Under the Surface Podcast

Listen to the next episode of our podcast, Under the Surface. In episode 18, The FoF (Filet-O-Fish) Turning Point to OpenFF (Open Force Field), we chat with @Lily Wang, Science Lead at the Open Force Field Initiative (@OpenFF), about the unexpected, very human moment that set her on the path to computational chemistry — a cold Filet‑O‑Fish eaten at 1 a.m. after a disastrous night in the lab.

Lily shares that she first wanted to study art. Still, a close friend's lupus diagnosis inspired her to choose science instead, leading to advancements in molecular simulation and force fields that benefit computational chemistry research.

We also cover recent advances in molecular modeling, such as neural-network-based charge models and improved protein force fields, to excite researchers about future innovations.

Topics:

• Lily's path from the arts to computational chemistry

• What OpenFF and OMSF actually do

• Building more advanced force fields

• Sage 2.3 and neural‑network charge models

• Expanding force fields for proteins and nucleic acids

• Funding open science and partnering with industry

Listener discretion is advised.

Timestamps:

• (02:27) What is OpenFF?

• (04:10) How to make models more accurate.

• (05:42) What made her want to be a scientist in the first place.

• (07:37) The moment she realized working with computers in chemistry was perfect for her.

• (15:42) How scientists use computers to study the outside of cells.

• (20:22) The difference between super-detailed and simpler computer models scientists use to study chemistry.

• (26:23) How sharing science models helps people in schools and company teams to make faster progress.

• (35:03) How scientists can share what they learn without giving away anyone's secrets.

• (46:18) What's new in Sage 2.3?

• (52:05) Why it's tricky to model electricity in molecules, and where scientists are going next with this research.

• (54:45) Two ways scientists build their models.

• (58:45) Looking ahead: Quantum mechanics and AI could change how scientists work in the future.

• (01:08:15) The Deschenes Dilemma: Lily shares what she might do if she weren't a scientist.

Resources & Links:

• Open Force Field Initiative 2.3

• Developing and Benchmarking Sage 2.3.0 with the AshGC Neural Network Charge Model

• OpenFF GitHub Repository

• OpenMSF (Open Molecular Software Foundation)

Connect with Lily Wang:

• LinkedIn

*Content Warning: This episode includes discussions of trauma, loss, and near‑death experiences. Please take care while listening, and reach out to a mental health professional or someone you trust if these topics become overwhelming.*

Listen to the next episode of our podcast, Under the Surface. In episode 17, Building Collaborative Drug Discovery Tools, we feature an in-depth interview with Barry Bunin, CEO of Collaborative Drug Discovery, about his journey from chemist to entrepreneur. He shares how his background and desire to make a difference have shaped his company's mission and technology.

Here's what we discuss:

• Barry Bunin's background and what inspired his purpose

• How CDD started and became a leader in sharing science safely

• Why CDD Vault was built to keep research private, secure, and easy to use

• How teamwork and sharing data make drug discovery faster

• Finding the right balance between sharing and privacy

• How new tech like AI helps scientists work together

• Caring about people, having an impact, and doing good in science

• Barry's book shows the power of working together and being creative

This episode brings together science, entrepreneurship, and the personal stories that inspire innovation.

Listener discretion is advised.

TIMESTAMPS:

• (03:00) Barry talks about starting out in science, wanting to make a difference, and how that shaped his work.
• (06:00) How Barry's personal experiences led to his book and his current journey.
• (06:33) Content Warning begins.
• (07:10) Content Warning ends.
• (10:00) Mixing hands-on chemistry with computer tools to get better results.
• (15:00) How Barry got interested in combining chemistry and technology early on.
• (20:00) Moving from lab work to starting software companies.
• (25:00) What CDD stands for: their values, company culture, and mission.
• (30:00) Working together in drug discovery, and how to keep things open but private.
• (33:24) Content Warning begins.
• (37:33) Content Warning ends.
• (35:00) Real stories from the field, and why being human matters in science.
• (40:00) Keeping data safe and models using tech like federated learning.
• (50:00) How Barry's book came together.
• (1:00:00) Looking ahead: AI, collaboration tools, and making a positive impact.
• (1:06:40) The "Deschenes Dilemma": What happens if you can't stop doing science?
• (1:08:00) Thinking about legacy, inspiring future generations, and making your mark.

