IIP Placements in Bioscience, Bioengineering, & Chemical Biological Engineering
Academy of Sciences of the Czech Republic (ASCR): Institute of Nanobiology and Structural Biology, Department of Structure and Function of Proteins
Location: Nové Hrady, Czech Republic
The Laboratory of Structural Biology was founded in 2002 as a joint laboratory of the Institute of Systems Biology and Ecology of the Academy of Sciences and the Institute of Physical Biology of the University of South Bohemia named Laboratory of High Performance Computing. The laboratory today combines methods ranging from computational and spectroscopic to molecular biological and biochemical--and, in collaboration with the Kuta Smatanova, lab protein crystallization. With its focus on molecular systems biology, the relationship between structure and function of proteins, dynamic changes related to functional processes on the level of proteins, and the mutual interaction of co-factors and subunits in protein complexes, the laboratory is an integral part of the new research concept of the Institute. IIP interns will be introduced to the computational methods for building and investigation of biological systems and will be able to analyze dynamical changes in systems and learn how to interpret generated data. IIP interns will use special software for modeling biological systems and carrying out molecular dynamics simulations, partly using massive parallel calculations on a beowulf-computer cluster. The underlying experimental basis of all structural information comes from protein crystallography done in house. After getting intense training during the first weeks, IIP interns will each be responsible for a sub-project that leads to a clear outcome/prediction that can be experimentally verified. Possible sub-projects include a computational project and an experimental project. The IIP interns may also have the opportunity to participate in a symposium on Structure Systems Biology in Bratislava, Slovakia, and/or the opportunity to visit biomedical institutes of the Academy of Sciences in Prague. Each IIP intern will be assigned to one of the following two projects:
- Computational Project: Modeling interactions in and between biomolecules and complex biologically relevant systems. The intern will mainly work with computational tools on data, that are produced in house. The IIP intern will get insight into how experimental data, such as X-ray structures, are generated and will collaborate directly with the scientists working in that area.
- Experimental Project: The experimental basis for modeling interactions in and between biomolecules and complex biologically relevant systems for the restriction modification system EcoR124I. The IIP intern will not repeat something somebody has done already, but would use a unique mutant that should alter the functionality of either the DNA translocation or the endonuclease activity. The project would involve: 1) Polymerase chain reaction using primers that would introduce the mutation, amplification of the DNA; 2) Growing of e.coli cells used later for over-expression; 3) Over-expression of protein in e.coli cells; 4) French pressing the cells to disrupt them; 5) isolation of protein from the crude extract using gel filtration and affinity and ion exchange chromatography; 6) Malachite green assay to monitor ATPase activity of your protein; 7) In vitro assay of DNA cleavage; 8) Limited proteoplysis. In nearly all steps SDS-phage electrophoresis is used to monitor either the successful amplification, the over-expression, the protein purity or the fragments after cleavage. In parallel the theoretical work would include: 1) Generation of a homology model of point mutation, 2) Docking of ATP into the system, 3) Molecular dynamics simulation of the system in simple-point water, and 4) calculation of the ATP binding energy.
Applicants should have academic interest in life sciences, an understanding of biologically relevant systems and how they can be understood by computational modeling, a good background in physics and mathematics;, and a good relation to computers as a scientific tool. General UNIX knowledge is welcome, but no programming is required. Two placements have been created for International Internship Program (IIP) interns.
Previous work responsibilities (in the words of the previous IIP intern): Intern 1: Learning basic Unix commands; Learning a number of types of simulation software (VMD, GROMACS, YASARA, PYMOL) ; Studying the model system of interest ; Performing the necessary modifications to the structures; Determining what sort of simulations to run and how to vary system parameters; Analyzing simulation results; Learning to use various tools to complement the analysis. Intern 2: Worked on project focused on determining the structure and function of HsdR's C-terminal domain.
Location: Singapore, Singapore
IMB is an institute in the biomedical sciences cluster of Singapore’s Agency for Science, Technology, and Research (A*STAR). It started operating in 2007 with a coalescence of research programs from the Centre for Molecular Medicine and the laboratories of the Singapore Stem Cell Consortium. It has been joined by groups from top institutions in Singapore and the U.S. and from the biotechnology industry. The overarching goal of the lab in which IIP interns would be placed is to develop efficient protocols that convert pluripotential hESCs into functional beta cells. If produced in bulk and in a clinically-compliant fashion, these cells could provide an inexhaustible supply of material for the treatment of type 1 diabetes. The lab focuses on three general questions: (1) how to produce bona fide DE from hESC; (2) how to assign pancreatic fate to this progenitor population; and (3) how to specifically direct the progressive specification of early pancreatic cells toward the mature beta cell fate. Manpower is apportioned equally among these aims, and successful IIP interns will be paired with a senior member of the lab to pursue one of these fast-moving projects. Applicants should have competency in basic molecular biology and a keen interest in biomedical research. One placement has been created for an International Internship Program (IIP) intern. This internship is offered in partnership with the Program in Global Health and Health Policy and can be used by GHP juniors for completion of the GHP Summer Research Requirement (please check the appropriate box on your application).
