The Expanding Frontiers of Carbon Nanotube Technology
3 Jul 2018
Summary
The Clean Water Project made an exciting discovery about the possible applications of carbon nanostructures to water purification, biomedical research, and energy research. Dr. Ming Ma, one of the scientists on the project, recently published a paper that summarizes the current status of work in this field.
The team at Tsinghua University includes (left to right) Ming Ma, Kunqi Wang, Wei Cao, and Jin Wang. Not pictured: Yao Cheng
Dr. Ming Ma (of the Computing for Clean Water project) at Tsinghua University recently published a paper in the Journal of Micromechanics and Microengineering entitled "Carbon nanostructure based mechano-nanofluidics." The paper is a thorough survey of all the recent research work on fluid flow in carbon nanostructures, such as carbon nanotubes and graphene sheets.
Carbon atoms can form single-atom thick sheets known as graphene. When these are rolled into tube shape, they are called carbon nanotubes. In recent years, there has been a flurry of research work with these nanostructures, called that because they deal with very tiny atomic structures measured in nanometers (billionths of a meter). The Computing for Clean Water project is one example of recent research in this area: By using World Community Grid to simulate water flow through carbon nanotubes at an unprecedented level of detail, the project's research team discovered that under specific conditions, certain kinds of natural vibrations of atoms inside the nanotubes can lead to a 300% increased rate of diffusion (a kind of flow) of water through the nanotubes.
Among their many surprising properties are the ability to dramatically enhance water flow through or past the nanostructures. There is much research being conducted to understand how this happens and ultimately how to make best use of this property to potentially purify water, desalinate water, and meet other goals in biomedical and energy research. Challenges remain in how to efficiently manufacture these materials and how to adjust their structures to achieve the best results.
You can read the paper at
Thanks to everyone who supported this project.
Project Update 26 Jun 2018 –The team ran Help Cure Muscular Dystrophy - Phase 2 ran 137 jobs 0:033 days:10hrs: 09min:16 sec
Great job to all that ran Help Cure Muscular Dystrophy Project
Data from Help Cure Muscular Dystrophy Project Helps Shed Light on the Mysteries of Protein Interactions
By: Dr. Alessandra Carbone Université Pierre et Marie Curie 26 Jun 2018
Summary
Protein-protein interactions are the basis of cellular structure and function, and understanding these interactions is key to understanding cell life itself. Dr. Alessandra Carbone and her team continue to analyze data on these interactions from the Help Cure Muscular Dystrophy project, and they recently published a new paper to contribute to the body of knowledge in this field.
3 Jul 2018
Summary
The Clean Water Project made an exciting discovery about the possible applications of carbon nanostructures to water purification, biomedical research, and energy research. Dr. Ming Ma, one of the scientists on the project, recently published a paper that summarizes the current status of work in this field.
The team at Tsinghua University includes (left to right) Ming Ma, Kunqi Wang, Wei Cao, and Jin Wang. Not pictured: Yao Cheng
Dr. Ming Ma (of the Computing for Clean Water project) at Tsinghua University recently published a paper in the Journal of Micromechanics and Microengineering entitled "Carbon nanostructure based mechano-nanofluidics." The paper is a thorough survey of all the recent research work on fluid flow in carbon nanostructures, such as carbon nanotubes and graphene sheets.
Carbon atoms can form single-atom thick sheets known as graphene. When these are rolled into tube shape, they are called carbon nanotubes. In recent years, there has been a flurry of research work with these nanostructures, called that because they deal with very tiny atomic structures measured in nanometers (billionths of a meter). The Computing for Clean Water project is one example of recent research in this area: By using World Community Grid to simulate water flow through carbon nanotubes at an unprecedented level of detail, the project's research team discovered that under specific conditions, certain kinds of natural vibrations of atoms inside the nanotubes can lead to a 300% increased rate of diffusion (a kind of flow) of water through the nanotubes.
Among their many surprising properties are the ability to dramatically enhance water flow through or past the nanostructures. There is much research being conducted to understand how this happens and ultimately how to make best use of this property to potentially purify water, desalinate water, and meet other goals in biomedical and energy research. Challenges remain in how to efficiently manufacture these materials and how to adjust their structures to achieve the best results.
You can read the paper at
Thanks to everyone who supported this project.
Project Update 26 Jun 2018 –The team ran Help Cure Muscular Dystrophy - Phase 2 ran 137 jobs 0:033 days:10hrs: 09min:16 sec
Great job to all that ran Help Cure Muscular Dystrophy Project
Data from Help Cure Muscular Dystrophy Project Helps Shed Light on the Mysteries of Protein Interactions
By: Dr. Alessandra Carbone Université Pierre et Marie Curie 26 Jun 2018
Summary
Protein-protein interactions are the basis of cellular structure and function, and understanding these interactions is key to understanding cell life itself. Dr. Alessandra Carbone and her team continue to analyze data on these interactions from the Help Cure Muscular Dystrophy project, and they recently published a new paper to contribute to the body of knowledge in this field.
In the video above, Dr. Alessandra Carbone gave an overview of the Help Cure Muscular Dystrophy project and its work as of 2014. Since that time, she and her team have published several papers using the project data, including the paper described in this update.
Dr. Alessandra Carbone (principal investigator of the Help Cure Muscular Dystrophy project) and team have published a paper entitled "Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions" in the journal Proteins.
Protein interactions are the basis for most biological functions. How they interact with each other and other compounds (such as DNA, RNA, and ligands) in the cell is key to understanding life and disease functions. Complicating things, proteins often interact with more than one other kind of protein. To better understand protein functions, tools are required to uncover these potential interactions.
