Date: Aug 15, 2023
Location: Oak Ridge, TN, US, 37830
Company: Oak Ridge National Laboratory
Requisition Id 11154
Overview:
Oak Ridge National Laboratory is the largest US Department of Energy (DOE) science and energy laboratory, conducting basic and applied research to deliver transformative solutions to compelling problems in energy and security.
We are seeking a Postdoctoral Research Associate who will support the Multiscale Biomedical Systems Group of the Advanced Computing in Health Sciences Section (ACH) in the Computational Sciences & Engineering Division, Computing & Computational Sciences Directorate at Oak Ridge National Laboratory (ORNL). In this role, you will be involved in cutting-edge computational science encompassing biophysics, chemistry, and materials. Your primary focus will be on developing and validating integrated molecular, cellular, and tissue-scale models that incorporate genetic signatures.
Your prime responsibility will be to develop models and simulation tools that incorporate genetic signatures for molecular, cellular, and tissue-scale systems. This includes building workflows to integrate AI models and optimizing performance by developing scalable tools on high-performance computing systems, utilizing existing GPU-accelerated software. Collaboration with interdisciplinary researchers at ORNL is essential to enhance your scientific profile, and key tasks involve optimizing molecular design processes, providing insights into radiation-induced effects on cellular components, and using agent-based modeling to create comprehensive simulation models for tumor cells that capture spatial and temporal complexities of the tumor microenvironment and patient heterogeneity. Additionally, you will establish practices for maximizing computational resource utilization, optimize bioinformatics and computational biophysics applications, and deploy scalable algorithms suitable for advanced computing systems.
The successful candidate(s) will receive mentorship and collaborate with the Multiscale Biomedical Systems group and the Advanced Computing for Health Sciences section at ORNL, as well as esteemed computer and computational scientists from both within ORNL and external collaborators. Their main focus will be on developing and applying innovative computational techniques specifically designed to address the project goals and align with the key missions of the DOE Office of Science.
Major Duties/Responsibilities:
- Optimize molecular design processes by utilizing and enhancing molecular dynamics algorithms and deep neural networks, with a specific focus on understanding radiation-induced effects on cellular components.
- Develop comprehensive simulation models for tumor cells using agent-based modeling techniques, effectively capturing the spatial and temporal complexities within the tumor microenvironment and accounting for individual patient heterogeneity.
- Establish and promote efficient practices for utilizing computational resources, ensuring effective and optimal utilization.
- Deploy scalable applications and algorithms suitable for advanced computing systems, ensuring practical usability in real-world applications.
- Create scalable tools on high-performance computing systems, integrating existing GPU-accelerated software to enhance efficiency and performance of modeling and simulation workflows.
- Optimize bioinformatics, computational chemistry, and materials applications through debugging, profiling, and performance optimization.
- Maximize computational resource utilization by optimizing bioinformatics and computational biophysics applications on advanced computing systems.
- Adapt, develop, and publish scalable applications and algorithms for deployment on advanced computing systems and Oak Ridge Leadership Computing Facility (OLCF) computers. Collaborate with a diverse team of scientists to conduct research and disseminate findings through journal publications, conference papers, and technical manuals.
- Engage in direct interaction with internal and external partners across various disciplines.
- Deliver presentations on research results at national scientific meetings.
- Contribute to project planning and execution efforts.
- Collaborate with staff members to develop new research proposals.
- Maintain accurate and detailed records of research activities.
- Gather and analyze data in accordance with project requirements.
- Deliver ORNL’s mission by aligning behaviors, priorities, and interactions with our core values of Impact, Integrity, Teamwork, Safety, and Service. Promote diversity, equity, inclusion, and accessibility by fostering a respectful workplace – in how we treat one another, work together, and measure success.
Basic Qualifications:
- A PhD in Computational Biology, Computational Chemistry, Bioinformatics, Engineering, Physics, or a related field completed within the last 5 years
- Basic knowledge of implementing parallel application development techniques, including parallel programming models, algorithms, and software.
- Experience in the field of computational biophysics, chemistry, biochemistry, or bioinformatics.
- Demonstrated expertise in utilizing domain-specific computational tool
Preferred Qualifications:
- Computational Modeling and Simulation Expertise: Possess a deep understanding of computational modeling and simulation techniques, including proficiency in utilizing prominent open-source high-performance computing (HPC) packages like HOOMD-blue, LAMMPS, AMBER, GROMACS, or NAMD. Experience with molecular dynamics algorithms, agent-based modeling techniques (e.g., Compucell or Physical), and other relevant computational approaches is crucial. Application these techniques to molecular, cellular, and tissue-scale systems effectively is important.