Additional background information on the project: A renewable supply of pancreatic beta cells would be invaluable for treating type 1 diabetes. However, despite considerable effort, it is not yet possible to generate functional beta cells from human Embryonic Stem Cells (hESC) in vitro. Interestingly, experiments conducted in mice demonstrate that interactions with the surrounding mesenchyme and endothelium orchestrate pancreatic development. The proposed project seeks to identify signals secreted by these tissues and determine how they affect beta cell development. Specifically, microtissues will be generated from different cell types and used to study the interactions between them. The first component of the project involves culturing and differentiating different cell types for inclusion in 3D microtissues. Microtissues will then be treated with inhibitors of signal transduction to determine the dynamics of cell-cell signaling during lineage commitment. The identity and behavior of different cell types will be determined by a combination of gene expression and immunofluorescence analysis and live cell imaging. The IIP intern will have the opportunity to learn a broad range of techniques selected from the following, depending on the placement duration and their interests: hESC differentiation, 3D microtissue generation, gene expression analysis, immunofluorescence, confocal microscopy/live cell imaging and R/Python programming for quantitative data analysis.
Location: Montpelier, France
The general objective of the Center for Structural Biochemistry (CBS) is to carry out research at the forefront of structural biology and biophysics as a means to reveal the fundamental physical mechanisms underlying biological activity and its regulation and, where possible, to exploit this knowledge in the conception of new therapeutic strategies in human health and disease. The selected IIP intern will be involved in one of the various research themes developed in the lab. One placement has been created for an International Internship Program (IIP) intern.
Previous work responsibilities (in the words of the previous IIP intern): My supervisor was working on a project to cure Hepatitis C. He already had the basic idea of what kind of molecule he needed for the project, so two people pursuing a masters in chemistry and I worked together to produce molecules. Because there were only two hoods and because some steps of the reactions would need to go for a long time, some days were very busy while others were much slower. Much of the chemistry was similar to what students do in labs in Princeton classes: turning carboxylic acids into esters, creating urea, turning esters back into carboxylic acids and adding amines. However, the chemicals were more powerful and the molecules themselves were much bigger and more complex.
Location: Palaiseau, France (near Paris)
École Polytechnique is a state-run institution of higher education and research, renowned for its Ingénieur Polytechnicien (polytechnic engineer) program. Established during the French Revolution in 1794, Polytechnique became a military school under Napoleon in 1804. It relinquished this status to become a public educational establishment in 1970, though it is still overseen by the Ministry of Defense. It is a founding member of the ParisTech grouping of leading Paris-area engineering schools, established in 2007. Students can apply for a research internship in any research group within one of the 22 laboratories at École Polytechnique (you may also want to peruse the internship subjects within the research groups). Two placements have been created for International Internship Program (IIP) interns. French is not required. Do not fill out the application on the École Polytechnique website. If you are applying for this placement, put École Polytechnique on the IIP Placement application as your first or second choice and then indicate your top three choices of research groups in the "additional information or comments" section of the IIP Placement application. In your personal statement, be sure to clearly indicate why you are interested in these research groups and why you are qualified to work on such projects.
Previous work responsibilities (in the words of the previous IIP intern): Before the internship, I did background readings on analytic combinatorics and on my supervisor's research, which involves word combinatorics and pattern searching, with applications in genomics. I used Java to implement two automata designed by my supervisor as well as a user interface for making relevant calculations using these automata, which supported my supervisor's theoretical results. We then wrote a paper about our results and submitted it to a conference.
INSERM (Institut National de la Santé et de la Recherche Médicale)
Location: Kremlin-Bicetre, Paris, France
INSERM is the French national research institute in the hospital of Kremlin-Bicetre, one of the oldest hospitals in Paris. Its laboratory specializes in the field of hemostasis and thrombosis and its research focuses on haemorrhagic disorders such as hemophilia. State-of-the-art technologies are available. For IIP candidates interested in exploring a scientific or medical career, this is a perfect opportunity to get a hands-on experience in an internationally recognized research unit, as well as getting to know a different culture. IIP interns will learn the techniques used in the laboratory and then contribute to specific projects in the research areas mentioned above, by performing bibliographic searches on the project and experimental work, and by anaylzing the data and drawing conclusions about the subsequent experiments. IIP candidates with interests in cell or molecular biology, biochemistry, or medical studies are encouraged to apply. Basic French would be an asset. One placement has been established for an International Internship Program (IIP) intern.
