MolSSI Intro
The Molecular Sciences Software Institute
A nexus for science, education, and cooperation for the global computational molecular sciences community.
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Education at the MolSSI

Education of students, post-docs, and faculty on programming and Best Practices in Software Development is a large part of MolSSI's mission. Our education program consists of our cohorts of Software Fellows, online training materials, and multiple workshops online and at various locations each year around the US.
Software Fellowships

Meet Our Fellows

The MolSSI continues to fund prestigious software fellowships that recognize advanced graduate students and postdocs pursuing the development of software infrastructure, middleware, and frameworks that will benefit the broader field of computational molecular sciences, including biomolecular and macromolecular simulation, quantum chemistry, and materials science.

Weiliang Luo’s interest in molecular science started early, sparked by a periodic table tucked into the back of a dictionary. What began as curiosity—wondering how matter is arranged and transformed—quickly deepened through hands-on exposure to simple experiments and vivid chemical reactions that felt almost magical.

Today, that curiosity drives his research at MIT, where he works at the intersection of quantum chemistry, machine learning, and scientific software. His primary focus is Enerzyme, a project centered on developing next-generation neural network potential (NNP) methods for enzymatic catalysis. The goal is to make AI-driven molecular simulations more accessible, robust, and scalable for complex biochemical systems. To do this, he combines modular, physics-inspired model design with large-scale quantum chemistry, transfer learning from biochemical data, and automated active learning workflows with uncertainty quantification.

Building Enerzyme has meant tackling both scientific and engineering challenges. Early versions of the framework were powerful but difficult to maintain, relying on fragile scripts and inefficient GPU usage. Through his MolSSI Software Fellowship, Weiliang worked with mentors—Drs. Benjamin Pritchard, Taylor Barnes, and Jessica Nash—to redesign the system from the ground up. By implementing best practices for multi-GPU PyTorch jobs on Slurm clusters and restructuring key workflows, he significantly improved performance and stability. He also reworked the NEB pipeline to better handle convergence issues, turning it into a more automated and reliable process.

These improvements went beyond speed. Standardizing data structures and configuration handling reduced user error and improved reproducibility, helping transform Enerzyme from a personal research tool into shared infrastructure used across his group.

The longer-term vision for Enerzyme is to become an open, extensible platform—accessible to experimental biochemists, flexible for developers, and aligned with rapid advances in atomistic machine learning. By accelerating simulations of enzyme catalysis, particularly in challenging systems like metalloenzymes, Weiliang hopes to enable new insights into complex biochemical processes. Ultimately, this work could support mechanistic studies, enzyme engineering for sustainable chemistry, and rational drug discovery.

The MolSSI fellowship has also given him the freedom to explore ambitious ideas while connecting with a broader community of computational scientists. These interactions have strengthened his interest in building software that is not only technically sound, but widely useful.

Looking ahead, he is open to paths in academia, industry, or startups, with a consistent goal: advancing molecular science through better computational tools. He is also motivated to mentor others as AI continues to reshape the field.

Outside the lab, Weiliang channels his creativity into the arts. He directs large-scale cultural performances and experiments with incorporating generative AI into storytelling and design. He also enjoys singing and arranging a cappella music, drawn to the same collaborative energy that defines his scientific work.

If you are interested in more of his work, please visit his GitHub and LinkedIn pages

The Accelerating Curricular Transformation in the Computational Molecular Sciences (ACT-CMS) program is pleased to announce that the 2026 round of Faculty Fellowship applications is now open.

ACT-CMS is an education and faculty development program from MolSSI. The goal of ACT-CMS is to transform science curricula by accelerating the integration of programming and computation into existing molecular science courses through faculty training and the development of open and reusable curricular modules.

The Faculty Fellows Program is the cornerstone of ACT-CMS. A Faculty Fellowship lasts one years and is awarded to a molecular science educator developing curricula integrating programming and computation into existing science courses. Throughout the program, Faculty Fellows will receive curriculum development and assessment training and will upskill their programming and computational skills. They will produce a curriculum module that uses programming and computation to teach STEM concepts in an existing course that they teach. These modules will be open and reusable, allowing other educators to adopt them in their classrooms.