- Deep Learning Frameworks: Preferably have experience with deep learning frameworks such as PyTorch, TensorFlow, and others. Understand dimension reduction techniques, generative models (e.g., RNN, GAN, AE), and large language models. Integrate these frameworks into modeling and simulation workflows to enhance performance and analysis.
- Proficient Programming Skills: Demonstrate proficiency in at least one high-level programming languages like Python, Julia, or R for implementing and manipulating computational models. Knowledge of at least one generic programming language such as C, C++, or Fortran is preferred for optimizing performance and interacting with lower-level libraries or HPC packages.
- High-Performance Computing: Proficiency in developing scalable tools on HPC systems and utilizing GPU-accelerated software is essential. Possess knowledge of parallel computing, optimization techniques, and resource utilization to ensure efficient simulations on large-scale computing resources.
- Integration of Genetic Analysis: Combine knowledge of genetics and familiarity with relevant data integration techniques to incorporate genetic signatures into modeling and simulation workflows. Understand how to effectively integrate AI models to optimize performance.
- Bioinformatics and Computational Biophysics: Possess a strong understanding of bioinformatics and computational biophysics applications to analyze molecular and cellular data. Familiarity with relevant algorithms, techniques, and tools in these fields is beneficial.
- Strong Analytical and Problem-Solving Skills: Demonstrate a high level of analytical thinking and problem-solving abilities, as computational modeling and simulation involve addressing complex challenges. Exhibit an aptitude for understanding and formulating mathematical and computational models.
- Collaboration and Communication: Exhibit effective collaboration skills, particularly with researchers from diverse disciplines, to contribute to interdisciplinary projects. Strong communication skills are vital for exchanging ideas, presenting findings, and engaging in scientific discussions.
- Mentoring and Continuous Learning: Display a willingness to receive mentorship and actively contribute within a research group. Remain open to learning from experienced scientists and staying updated with the latest advancements in the field.
- Motivated self-starter with the ability to work independently and to participate creatively in collaborative teams across the laboratory
- Ability to function well in a fast-paced research environment, set priorities to accomplish multiple tasks within deadlines, and adapt to ever changing needs
Please submit three letters of reference when applying to this position. You can upload these directly to your application or have them sent to postdocrecruitment@ornl.gov with the position title and number referenced in the subject line.
Instructions to upload documents to your candidate profile:
- Login to your account via jobs.ornl.gov
- View Profile
- Under the My Documents section, select Add a Document
Applicants cannot have received their Ph.D. more than five years prior to the date of application and must complete all degree requirements before starting their appointment. The appointment length will be for up to 24 months with the potential for extension. Initial appointments and extensions are subject to performance and the availability of funding.
Moving can be overwhelming and expensive. UT-Battelle offers a generous relocation package to ease the transition process. Domestic and international relocation assistance is available for certain positions. If invited to interview, be sure to ask your Recruiter (Talent Acquisition Partner) for details.
Benefits at ORNL:
ORNL offers competitive pay and benefits programs to attract and retain talented people. The laboratory offers many employee benefits, including medical and retirement plans and flexible work hours, to help you and your family live happy and healthy. Employee amenities such as on-site fitness, banking, and cafeteria facilities are also provided for convenience.
Other benefits include: Prescription Drug Plan, Dental Plan, Vision Plan, 401(k) Retirement Plan, Life Insurance, Pet Insurance, Generous Vacation and Holidays, Parental Leave, Legal Insurance with Identity Theft Protection, Employee Assistance Plan, Flexible Spending Accounts, Health Savings Accounts, Wellness Programs, Educational Assistance, Relocation Assistance, and Employee Discounts.
This position will remain open for a minimum of 5 days after which it will close when a qualified candidate is identified and/or hired.
We accept Word (.doc, .docx), Adobe (unsecured .pdf), Rich Text Format (.rtf), and HTML (.htm, .html) up to 5MB in size. Resumes from third party vendors will not be accepted; these resumes will be deleted and the candidates submitted will not be considered for employment.
If you have trouble applying for a position, please email ORNLRecruiting@ornl.gov.
ORNL is an equal opportunity employer. All qualified applicants, including individuals with disabilities and protected veterans, are encouraged to apply. UT-Battelle is an E-Verify employer.