Previous work responsibilities (in the words of the previous IIP intern): HPLC purification of von Willebrand factor; weekly meeting with PI; read literature
Karolinska Institute, Division of Molecular Structural Biology, Department of Medical Biochemistry and Biophysics
Location: Stockholm, Sweden
The IIP intern will participate in an ongoing project in the lab, working alongside a graduate student or researchers. It is highly likely that the project will be working towards structural studies of proteins from the Endoplasmic reticulum (ER) of the human cell, but the exact target will be decided later. This group uses a wide range of techniques including cloning, recombinant protein expression and purification, crystallization and X-ray structure determination. The lab will try to ensure that the IIP intern experiences as much of this process as possible, but it is almost certain that the project will include purification of protein from recombinant E. coli cells and screening for crystallization conditions, as well as other techniques. This IIP placement is ideal for IIP candidates with a background in biological sciences and an interest in biophysics or in the structure and function of proteins. Experience in the basic lab techniques of biochemistry/molecular biology, such as the use of pipettes, electrophoresis, preparation of buffers etc., would be an asset. One placement has been created for an International Internship Program (IIP) intern.
Previous work responsibilities (in the words of the previous IIP intern): Cloning protein constructs of proteins involved in the transport pathway from the endoplasmic reticulum to the Golgi apparatus into bacteria and insect cells to generate protein that could be purified and crystallized for structural studies. Work responsibilites: Performing the cloning procedures, Western blots, SDS-PAGE gels, etc. The work is heavily lab based and is perfect for Molecular Biology majors. Occassionally you will write protocols outlining the modifications used in your procedure, or will analyze DNA sequences and primers on the computer.
Newcastle University, Institute of Neuroscience
Location: Newcastle-upon-Tyne, England
The Institute of Neuroscience at the University of Newcastle works in the novel field of connectomics and authored the first review in this area (Trends in Cognitive Sciences, 2004). IIP Interns will be involved in pilot studies or ongoing studies in the field of neuroinformatics. The Institute is interested in using computational tools to understand mechanisms leading to brain diseases, diagnose brain diseases, and predict what intervention would be most beneficial for an individual patient. Topics include the analysis of neuroimaging or electrophysiology data, developing tools for network analysis, and simulating brain activity and development. IIP Interns will be involved in ongoing research and might become co-authors on journal manuscripts. Even though programming and statistics skills are highly beneficial for such projects, a keen interest in understanding how the brain works as a network is the key component of a successful IIP intern. Projects are available in the following areas for IIP interns: (1) Simulation of dynamics and development of large-scale human neural networks involving high-performance computing, cloud computing, and grid computing; (2) Analysis of structural and functional brain connectivity in human subjects; in particular of patients with developmental disorders leading to schizophrenia and (childhood-onset) epilepsy; and (3) Development of novel tools for neuroimaging and connectome analysis. Visit http://www.biological-networks.org/ to learn more about the School of Computing Science’s research. IIP candidates with interests in physics, mathematics, computing, engineering, or medicine are encouraged to apply. Analytical, mathematical or programming skills would be an asset. Three placements have been created for the International Internship Program. This internship is offered in partnership with the Program in Global Health and Health Policy and can be used by GHP juniors for completion of the GHP Summer Research Requirement (please check the appropriate box on your application).
Previous work responsibilities (in the words of the previous IIP intern): Intern 1: Working on the assigned research project (usually coding in Matlab); attending weekly lab meetings; preparing final report. Intern 2: Building a database for epilepsy patient data as a medical aid for clinicians to extract features from recordings and search for similar recordings based on comparison of features or metadata. The project involved designing the system and programming all the different pieces of the puzzle. A significant portion of the programming was done in MATLAB for extracting particular features for EEG recordings and MySQL was used for designing the database. I also used Perl and HTML to build a web application that interfaced with MATLAB and the database.
Pasteur Institute, Department of Cell Biology and Infection
Location: Paris, France
Since its creation in 1887, the Institut Pasteur has become famous throughout the world as a symbol of science and French culture. For 120 years, its foundation has contributed to the prevention and treatment of infectious diseases through research, teaching, and public health initiatives. The Institute enjoys an independent status and has numerous other assets, with its research laboratories, technological platforms, teaching center, and medical center all located on one campus in the heart of Paris. The laboratory in which the IIP intern will be placed is interested in deciphering the molecular and cellular mechanisms of bacterial invasion of host cells. The host laboratory has developed several novel approaches to investigate the intimate interactions between the host and invading pathogens in single cells in space and in real time developing novel microscopic techniques. They employ their innovative, single-cell based, microscopic approaches to elucidate the apparent contradictory effects of multiple secreted effector proteins processes. The IIP intern will participate full-time in this ongoing research project in molecular genetics. IIP candidates with interests in cell biology, biochemistry, biophysics, microbiology, and immunology are encouraged to apply. Basic molecular biology and/or cell biology skills would be helpful. French is not required but would be an asset. One placement has been been created for an International Internship Program (IIP) intern.
