From Atoms To Words #13: From Gecko Feet to The Origin of Life ??

?? Greetings to you, curious minds! As May ushers in the first gentle sunlight, we set off on a warming adventure through a spectrum of topics, from the Spider-Man-like powers of gecko feet to the profound question of life’s origins. Our explorations are powered by advanced multiscale simulations, spanning from quantum chemistry to coarse-graining. But before we dive deeper, let's start with a philosophical musing: How is the concept of scientific understanding evolving in the age of AI? What exactly does this entail, and why does it matter?

Alright, let's go!

Scientific Understanding in the Age of AI Oracles: A Journey Beyond Discovery

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?? The first time I laid eyes on an iPhone, a thought thundered through my mind: "This can't be real; we've stepped into the future." Yet it was real indeed, and it took me—us, really—only a few days to acclimate to its existence.

Quite astonishing, isn't it? This sense of disbelief mirrors my feelings towards machine learning and AI.

We've become accustomed to a world where large language models and other AI systems enhance our everyday lives, a scenario that equally applies to science. We're at a crucial juncture, a tipping point, where change occurs at breakneck speed.

?? What future does AI hold for us in science?

Just a few weeks ago, during one of our conversations here on LinkedIn, we were dissecting the role of simulations and AI in scientific discovery. In that discussion, a bold reader suggested that by 2026, AI might replace both traditional experiments and simulations.

Hard to agree, right?

I can concede that, eventually, we may possess AI capable of providing the correct answers, but how do we train such AI without data from simulations or experiments? And more critically, how will we understand the mechanisms and principles behind these answers?

?? This brings us straight to today's story: how is the concept of scientific understanding evolving in the age of AI? What exactly does this entail, and why does it matter?

?? We will explore:

? The concept of Scientific Discovery vs. Scientific Understanding

? Six Concrete Examples of Discovery without Scientific Understanding

? The Three Dimensions of Computer-assisted Scientific Understanding

• including: the Computational Microscope, AI as a Resource of Inspiration, and AI as the Agent of Understanding

Shall we begin?

?? Discover more on From Atoms To Words ?? Scientific Understanding in the Age of AI Oracles: A Journey Beyond Discovery

Can Quantum Chemistry Simulations Help Trace the Origin of Life?

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?? Are we alone in the universe? Where does life come from? Let's dive into the heart of these age-old questions with... quantum chemistry! ??

Following Petrucci’s recent review article, we explore four prebiotic scenarios, each revealing potential beginnings of life through the lens of quantum chemistry, from DFT to Ab Initio Molecular Dynamics:

1?? Interstellar Medium: Venture into the cosmic cold where simple molecules like NH2 and H2CO mingle to possibly forge life's early precursors like formamide. Picture icy comets and dust grains as cosmic crucibles catalyzing complex molecules such as amino acids in reactions energized by the chilling vastness of space.

2?? Radiation on Early Earth: Under the nascent glow of a young sun, Earth’s primordial atmosphere was a stage set for molecular ballet under UV rays, potentially fostering the formation of vital biomolecules, resilient even in harsh environments.

3?? Mineral Surfaces: Earth’s craggy rocks could have been the very catalysts in life's complex chemistry, where minerals like clays might help piece together simple organic compounds into the precursors of proteins.

4?? Extreme Conditions: From meteoric impacts to seething hydrothermal vents, Earth's tumultuous early conditions might have been the incubators forging simple organic molecules.

Through the lens of quantum chemistry, each scenario not only suggests a potential pathway in our molecular origins but also emphasizes how Earth's most extreme conditions could have been the perfect nurseries for life's emergence.

So, are we alone?

Well, I'm not claiming that quantum chemistry simulations have the definitive answer. Ahem, no. ?? But, they do offer a glimpse into the atomistic subtleties of life’s origins.

Did I make you curious?

?? Get the full picture, along with the technical juice and plenty of scientific references, at ?? Can Quantum Chemistry Simulations Help Trace the Origin of Life?

How Can Coarse-Grained Simulations Reveal Geckos' Wall-Clinging Skills?

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?? The secret to gecko adhesive success lies in the sophisticated architecture of their toes.

The gecko's digits are sheathed in millions of fine hairs known as setae, which terminate in billions of even tinier structures called spatulae. I imagine them as the branching roots of a tree or the fine veins of a leaf—this is the hierarchical structure that allows a gecko to grip.

?? Ah, Mother Nature!

At the microscopic scale, the setae exhibit a complex design: stiff fibrils embedded within a softer matrix. This structural composition, along with the chemical makeup of β-keratin, facilitates the spatulae's interaction with any surface through van der Waals forces.

?? As we've previously explored on From Atoms To Words, this type of noncovalent binding—van der Waals interactions—may seem weak when considered individually. However, when these interactions work together, they create a bond robust enough to support the gecko's weight as it traverses various substrates.

But here’s where geckos really show off: they can unstick their feet with a mere thought, a feat dubbed smart adhesion. While their adhesive pads need to stick firmly to facilitate climbing, they must also be able to let go for the gecko to walk freely. It's a delicate balance between friction and adhesion, all playing out in the span of a step.

?? Now, how have we learned all of this?

Well, since the advent of electron microscopy in the mid-20th century, researchers produced a rich body of information about the mechanism of gecko adhesion. But what's truly exciting is that this isn't just limited to experimental work. There's a wealth of theoretical and computational studies too.

So, how do geckos' little molecular devices work their adhesion capabilities?

?? Today, we find the answer in three studies on gecko adhesion, all through the lens of coarse-grained simulations. Here’s what we learn:

? The mechanical properties of gecko-foot β-keratin

? The key role of water in gecko adhesion on wet surfaces

? The dynamics of gecko adhesion on rough surfaces

Craving some scientific juice?

?? Get the full gecko-picture, along with stunning animations, at ?? How Can Coarse-Grained Simulations Reveal Geckos' Wall-Clinging Skills?

+3 Bonus Stories

1?? Anion-Pi Interactions: Exploring The Land of Opportunity in Chemistry

Once theoretically predicted, then experimentally confirmed, anion-pi interactions have become central in various fields of chemistry. [Read the full article]

2?? Water’s Hydrogen Bonds: What Makes Them Vital for Life As We Know It?

How can water's hydrogen bonds have such a colossal impact on the existence of life on Earth and, potentially, everywhere else? [Read the full article]

3?? Enzymatic Reactions: Quantum Chemistry Modeling of Life’s Catalysts

Can we really investigate enzymatic reactions and estimate their activation energies with quantum chemistry? Let's talk "cluster approach." [Read the full article]

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[Arturo Robertazzi | From Atoms To Words]