Different parts (surfaces) of the protein can be binding sites that attract another protein. This paper describes a methodology the research team developed to better predict these alternative binding sites. A subset of the Help Cure Muscular Dystrophy project data was used to validate their technique, which will be subsequently applied to the whole dataset computed via World Community Grid.
Microbiome Immunity Project Researchers Create Ambitious Plans for Data
By: Dr. Tomasz Kościółek and Bryn Taylor University of California San Diego 19 Jun 2018
Summary
19 Jun 2018
The Microbiome Immunity Project researchers—from Boston, New York, and San Diego—met in person a few weeks ago to make plans that include a 3D map of the protein universe and other far-ranging uses for the data from the project.
The research team members pictured above are (from left to right): Vladimir Gligorijevic (Simons Foundation’s Flatiron Institute), Tommi Vatanen (Broad Institute of MIT and Harvard), Tomasz Kosciolek (University of California San Diego), Rob Knight (University of California San Diego), Rich Bonneau (Simons Foundation’s Flatiron Institute), Doug Renfrew (Simons Foundation’s Flatiron Institute), Bryn Taylor (University of California San Diego), Julia Koehler Leman (Simons Foundation’s Flatiron Institute). Visit the project's Research Participants page for additional team members.
During the week of May 28, researchers from all Microbiome Immunity Project (MIP) institutions (University of California San Diego, Broad Institute of MIT and Harvard, and the Simons Foundation’s Flatiron Institute) met in San Diego to discuss updates on the project and plan future work.
Our technical discussions included a complete overview of the practical aspects of the project, including data preparation, pre-processing, grid computations, and post-processing on our machines.
We were excited to notice that if we keep the current momentum of producing new structures for the project, we will double the universe of known protein structures (compared to the Protein Data Bank) by mid-2019! We also planned how to extract the most useful information from our data, store it effectively for future use, and extend our exploration strategies.
We outlined three major areas we want to focus on over the next six months.
The future of the Microbiome Immunity Project is really exciting, thanks to everyone who makes our research possible. Together we are making meaningful contributions to not one, but many scientific problems!
During the week of May 28, researchers from all Microbiome Immunity Project (MIP) institutions (University of California San Diego, Broad Institute of MIT and Harvard, and the Simons Foundation’s Flatiron Institute) met in San Diego to discuss updates on the project and plan future work.
Our technical discussions included a complete overview of the practical aspects of the project, including data preparation, pre-processing, grid computations, and post-processing on our machines.
We were excited to notice that if we keep the current momentum of producing new structures for the project, we will double the universe of known protein structures (compared to the Protein Data Bank) by mid-2019! We also planned how to extract the most useful information from our data, store it effectively for future use, and extend our exploration strategies.
We outlined three major areas we want to focus on over the next six months.
- Structure-Aided Function Predictions
- Map of the Protein Universe
- Structural and Functional Landscape of the Human Gut Microbiome
The future of the Microbiome Immunity Project is really exciting, thanks to everyone who makes our research possible. Together we are making meaningful contributions to not one, but many scientific problems!
Smash Childhood Cancer Researchers Choose New Target Molecules
05 Jun 2018
By: Dr. Akira Nakagawara, MD, PhD CEO of the Saga Medical Center KOSEIKAN and President Emeritus, Chiba Cancer Center 5 Jun 2018
Summary
The Smash Childhood Cancer research team recently chose several new target molecules as the focus of their current work. Learn more about the significance of these molecules in this update.
05 Jun 2018
By: Dr. Akira Nakagawara, MD, PhD CEO of the Saga Medical Center KOSEIKAN and President Emeritus, Chiba Cancer Center 5 Jun 2018
Summary
The Smash Childhood Cancer research team recently chose several new target molecules as the focus of their current work. Learn more about the significance of these molecules in this update.
Almost a year and a half has passed since we kicked off the Smash Childhood Cancer project. On behalf of all the team members, I really appreciate volunteers' contributions to this project.
By adding new members to the original group from the Help Fight Childhood Cancer project, our research team for Smash Childhood Cancer has become quite international, with pediatricians from Japan, Hong Kong, and the United States involved in this big, new drug development project.
While the Help Fight Childhood Cancer project's goal was to search for new and better treatments for neuroblastoma, Smash Childhood Cancer addresses not only neuroblastoma, but other childhood cancers such as brain tumors, osteosarcoma (bone cancer), germ cell tumors, hepatoblastoma (liver cancer), and others.
Several proteins--beta-catenin, LIN28B , N-CYM and others--have been newly chosen as target molecules. The structures of the beta-catenin and LIN28B proteins have been determined, so in silico screening for these has been started, looking for high binding affinity compounds from a library of more than 3 million small molecules.
The N-CYM protein, which was discovered by my team and myself, is the novel driving gene product of neuroblastoma. The protein is only found in humans and chimpanzees, and is created through de novo evolution (meaning it is part of the evolution of the cancer). The protein is quite difficult to crystallize for some reason and we are still working on determining its exact structure so that drug discovery against it could begin.
Recently, we received a grant from Japanese government to support our drug discovery against the LIN28B protein, which may help accelerate our progress on Smash Childhood Cancer.
Once again, I would like to express our gratitude for volunteers all over the world who have been supporting the project. For children who are fighting childhood cancer, we would like to discover a new drug as soon as possible and develop a treatment without subsequent side effects.