Universiti Teknologi PETRONAS
Location: Tronoh, Perak, Malaysia
Universiti Teknologi PETRONAS (UTP) was established in 1997 when PETRONAS was invited by the Malaysian government to set up a university. UTP offers a wide range of engineering and technology programs at undergraduate and postgraduate levels complemented with a strong focus on Research and Development. The programs are designed with high industry relevance to provide a dynamic learning environment. The Civil Engineering Department involves the application of engineering principles and applied sciences to the design, construction, operation, and maintenance of capital projects in a typical asset life cycle. This includes buildings, roads, bridges, dams, airports, water and wastewater treatment plants, oil and gas production facilities, special purpose structures and any engineered structures for the comfort of mankind. Research projects of the department include focuses in computer aided design, surveying, transportation engineering, environmental engineering, geotechnical engineering, structural engineering, pavement and materials engineering, construction and project management, steel and concrete design, water and wastewater engineering. IIP interns will work on a research project on rice husk ash. Two placements have been established for International Internship Program (IIP) interns. Here is some background information on the projects:
- Rice husk ash project: About 600 million tons of rice is produced each year throughout the world, which generates about 120 million tons of rice husk. Disposal of the rice husk has become a big problem and usually rice husk is burnt in open air or stacked on farmland, releasing large amounts of hazardous substances, occupying land resources, and polluting the environment. The utilization of rice husk ash as a pozzolanic material in cement and concrete provides several advantages such as improved strength and durability, reduced materials cost due to cement savings and environmental benefits related to the disposal of waste materials and reduction of carbon dioxide emissions. It has been demonstrated that in order to produce reactive rice husk ash, specific temperature and duration of burning has to be maintained. Controlled burning can produce amorphous rice husk ash with high silica content and this can significantly enhance the properties of concrete. Recent studies have shown that RHA, rich in silica (about 85% to 90%), can be utilized in construction materials by controlling the burning temperature. Replacing the cement by RHA burned under controlled temperature, the compressive strength of the concrete increased. The concrete with RHA also lowers initial surface absorption, lowers the permeability, and increase the resistance of concrete to chloride ion penetration in comparison to conventional concrete. One of the controlled burning methods is using a microwave incinerator. Microwave Incinerator Rice Husk Ash (MIRHA) is obtained by burning rice husk in UTPMI--a microwave incinerator at Universiti Teknologi PETRONAS, with a controlled temperature. The UTPMI used for the burning process produce good quality MIRHA. Concrete and cement industry can contribute to sustainable development by adopting MIRHA as cement replacement material to save natural resources, energy, reducing CO2 emissions, and protect the environment. Through this IIP placement, the IIP intern will learn how to evaluate the microstructure of cementitious materials using equipment such as: ESEM, FE-SEM, XRD, X-ray tomography etc., and will gain the knowledge of the basic principles of mix-designing various types of concrete as well as knowledge of the production process of concrete and how to evaluate the properties of concrete such as compressive, flexural and tensile strengths, workability, including rheology and microstructure. Interested IIP candidates should possess a systematic understanding and advanced knowledge of various cement replacement materials, their effects on concrete properties, and their suitability for concrete production.
- Fly ash/palm oil fuel ash project: Steel coating requires anti-corrosion property to expand the lifespan of the equipment especially for pipes or instruments that are used in abrasive environment. Severe corrosion can be observed in equipments made from steel alloy that is operated in very abrasive environment. Operating under high pressure or/and high temperature (a temperature about 35% of the absolute melting range of a given metal or alloy) for a period of time and exposing the equipment to chemical attack, will degrade the effectiveness of the coating. Looking at a greener alternative of coating material, geopolymer material seems to be promising to be used as steel coating. Geopolymer, which is an inorganic polymer, is prepared by alkaline activation of an aluminosilicate source such as fly ash, metakaolin, slag or agriculture waste such as palm oil fuel ash/rice husk ash etc.; that can form amorphous to semi-crystalline three-dimensional silica-aluminate material. Geopolymer possess excellent mechanical properties, impressive fire resistance and high resistance to chemical attack. The proposed work will provide the intern with more information and hands-on laboratory work in the development of green coating materials for steel substrate using waste materials which are in abundance worldwide. Through this placement the IIP intern will need to conduct a brief literature review on coating material (with emphasis on geopolymer-based coating material) for metal substrate to gain better understanding of the project; will learn how to prepare specific material (in this case geopolymer-based coating material) using fly ash/palm oil fuel ash or fly ash/metakaolin as the basic raw materials; will conduct various experiments will be to obtain reasonable geopolymer product for the application on steel substrate, evaluate the coating properties of geopolymer products, as well as, the chemical, physical and micro-structural properties of the raw materials, geopolymer product and the coating properties using equipments such as FESEM, XRD, XRF, FTIR, and other related analytical tools. This IIP intern will gain the knowledge of the basic principles and hands-on material preparation, synthesis, characterization and properties of coating material and coating application. IIP candidates with interests in material development and chemical engineering are encouraged to apply. Technical skills in material processing and characterization would be an asset.