Applications for the next cohort of Faculty Fellows open in January 2026 and close on February 28, 2026. A Faculty Fellowship has the following benefits:

  • $5000 support (stipend + travel funding) stipend each year of the fellowship.
  • Mentorship from an ACT-CMS Programming and Computation Mentor and an ACT-CMS Curriculum Mentor.
  • Annual meeting at MolSSI headquarters for training and networking.

Application Link: Click Here.

If you are interested in applying and have questions, please register for information session Here. The information session will be held on January 30, 2026, at 1:00 PM ET (10:00 AM PT)

For more information about the ACT-CMS Fellowship Program, please visit the ACT-CMS website.

The Molecular Sciences Software Institute (MolSSI) is proud to announce the release of a new Udemy course: C++ Project Management: CMake, CPack, and Beyond, created by MolSSI Software Scientist Taylor Barnes.

Becoming an expert C++ software engineer requires much more than writing code. Successful developers also need to navigate the complex world of compilers, build systems, package managers, containerization tools, and debuggers that power serious scientific software. This course provides a natural next step for students and researchers who know the basics of C++ and are ready to tackle real-world project management.

🎓 Upon completion, you’ll receive a shareable credential to highlight your training on LinkedIn or your CV.

Special Offer: Just $12.99!

Use coupon code C63D76238F8CA8A16BCF at checkout to get the course for only $12.99
👉 Enroll here: C++ Project Management: CMake, CPack, and Beyond

Offer valid until Oct 4, 2025.


What You’ll Learn

This hands-on course dives into the practical aspects of building, distributing, and maintaining C++ software:

  • CMake: Configure builds, compile executables and libraries, and manage dependencies.
  • CPack: Create distribution-ready packages for your projects.
  • Debian packaging: Understand package structures and run your own test APT server.
  • Debugging tools: Use sanitizers and language servers to improve project reliability.
  • Container-native development: Explore Docker-based workflows that can streamline and modernize your development environment.

The course also addresses advanced CMake concepts such as variable substitution, scope handling, and creating packages that are easy for others to consume.

Course Format

All lessons are recorded inside a Docker development environment, with support for both Neovim and VSCode. This setup ensures participants can follow along step by step while experiencing the benefits of container-native development.

Who Should Enroll?

  • Students with a basic foundation in C++ who want to take the next step.
  • Developers interested in contributing to real-world scientific projects.
  • Coders looking to create and distribute libraries for others to use.

Prerequisites: Basic familiarity with C++ (conditions, loops, simple classes) and some experience with Git are recommended.

Are you an early-career graduate student or researcher new to quantum chemistry and looking to expand your skillset? Have you ever attended a MolSSI training and wished you had a credential to show off on your professional profiles?

We have good news for you!

The Molecular Sciences Software Institute (MolSSI) has launched its first self-paced Udemy course: Introduction to Quantum Chemistry Simulation, taught by Dr. Taylor Barnes. This course introduces the core concepts of quantum chemistry simulation through practical, hands-on work with Psi4, a widely used open-source package for quantum chemistry. You can run calculations directly in Google Colab or set up a local installation, whichever fits your workflow.

🎓 Upon completion, you’ll receive a shareable credential to highlight your training on LinkedIn or your CV.

Special Offer: Just $12.99!

Use coupon code D8A475313E0A94E03FFB at checkout to get the course for only $12.99
👉 Enroll here: Introduction to Quantum Chemistry Simulation

Offer valid until May 17, 2025.


Who Should Take This Course:
  • Undergraduate and first-year graduate students
  • Researchers looking to break into quantum chemistry
  • Anyone with a basic chemistry background (advanced high school level)
  • No programming experience required!
Course Overview:

Learn how to use the laws of quantum mechanics to simulate the world at the molecular level.  We’ll be focusing on gas-phase quantum chemistry using Gaussian based wavefunction theory methods.  You’ll use Psi4, a popular open-source software package regularly used by professional researchers, to run simulations of small chemical systems.  Don’t worry if you’re not a math genius; this course avoids down-in-the-weeds mathematical analysis in favor of conceptual overviews and practical advice.  Anyone with basic chemistry familiarity (equivalent to an advanced high school course) will be able to start running interesting calculations on real-world systems by taking this course.

