Computational Biophysicist - Postdoctoral Researcher

Lawrence Livermore National Laboratory

Mar 31

Applications are closed

Job
Full-time
Entry Level
Science
Software Engineering
$108.8K
Livermore

Requirements

PhD in computer science, computational biology, computational physics, computational chemistry or equivalent combination of education and related experience.
Knowledge and experience in developing novel machine-learning based methods for enhancing the sampling of rare events, using free energy methods to model protein-protein binding affinities and developing statistical analysis of large-scale molecular dynamics datasets.
Experience at the postdoctoral or higher level in the fields of molecular dynamics simulations, free energy calculations, transition path theory, enhanced sampling methods, machine learning, and statistical mechanics.
Demonstrate advanced computer skills including programming experience with Python or C++ in a UNIX environment as well as experience using large high-performance computing clusters, including the use of job schedulers such as SLURM, PBS or Flux.
Ability to work independently on defined research projects, as well as a member of a large team.
Ability to develop independent research projects as demonstrated through publication of peer-reviewed manuscripts in the field of molecular modeling and simulations.
Ability to travel, as necessary, to interact with sponsors, customers and collaborators.
Proficient written, verbal communication and interpersonal skills necessary to deliver presentations, prepare written reports and to interact with a diverse set of scientists, engineers, and other technical and administrative staff.
Qualifications We Desire:
Experience in collaborating with experimental biologists as well as understanding and using experimental data in combination with computational research.
Experience in developing and training machine-learning based models in high-performance computing systems.
Experience computing binding affinity, stability and/or other metrics using scoring functions like Rosetta.
Experience with parallel programming tools used to develop high performance code on GPU’s and/or CPU’s, such as OpenMP, MPI, CUDA or OpenCL.
Experience using collaborative programming workflows and tools such as git, Gitlab, or subversion.

Responsibilities

Conduct advanced independent research to create a novel high performance computing capability for predicting the binding affinities and kinetics of protein-protein interactions at the atomistic and coarse-grained levels.
Contribute to the software development of high-performance computing tools for robust calculations of binding free-energies and kinetics.
Develop novel machine-learning based path-sampling methods for estimating protein binding rates and free energies.
Develop new workflows to analyze and visualize results from complex and large-scale molecular dynamics datasets.
Develop collaborations with external partners (Universities, Industry, other National Laboratories) to advance computational biology simulation efforts.
Prepare complex and detailed weekly progress reports to support project needs and deadlines. Prepare complex written analyses and verbal briefings, and present research results at scientific meetings.
Develop new and innovative research methods relevant to the needs of Laboratory programs and/or external funding agencies and interact with senior project staff and management to influence programmatic decisions.
Write proposals, secure funding, and establish independent research projects.

Lawrence Livermore National Laboratory

Science and technology on a mission

Science & Healthcare

Industry

5001-10,000

Employees

1952

Founded Year

Mission & Purpose

Lawrence Livermore National Laboratory, located in the San Francisco Bay Area, is a premier applied science laboratory that is part of the National Nuclear Security Administration within the Department of Energy. LLNL's mission is strengthening national security by developing and applying cutting-edge science, technology, and engineering that respond with vision, quality, integrity, and technical excellence to scientific issues of national importance. The Laboratory's science and engineering are being applied to achieve breakthroughs for counterterrorism and nonproliferation, defense and intelligence, energy and environmental security. The world-class programs and capabilities at the Lawrence Livermore National Laboratory span one square mile, what many consider to be "the smartest square mile on Earth."