- Offshore Structures: There are about ten thousand offshore platforms located in various water depths ranging from 30m to 2,500m all over the world. The majority of these are fixed platforms located in water depths up to about 20m. For deeper regions, floating platforms are installed connected by mooring lines to the seabed. These structures are planned, designed, fabricated, transported, installed, operated, maintained, and decommissioned by civil engineers. This training will give the student insight into all aspects related to the analysis and design of offshore platforms. The trainee will get an exposure to model tests being conducted in very costly and sophisticated wave tanks fitted with the latest instrumentation such as optical motion capture system. Also, the trainee will get some exposure to using very costly commercial software used in the oil and gas industry. IIP intern responsibilities will include: attending the course "Offshore Structures," conducting an assignment for generating random waves and determining wave forces on members of jacket platforms; modeling tests in offshore laboratory on floating platforms subjected to waves and current and using commercial software for design of jacket platforms. IIP candidates with interests in the theory of structures or fluid mechanics are encouraged to apply.
- Ionic Liquids Project: Most of the heavy metals that occur in the environment are toxic and persistent. The occurrence of the heavy metals in the environment would therefore be particular dangerous even though it may only be a trace amount. The recent European Union Water Framework Directive (WFD) sets high Environmental Quality Standards (EQS) for priority substances in surface water regulating the annual averages and maximum allowable concentration in surface water. Most of the heavy metals and their compounds belong to the list of priority substances due to their level of toxicity, bioaccumulation and other constraints. There are many approaches developed for the metal extraction from liquid effluents. This includes dissolving an organic solvent such as kerosene, toluene, or using an extraction agent. However, the extraction process could not be regarded as green technology as they would cause detrimental effect to the environment and the human body. Furthermore, some other drawbacks include cost and disposal problems associated with the resin, decrease of removal efficiency when multiple metals are present. Study was conducted by using ionic liquids for selective liquid/liquid extraction of heavy metals. Ionic liquids are generally defined as molten salts, consisting entirely of anions and organic cations, and and exist in liquid form at temperatures below 100°C. Integrating imidazolium cations with functionalized groups act as metalligating moieties. The scope of this work will cover the synthesis of ionic liquids and apply them in separation of heavy metals from waste water. Characterization and instrumentation work using analytical equipment such as NMR, HPLC, FTIR and AAS will be included in this work. IIP intern responsibilities will include synthesizing a range of imidazolium ionic liquids using the quaternisation reactions; characterizing the ionic liquids using NMR, HPLC and FTIR instruments. The IIP intern will gain basic knowledge in designing separation parameters for the removal of metals from waste water and learn the ionic liquids properties in relations to its design of cations and anions. IIP candidates with interests in Chemistry or Chemical Engineering are encouraged to apply. A basic knowledge in chemistry practicals is essential.
- Glycerol project: A growing environmental concern, a rapid increase of oil price and political fallout arising from the escalating fossil fuel based-energy demand constitute the primary impetus behind the search for renewable sources of energy and chemicals. In recent findings, the biomass (oxygenated hydrocarbon) transformations over supported transition metals are touted as promising routes towards sustainable production of fuel precursors. Fuels derived from biomass are considered CO2-neutral since they provide a closed carbon cycle, therefore, eliminating greenhouse gas (CO2) emission to atmosphere. One of the key solutions is employing glycerol as a reactant in dry reforming process to produce syngas (mixture H2, CO and CO2). Thus, we propose to investigate the use of chemically treated limestone based catalyst for glycerol reforming using CO2. Furthermore, this process will address the environmental-degradation issue associated with greenhouse gas (CO2) emission. More importantly, dry reforming of glycerol remains elusive and its potential has yet been explored. During glycerol steam reforming, carbon laydown was substantial, hence affecting its longevity performance. This IIP intern will be expected to synthesize the catalysts that would be used in syngas production. The IIP intern will learn to evaluate the characteristics of the catalysts using XRD, SEM and other related instruments. Finally, the IIP intern will run a few experiments related to syngas production.IIP candidates with interests in chemical engineering or chemistry are encouraged to apply.