Course Highlights:
  • Installation and usage of Psi4.
  • The key choices that go into running a quantum simulation, such as method and basis set.
  • The differences between popular wavefunction methods, such as Hartree-Fock theory and Coupled Cluster theory.
  • How basis sets work.
  • Basis set selection.
  • Calculating energies.
  • Defining molecular geometries using both Cartesian coordinates and Z-matrices.
  • Running geometry optimizations.
  • Dealing with Basis Set Superposition Error.
  • A basic introduction to multiconfigurational methods.
  • Calculating thermodynamic quantities, such as heat of formation.
  • Evaluating excited states.

Early Steps in Computational Science

Dr. Carlos Bueno’s journey into computational biophysics started by helping his father to automate scheduling tasks in Excel. This early exposure to programming sparked a lasting interest, evolving into writing simple programs in Visual Basic, such as a titration calculator, where he found that “even simple chemical models hide multiple complexities”. His academic path then took him to Dr. Mirko Zimic’s bioinformatics lab in Peru, where he navigated at the interface between biology, chemistry, physics, and programming. Whether setting up computing clusters or diving into biophysical modeling for tuberculosis research and poultry vaccine development, Carlos’s work was deeply informed by the proximity and insights gained from Dr. Patricia Sheen’s experimental lab, whose lab benches were next to their computers. This closeness between the labs allowed him to bridge computational and experimental perspectives.

Building Open-Source Tools and Leadership

At Rice University, Carlos joined Professor Peter Wolynes’ group at the Center for Theoretical Biological Physics, focusing on mesoscale biophysical models of complex protein interactions. His research evolved through close collaborations with faculty across disciplines, including Dr. Margaret Cheung, Dr. M. Neal Waxham, Dr. José Onuchic, which enriched his perspective on both the biological relevance and computational demands of his work. Within this collaborative environment he faced the challenge of managing and developing software that organically developed in a fast-paced academic environment, such as multiple versions of the code coexisting without version control or insufficient documentation. This led him to the MolSSI best practices, a turning point in his approach to scientific software.

“The MolSSI best practices completely reshaped how I approached scientific software,” Carlos reflects. He began implementing version control, unit testing, continuous integration, and thorough documentation, contributing to the development of OpenAWSEM in collaboration with Dr. Nick Schafer and Dr. Wei Lu for protein modeling and Open3SPN2 for DNA simulations in OpenMM.

The MolSSI Software Fellowship, alongside the mentorship of Dr. Jessica Nash, proved instrumental in Carlos’s growth as a software leader. He states, “Working with Jessica has helped me tackle problems leading open-source collaborative software projects with large teams, collaborating effectively with the bigger scientific computing ecosystem, and adopting more effective coding styles and design patterns to ensure our software tools can be easily adapted to tackle a vast range of problems.” This guidance, combined with insights from other mentors like Levi, who emphasized long-term software design, solidified his confidence in leading projects, particularly in prioritizing requirements and refining communication.

Carlos highlights specific areas where Jessica’s mentorship was invaluable: “Her feedback has helped me think more deliberately about design patterns and how to structure codebases, so they are easier to extend and maintain. She has also introduced me to valuable resources and best practices that I now apply regularly in my projects for testing and benchmarking. We have also had discussions about licensing, community contributions, and interoperability with other tools like MDTraj, and MDAnalysis. She has help us to develop new methods and interfaces for the Frustratometer project, making it more flexible and accessible.”

A Vision for Science and Mentorship

Carlos’s vision extends beyond immediate projects. He aims to remain at the intersection of theory and experiment, bridging biology, chemistry, and physics through computational modeling. His immediate goal is to expand the AWSEM ecosystem into a robust, well-documented platform for future collaborators.