Resources & Links:

• Inside CDD Vault — A Different Kind of Silicon Valley Success Story: Behind the Code: The Human Side of Collaborative Drug Discovery (on Amazon)

• Collaborative Drug Discovery (CDD)

• The Human Side of Collaborative Drug Discovery

• How Do B2B Companies Hold Onto Their Purpose as They Grow?

Connect with Barry Bunin:

• LinkedIn

Check out the next episode of our podcast, Under the Surface. In episode 16, When Proteins Move: Woody Sherman on Computational Chemistry, Molecular Simulation, and the Future of AI in Drug Discovery, we chat with Woody Sherman, Founder and Chief Innovation Officer at PsiThera, and a longtime leader in computational chemistry, about how he went from studying quantum polymers to shaping modern tools like Induced Fit Docking.

Woody shares the moment that pulled him into protein simulations, his early exposure to AI at MIT, and how an internship at Biogen set him on the path to industry. He also reflects on his years at Schrödinger, building solutions, writing code, and learning how to solve real problems for scientists.

• How application scientists help connect research with real-world industry needs

• Woody's journey from university research to starting Silicon Therapeutics

• How tools like induced fit docking were created

• How drug discovery platforms have changed over time

• What's different between working in industry and in academia

• What's next for open molecular software and AI working together

(02:05) Why mentorship matters for scientists

(04:15) Woody's path through school and research

(09:10) Shifting into custom molecular simulations

(12:00) Going from the academic world to industry

(15:00) Creating new tools for drug discovery at Schrodinger

(22:10) Putting together a team of experts

(26:15) Working together on drug design platforms

(34:00) Leading application science teams around the world

(41:45) Starting up Silicon Therapeutics

(45:58) Progress in the development of the STING agonist medicine

(49:00) Launching PsiThera

(56:30) Focusing on inflammation and the immune system

(60:15) Sharing science and data openly

(69:00) How AI will shape the future of drug discovery

(80:30) What Woody enjoys outside of work

(82:20) Final thoughts and getting involved with the community

Listener discretion is advised.

Check out the next episode of our podcast, Under the Surface! In episode 15, Fells' Elements of Success: A Periodic Journey, we immerse ourselves in the world of chemistry and career alchemy with James Fells. From his early days as a curious freshman to his role as an Associate Director, In Silico Discovery at Johnson & Johnson Innovative Medicine, James recounts his journey through the ups and downs of the scientific realm and the importance of guidance along the way. Hear how his childhood curiosity about Gargamel inspired his success, how he moved between academia and industry, and why his story stands out. We think this episode will really connect with you. Listener discretion is advised.

(02:12) The story behind the early use of MOE software in 1999 (03:36) Childhood obsession with potions and how it sparks real science (07:00) Funding, scholarships, and the importance of independence (08:41) Making the leap from academia to industry: speed and culture shock (12:33) The value of humility, openness, and collaboration in pharma (16:15) Crafting winning fellowship applications and proactive networking (20:19) Transitioning from postdoc to industry: timing and strategy (24:17) How industry teams differ from academia in hierarchy and respect (37:33) The big cultural shifts moving from Merck to Johnson & Johnson (45:18) The importance of company culture, openness, and shared lessons learned (49:12) J&J's evolving approach to science, leadership, and opportunity (57:47) Reflections: What he'd do differently, advice for future scientists (62:03) If not in science, what would James do? Coach? Math teacher? (63:53) Final thoughts: Exploring opportunities, being adaptable, and following your curiosity

Subscribe & listen to all episodes of our podcast: https://sites.libsyn.com/459216/underthesurface Follow us on LinkedIn & X

Welcome to the last episode of 2025 for our podcast, Under the Surface! In this episode, SVL: Santavy vs Labute - The HoliDAVE Edition, get cozy with this special holiday edition of "Under the Surface"! Chris Williams and Dave Thompson are here to share laughs, swap stories, and spread some cheer as they chat with CCG's always-jolly Principal Scientist, Martin Santavy. From the wild beginnings of programming to the everyday adventures of debugging, this episode takes you on a fun-filled ride through the world of computational chemistry. There's plenty of laughter, a sprinkle of science magic, and a whole lot of heart as we talk about the quirks of coding and the power of good communication. Whether you're a science fan or just love a great story, come join us—grab your favorite mug, settle in, and let's celebrate the season together!

Listener discretion is advised.