- Engineering Cementitious Composite Material project: Increasing pressure on bridge designers to eliminate existing expansion joints on bridge decks in order to reduce maintenance and long-term rehabilitation cost led to an innovative solution by replacing these joints using concrete link slab. A concrete link slab is relatively thin reinforced concrete slab that typically connects simply supported deck spans. However, concrete link slabs do not possess the large tensile strain capacity and micro-cracking behavior and therefore mustbe heavily reinforced to keep crack widths within the concrete link slabs below acceptable serviceability limits allowed by the AASHTO bridge design code. This high reinforcement ration within concrete link slabs unnecessarily stiffens the link slabs. In addition, it was found that these slabs are sensitive to poor construction practices. The unique capability of engineering cementitious composite (ECC) material to deform up to 4% strain in uniaxial tension while maintaining low crack widths allows the ECC link slab to accommodate the deformations imposed by the adjacent decks (i.e. due to thermal expansion and contraction). However, the ability of these slabs to withstand the rigors of repeated deflection caused by cycling loading of the bridge structure is stil unclear. Therefore, the main objective of this proposed research work is to develop a fatigue models for ECC link slabs. Investigate experimentally and theoretically (using 3D nonlinear finite element method) the load capacity and fatigue performance of ECC link slabs, along with the development of cracking on the tensile face of the ECC link slab. The expected outcome of this research is the development fatigue model of ECC link slabs that will encourage the authorities on using them to replace the current joint system. This research works will also establish a necessary data and aid on the design and analysis of ECC link slabs. The IIP intern will contribute to this research. IIP candidates with interests in concrete engineering are encouraged to apply. Technical knowledge in structural behavior would be an asset.
- High Performance Cloud Computing project: High Performance Cloud computing is a set of infrastructure that is able to provide services that is able to compute jobs that are data intensive (processing big data) and computationally intensive.
Sub-Project 1: Towards reliable, maintainable and high performance cloud computing: A high performance cloud services must be reliable and maintainable to provide high quality services to its continuing expanding sets of users and increasing number of complicated services. Performance is also crucial when considering the various parallel high computation and data intensive jobs that are running on limited amount of physical resources. As such, design of the services and cloud infrastructure are very crucial to ensure that the services are reliable, maintainable and have acceptable performance. The quality of the services and infrastructure must also be verified. Formal methods for verification have the advantage where it provides better assurance on the quality of the computer systems. However, formal methods have always had the problem with scalability where these methods are difficult and not applicable to verify large and complex systems; a cloud-based system is a complex computer system. The research work will focus on enabling formal verification of cloud computing services for performance, reliability and maintainability.
Sub-Project 2: Advanced Computational and Simulation Study of Lithium Batteries over the Cloud: The focus of this research is the development of a high performance cloud computing platform for the computational and simulation studies of lithium batteries. The system is expected to as fast and as accurate as possible compared to a conventional computing platform. High performance cloud offers many advantages compared to HPC clusters: Computational tasks are no longer bound to a fixed number processors and job waiting queues, as resources are now made scalable. Resources can be made available on demand when an increasing number of jobs were required to be processed; thus I/O and compute intensive simulation tasks will not experience any waiting time or job queue.
Processing in the clouds is not bound to a location as it is with HPC clusters. Cloud users are able to submit their computational jobs via the network (Internet or intranet) to the clouds, which may consist of many other HPC clusters located at different geographical locations to give the computational power needed. Therefore, this offers ubiquitous access to the simulation and modelling.
Sub-Project 3: 3D Cloud Interface for Distributed Interactive Genetic Algorithm: Interactive Genetic Algorithm (IGA) allows users to influence the outcome of a Genetic Algorithm (GA) search through visualization and interaction. Thus far IGA has been applied for relatively simple form of GA problems. More complex form of GA, such as highly distributed, parallel population GA, would need a more complex interface, and such interface has to be systematically investigated so as not to require too much user effort and so as to be accessible via a cloud-based interface. The use of systematic Human-Computer Interaction methods together with 3D user interfaces and immersive visualization will be investigated as part of the research.
Sub-Project 4: GPU-ization and GPU Virtualization over the Cloud: The use of GPU nowadays has extended from gaming and graphics to non-graphical applications such as numerical computing and data sorting. While much work has been done on single-GPU programming for a variety of applications, a systematic approach to application development for multiple, heterogeneous GPU is still lacking. Further, little work has been done on making GPU applications be cloud-accessible. The main focus in this research is hence two-fold: develop a methodology for converting non-GPU applications to GPU versions, and studying the cloud-accessibility of the applications via GPU virtualization. Applications to be considered include the following: 1. finite-element simulation 2. neural network. 3. ray tracing. IIP candidates for this project should have interests in computer science and experience/ skills in C++ and Java programming, scripting for Linux operating system, working in Linux environment, design of computer system using modeling languages such as UML, and verification of computer systems preferably using formal techniques. Two placements have been established for International Internship Program (IIP) interns.