Beyond his research, Carlos is passionate about mentorship and science education, contributing to programs like Science Clubs Peru, iGEM, the Serendipity Program, and the Frontiers in Science Program. He is particularly proud of his open-source contributions, OpenAWSEM and Open3SPN2, which are now being used and extended by others.

Above all, Carlos finds joy in spending time with his son, seeing the world through his eyes and reminding himself of the constant learning and growth that defines human experience.

If you are interested in more of his work, please check his GitHubLinkedIn, or personal website.

2024-25 MolSSI Software Fellow Yiwen Wang did not initially envision a PhD in chemistry, having started her academic journey in the realm of physics. However, being surrounded by friends immersed in chemistry—many of whom later became computational chemists—exposed her to a world where physics, chemistry, biology, and computer science seamlessly intersect in fascinating ways. Daily discussions ranging from quantum chemistry to molecular dynamics ignited her interest in molecular science, ultimately leading her to pursue a Ph.D. in computational and theoretical chemistry. 

Her current research focuses on advancing constrained nuclear electronic orbital (CNEO) theory, a framework that incorporates nuclear quantum effects (NQEs) into electronic structure methods. As part of the Prof. Y. Yang group, Yiwen is developing constrained multicomponent time-dependent density functional theory (CNEO-TDDFT) to extend CNEO methodologies from ground-state to excited-state calculations. By integrating NQEs—particularly quantum nuclear delocalization effects—into an effective potential energy surface (PES), her work aims to provide a more accurate description of excited-state dynamics, an area where conventional electronic structure methods often fall short. 

The Challenge of Scientific Software Development 

Implementing these advanced methodologies in real-world software is no small feat. Under mentorship of MolSSI Software Scientist Dr. Sina Mostafanejad, Yiwen has been working on incorporating the CNEO framework into NWChem and PySCF, two open-source computational chemistry packages written in Fortran and Python, respectively. Despite having no prior experience with Fortran, she embraced the challenge head-on and made substantial contributions to NWChem. She has successfully implemented CNEO ground-state energy and its analytic gradients, as well as CNEO excited-state energy and its analytic gradients. While further refinements remain—such as integrating the framework into NWChem’s workflow, optimizing code structure, and finalizing the compilation process—she anticipates that by the end of her MolSSI Fellowship, the full CNEO functionalities will be implemented and ready for broader use. This will enable researchers studying systems with significant NQEs to leverage CNEO-based methods in their calculations. 

A Defining Accomplishment: Turning 40 Pages of Theory into Code 

Among her many achievements, one stands out as a particularly defining moment. The successful execution of her code for calculating analytic gradients was the culmination of months of work and theoretical derivations spanning over 40 pages. Seeing those equations come to life in functional computational code was an incredibly rewarding experience—one that still brings her a deep sense of satisfaction. 

Beyond Research: A Love for Cooking, Baking, and Nature 

While Yiwen’s research keeps her engaged in the world of molecular science, she finds balance in everyday joys. She has a hidden talent for cooking and baking, with a particular fondness for making chocolate or blueberry bagels on weekends. Long walks along the lakeshore of the University of Wisconsin campus provide moments of reflection and connection, often accompanied by phone calls with family and friends. 

Looking Ahead: Future Goals and Aspirations 

As she continues her Ph.D. journey, Yiwen remains focused on exploring new chemistry problems, conducting impactful research, and ultimately completing her doctoral studies. Whether in academia or industry, her passion lies in developing computational tools that enhance our understanding of molecular systems, with potential applications in drug design, materials science, and beyond. 

Through a unique blend of theoretical insight, software development, and interdisciplinary collaboration, Yiwen Wang is making strides in computational chemistry—bringing molecular science and computing together to push the boundaries of what’s possible. 

For more about her work, visit her GitHub or LinkedIn

MolSSI Workshops

The MolSSI’s Software Workshop program is a community-driven effort in which researchers from academia, industry, and national labs propose timely and important topics focused on the software needs of the molecular sciences, and the MolSSI organizes or facilitates the event.