03:45 The Journey to CCG: Early Days and Influences 10:02 The Development of SVL: A New Programming Language 14:56 Challenges and Innovations in Computational Chemistry 20:55 The Evolution of CCG and Its Market Position 22:23 Reflections on Missed Opportunities 24:25 The Evolution of Software in Chemistry 26:50 Navigating the Language of Chemistry 30:54 The Importance of Communication in Science 35:32 Debugging and Problem Solving 42:45 The Joy of Software Development 50:35 Passion for Science and Software

Subscribe & listen to all episodes of our podcast: https://sites.libsyn.com/459216/underthesurface Follow us on LinkedIn & X

In episode 13, Unfiltered Leadership, we dive into the fascinating journey of Erin Davis, who proves that the path to becoming a CTO at X-Chem is paved with caffeine, coding, and a touch of chaos.

Erin's story is a masterclass in creativity and resilience. Tune in for tales of tech debt, DNA-encoded libraries (DELs), questioning authority, and why she believes humans are just 'meat sacks' trying to make sense of it all.

This episode is a delightful mix of humor, inspiration, perfect for anyone who loves a good science story with a side of laughter. This episode will leave you inspired and entertained! Listener discretion is advised.

Subscribe & listen to all episodes of our podcast: https://bit.ly/3WQGPKY Follow us on LinkedIn & X

In episode 12, Never Mind the Woman Behind the Curtain, we welcome Dr. Sarah Witzke, Senior Application Scientist at CCG, who spills the beans on the not-so-secret life of support scientists in drug discovery. Think of it as a behind-the-scenes tour as to why you shouldn't ignore the people behind the curtain.

Sarah shares her multifaceted journey, hopping from academia to the industry, kind of like a superhero changing outfits—except her cape was probably a lab coat. She unpacks the art of juggling her responsibilities and her knack for customer interaction.

Spoiler alert: building trust with clients is crucial, unless you want them to think you're just some mad scientist in a basement! They explore how remote work has flipped team communication on its head. You might think it's just a lot of Zoom calls and pajama pants, but there's more to it. Sarah reflects on her career path, her growth, and the ups and downs with impostor syndrome along the way. And to top it all off, she dishes out some golden advice for aspiring application scientists — hint: humility and adaptability are your BFFs. So, grab a snack and settle in for a fun and insightful chat that might just inspire you to embrace your inner scientist — or perhaps become one.

In our next episode, we're joined by Jason Cole, a Senior Research Fellow at the Cambridge Crystallographic Data Center (CCDC). He shares his fascinating journey, starting from his childhood in Italy, where his love for science blossomed, all the way to his impressive career in computational chemistry and crystallography. We chat about what CCDC does in terms of gathering and sharing crystallographic data, the ups and downs of software development in this field, and why it's so crucial to validate docking software. Jason also highlights the importance of data standards, the philanthropic mission of CCDC, and what the future holds for drug discovery, particularly with the exciting possibilities of artificial intelligence (AI) and quantum computing. It's a great conversation packed with insights!

In our first episode of 2025, our hosts, Chris Williams and Dave Thompson, have the pleasure of speaking to Fernando Garces, CEO and co-founder of BioGlyph. Leading us from the sunny climes of Portugal through the tropical paradise that is London, on route to the West Coast of the US and A, Fernando shares his evolving love of science through the heights of academia, into industry, and now as CEO of a software company he co-founded to improve the modeling of complex multispecifics. Important questions are unpacked throughout - is London really a tropical paradise? How long can we keep milking podcast episode titles that take advantage of the homophonic property of pharma and farm? Oh, and we have another surprising guest answer to the 'Deschênes Dilemma'… It is not to quote G. K. Chesterton, a proper nailbiter!

In our final episode of 2024, host Chris Williams and guest co-host, Under the Surface Executive Producer and CCG Vice President, Alain Deschênes have a long overdue chat with computational drug discovery rock star Rebecca Swett. Rebecca shares her journey from her academic beginnings to her current role at X-Chem, via roles at Novartis, Vertex, and Relay. Rebecca's wide-ranging experience shines through as the conversation wends its way through cutting-edge computational chemistry covering machine learning, molecular dynamics, and DNA-encoded libraries. At the scale Rebecca works at, automation is key, so this topic comes up too. We're not going to lie; it's a lot. And, of course, there's more … Rebecca highlights the significance of allyship and representation for women in science, and the role of community (with a shout-out to the long-running BAGIM modeling forum). Also, in the inaugural asking of the 'Deschênes Dilemma,' we find out what Rebecca would be doing if she wasn't doing all of the above …