Previous work responsibilities (in the words of the previous IIP intern): Reading and researching scientific literature to acquire knowledge on a particular study. Calculating different ratios of materials for concrete mixes. Batching and casting concrete and/or cement mixtures in various sized molds.
University of Edinburgh, School of Chemistry
Location: Edinburgh, Scotland
The School of Chemistry (SoC) is part of EaStCHEM, the joint Chemistry Research School of the University of Edinburgh and St. Andrews University. EaStCHEM scored highest in the U.K. in the most recent Research Assessment Exercise (meaning that its research is ranked highest in the country). Within the SoC, there is research being carried out in a wide variety of areas. The primary research area is in measuring and understanding redox potential in cells. Intern responsibilities may include designing or synthesizing a new reporter that can be used to study redox processes in cells or using systems biology and computational approaches to interpret and model redox processes in cells. This is an extremely interdisciplinary area where a keen interest in biology/medicine is required as well as an understanding of chemistry. In previous years IIP interns have been responsible for designing and synthesizing new reporters that can be used to study redox processes in cells; using systems biology and computational approaches to interpret and model redox processes in cells; developing new MALDI imaging techniques to image distributions of metabolites in cells and tissues; or developing new catalytic strategies for cheap and environmentally friendly synthesis. IIP candidates with interests in chemistry, biology, or electrochemistry are encouraged to apply and should be comfortable working in an organic chemistry lab. Experience working in an organic chemistry lab would be an asset. Four placements have been created for an International Internship Program (IIP) interns.
Previous work responsibilities (in the words of the previous IIP intern): Intern 1: Determining optimal reaction conditions for iron catalysis of nitroarenes. Intern 2: Prepared mouse brain and kidney samples for MALDI imaging, ran MALDI imaging on samples, analyzed data to see how oxidized and reduced lipids were distributed over tissue samples. Intern 3: Two primary responsibilities: creating a mapping of redox-dependent pathways in a cancer cell (involved mostly literature research) and developing nanoshell-based intracellular pH sensors.
University of Oxford, Weatherall Institute of Molecular Medicine
Location: Oxford, England
The MRC Weatherall Institute of Molecular Medicine (WIMM) at the University of Oxford is one of the world’s premier institutes where basic research in cell and molecular biology is applied to the improvement of human health. Located next to the John Radcliffe Hospital, clinician/scientists and basic researchers work hand in hand with clinicians in the hospital to tackle both rare and common diseases. The WIMM incorporates programs on blood diseases and stem cell disorders (leukemia, lymphoma, and thalassaemia); immunological disorders (HIV AIDS, multiple sclerosis, inflammatory bowel disease, and eczema); cancer (bowel and breast); infectious disease (malaria); and a wide range of genetic diseases, including abnormalities of facial development and disorders of the neuromuscular junction. IIP interns will join in the basic and medical research being undertaken at the WIMM providing an introduction to the new revolution in molecular medicine. Three placements have been created for the International Internship Program. This internship is offered in partnership with the Program in Global Health and Health Policy and can be used by GHP juniors for completion of the GHP Summer Research Requirement (please check the appropriate box on your application).
Previous work responsibilities (in the words of the previous IIP intern): Intern 1: I worked on a project to create a circular RNA to serve as a microRNA sponge with a graduate student. He would help plan the experiments and tell me what needed to be done, but I was responsible for carrying out all of the experiments. I used a variety of different lab techniques, including cloning, tissue culture/transfection, and FACS. At the end of my time I presented my data in a lab meeting. Intern 2: Conducted flow cytometry experiments to characterize surface marker expression patterns in leukemic stem cell populations at different time points of acute myeloid leukemia.
University of Queensland, Institute of Molecular Bioscience (IMB)
Location: Brisbane, Australia
The Institute for Molecular Bioscience's mission is to decipher the information contained in the genes, proteins, and molecules of humans, animals, and plants. Since its establishment in 2000, the IMB has earned a reputation as one of the Asia Pacific region's leading research institutes. By understanding the development process and aspects that go awry in complex diseases, IMB aims to develop pharmaceutical and cellular therapies, technologies, and diagnostics to prevent or treat such diseases.
