMD Ryzen. I was a little skeptical about Ryzen at first, but I found it easy to benchmark myself and the performance is excellent.
And above all, the trust I felt after my first purchase was immense.
In fact, the calculation speed of the PCs we installed improved by 1.2 to 1.3 times. For example, a calculation that took 22 hours can now be completed in 18 hours. This not only improves the efficiency of a single calculation, but also makes a big difference when multiple calculations are performed.
Comparison of calculation processing time between new and existing workstations
In addition, by increasing the number of machines, students no longer have to wait. When there is no waiting time, the hurdle to doing calculations is lowered, and I feel that students are now motivated to try doing calculations on their own.
The fan noise is a little more noticeable than with the previous model, but this is something that will affect the machine's lifespan, so overall I'm satisfied.
Q5.
You mentioned that trust was important, but how do you feel about Tegara's support?
Professor Kitamoto:I mentioned the pre-purchase support earlier, but I feel that the after-sales support is also excellent.
Regarding maintenance, we were told that "after about five years, the water cooling system itself becomes outdated, so we can ask for replacement and grease reapplication." It's also helpful that we only need to wipe off the dust on a regular basis. We feel reassured by the solid support we receive for parts that we don't want to touch ourselves.
Also, since calculations are constantly being performed, we were concerned about the power supply, but they also consulted us about installing a UPS (uninterruptible power supply).
Even if the Tegara staff can't answer right away, they'll say, "Please wait a moment." They don't give vague answers. Everyone is so busy these days, and just hearing a simple reply like, "I'm checking right now," is very reassuring. Response is important.
Newly introduced Tegsys PC
Q6.
What are the future prospects for your research?
Professor Kitamoto: The material we developed, which has a sharp emission spectrum, is expected to be used in high-definition displays and medical applications. Conventionally, unnecessary wavelengths have been removed using a cut filter, but if the material itself exhibits sharp emission, it will lead to improved energy efficiency.
Currently, we are mainly able to design single molecules, but in the future, more complex calculations will be required. For example, in organic light-emitting devices, the main emitting molecules we focus on make up about 5% of the total, with the remaining 95% being host materials. Therefore, we need to consider the effects of these molecules being mixed together.
In the future, I think that more accurate material design will be possible by combining not only conventional DFT methods but also molecular dynamics calculations and by considering more efficient calculation methods. This is an area that will be deepened not only in our laboratory but in the entire research field, and the calculation methods themselves will also be new. Depending on the content, more computing power may be required in the future.
Q7.
Who would you recommend this service to?
Professor Kitamoto:This is perfect for those who want a flexible computing environment in their lab, especially those who want to increase the number of computers to improve efficiency.
In order to use a supercomputer, you need to use Linux and make various settings, which can be a hurdle before you can even start calculating, and I think that's a waste. In particular, when considering ease of use for students, I think a Windows environment is important. If students can operate it intuitively, they can use it without feeling any hurdles, and as a result, they can advance their research more quickly.
Computational chemistry is now becoming essential for research papers. Backing up experimental chemistry results with calculations increases their persuasiveness, which can lead to new research. Mastering its use as a tool should greatly expand the scope of research.
I think Tegara's services are ideal for people who need specialized calculations but also value ease of use and want to get the most performance out of their system within their budget.
I also think it's recommended for people who use a variety of systems and software. I have an acquaintance who works as a translator, and he often uses systems specifically for translation and Adobe software. That requires a fair amount of GPU and memory, so I think it's good for people like him.
Q8.
What advice would you give to students and young researchers?
Professor Kitamoto:I want students to be able to experience the joy of getting to the bottom of things.
Research, in particular, is the process of discovering something that has never existed before and then giving it form. The moment your intellectual curiosity is satisfied, there is a sense of fulfillment that cannot be found anywhere else.
There may be more difficult times in the research process. However, the experience of presenting at an academic conference and being able to discuss something that no one else in the world has done as if you were the most knowledgeable person, and publishing that in the form of a paper and putting it out into the world, gives you a sense of fulfillment that can only be obtained from these experiences, and is the true joy of research. I hope you will experience this.
However, in order to advance research, it is essential to gather colleagues and work together, and it is important to remember that relationships of trust are also important for this.
I believe that the doctoral program in particular is a time to acquire the ability to turn 0 into 1 and bring about innovation. I believe that this will be a skill that you can use not only to become a researcher, but also after you become a researcher, so I hope you will do your best.
Yuichi Kitamoto
field of study
Organic synthesis, supramolecular chemistry, functional organoboron compounds, optical functional materials, optical resolution
Research Projects
- Creating new functional materials for everyday electronic devices
- Creating new organic molecules containing boron using a unique synthesis method
After enrolling in the Faculty of Engineering at Tohoku University, he went on to graduate school. He completed his major in bioengineering in April 2014, receiving his PhD in Engineering. He then worked as a researcher at the Ooi Laboratory at the same university, Konica Minolta, Inc., and the Global Prominent Research Center at Chiba University (Yagai Laboratory), before being hired as an assistant professor at the Graduate School of Engineering at Tohoku University in April 4, where he continues to work today. During his student days, he was involved in research into highly efficient resolution of chiral compounds by controlling the association state of molecules. During his time as a researcher, he was involved in research into organic electronic materials and the synthesis of supramolecular polymers with various shapes. He is currently mainly involved in the design and synthesis of functional boron compounds and the development of their functions.
*From the Tohoku University Graduate School of Engineering and Faculty of Engineering, Department of Chemistry and Biology Faculty Introduction Page
Please see the link below for communication between Professor Kitamoto and Tegsys during the composition review.
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