The IIP intern will worki in medicinal chemistry aiming towards molecules of therapeutic application. The IIP intern will conduct synthetic organic chemistry of small heterocyclic drug-like molecules, purification (HPLC) and characterization (LCMS, NMR, Mass Spectrometry). Although the IIP intern will be primarily conducting synthetic chemistry, there will be significant opportunity to learn about multiple areas of drug discovery and related biology through the multidisciplinary team within which the intern will work. Two main areas of interest: (1) novel therapies to treat inflammatory disease (asthma / type 2 diabetes / inflammatory disorders of the brain) via targeting the NLRP3 inflammasome and (2) drugs against pathogenic fungi, in particular, the human pathogenic fungus cryptococcus neoformans a common cause of fatal fungal meningioencephalitis in immunocompromised individuals. Additional background information on the two research areas:
- Novel Therapeutics for Anti-inflammatory Disease: Working as part of an international multidisciplinary team in the field of synthetic medicinal chemistry, the intern will synthesize novel members of an exciting compound series, targeting the NLRP3 signalling cascade, aimed at reducing levels of a potent pyrogen interleukin 1β. Such molecules have significant utility in inflammatory diseases including asthma, type 2 diabetes and also in disorders of the brain, Parkinsons and Alzheimers. The lead molecule is showing excellent activity in murine models and IMB is looking to advance the series. There is a unique opportunity to learn and develop synthetic, purification, and analytical skills contributing to the series for future patent and/or publication and the intern will be included on this as appropriate to the work conducted. The student can expect to complete his/her project with an excellent understanding of the structure activity/property relationships within the series and the underlying biology of the disease area.
- Drugs against pathogenic fungi: The human pathogenic fungus Cryptococcus neoformans is a common cause of fatal fungal meningioencephalitis in immunocompromised individuals, typically AIDS patients and persons undergoing immunosuppressive treatment such as transplant and chemotherapy. In sub-Saharan Africa, cryptococcosis is the second most deadly infectious disease behind only malaria. Infections of humans caused by pathogenic fungal species such as C. neoformans are highly refractive to pharmacological intervention due to similarities in our shared eukaryotic physiology. Antifungals are few in number, often expensive, frequently toxic to humans, and have notoriously variable efficacy across the spectrum of human fungal pathogens.The aim of this internship is to develop promising new antifungal lead compounds. An approach of particular interest is exploiting differences in essential enzymes that are well characterized in both the human host and the fungal pathogen to gain selective antifungals through structure based drug design. IMB has already conducted an extensive screening campaign where a number of hits have been selected for further work. This project will require a talented and creative synthetic chemist willing to work across multiple scientific disciplines to progress the project.
IIIP candidates with experience in synthetic organic chemistry and an interest in therapeutics are encouraged to apply. Laboratory experience particularly organic synthesis work is required. One placement has been established for an International Internship Program (IIP) intern.
University of South Bohemia, Institute of Physical Biology
Location: South Bohemia, Czech Republic
This project is part of the Biological Engineering Group in the Institute of Physical Biology. IIP interns may choose from a few existing projects. In addition, projects that align with the IIP intern's own interests may be arranged. Here is some brief background on the Group's main project: Frontiers of biology lie now in exact evaluation of biological processes, whether the field is called Systems Biology, Biological Engineering, or another name. There is currently discrepancy between processes observed in living cells, for example by microscopy, and models that are based mainly on biochemical observations--that is, interactions of proteins and metabolites extracted from the cell culture and examined in the test tube. There are many examples of non-homogeneous behavior in cells that have essential functional meaning and may be crucial for discrimination between living and non-living matter. In contrast to the prevalent approach the Group examines the macroscopic properties of cells and uses a stochastic systems approach from control engineering for model building. For that a new mathematical method of point information contribution and point information entropy hsa been developed, which is implemented into software used for evaluation of processes in living cells. IIP intern responsibilities will include work in one or more of the following areas: 1) cell monolayer cultivation, cell time-lapse microscopy, simple data evaluation all with relation to cancer research, implantology, intestinal tract diseases, etc. 2) software testing, participation in image analysis or chromatography data analysis software development, building of data storage systems; 3) mathematical modeling of biological processes, fluid flow description in bioreactors by CFD (Computational Fluid Dynamics) codes, laboratory Couette-Taylor bioreactor testing, design of experiments to identify model parameters, proposal of new experimental protocols for essential biotechnology processes. At the end of the summer, the IIP interns will participate in a project presentation. IIP candidates should have an academic background in experimental or theoretical physics, chemistry, biology, mathematics, informatics, or mechanical, chemical, or electrical engineering. Basic chemical or biological laboratory skills, teamwork skills and computer knowledge are recommended. Skills in Spanish, Czech, German, or Swedish would be an asset but are not required. Three placements have been established for International Internship Program (IIP) interns.
Previous work responsibilities (in the words of the previous IIP intern): Tested and calibrated microscope equipment to determine its optimal functional limits; analyzed data from these tests using the lab's computational analysis protocols; and made a final poster and presentation.