molecular dynamics simulation

A protein in a cell doesn't hang motionless like a mannequin in a store window. Its atoms are constantly jiggling, stretching, and bending, like a plucked guitar string that keeps vibrating after you strum it. To understand how a protein works, you need to know how tightly each part holds onto its neighbors.

A tennis ball hits a sandcastle. The castle crumbles, but by where and how far the grains of sand fly, you can guess the castle's shape. That's roughly how the method of exploding proteins with X-rays works. The laser beam is so powerful that the protein molecule loses electrons and flies apart into charged fragments, like the castle under the ball's impact.

A protein is like a tiny machine that switches on and off on command. The command arrives when another molecule sticks to it, like a key in a lock. The protein then changes shape and passes the signal along. But exactly how the signal travels inside the protein has long been a mystery.

A perovskite solar cell is like a young athlete: it performs brilliantly at first, but tires with age. Over eight hours, its performance drops noticeably, with no visible cause like cracks or dust. Scientists took one cell and recorded its performance at 0, 90, 280, and 480 minutes of its life.

When sugar goes into tea, it dissolves. But why doesn't it just fall back out? It's all about chemical potential — a quantity that shows how 'favorable' it is for a substance to be in a given place and state. For a pure substance, it's easy to calculate, but for a mixture of several components, it's a real puzzle.

A kitchen mixer runs at a single speed, but start jabbing the button and the mixture whips up differently. Chemical reactions behave much the same way when the rates of their individual steps are not constant but pulse over time.

Hybrid perovskites are the rising stars of photovoltaics: their efficiency is growing so fast it feels like we're on the brink of a solar revolution. But these materials, like intricate atomic mosaics, are extremely vulnerable — moisture, heat, and light quickly turn them to dust.

A protein in a cell is not a frozen sculpture. It is constantly in motion: bending, breathing, jittering. This motion, its dynamics, determines how the protein works. But peering directly into the dance is hard, and computer simulations often demand enormous computing power. A new approach, named DynaMode, views protein motion as a musical piece.

Inside a fusion reactor, plasma rages — a gas heated to millions of degrees. There are no direct windows, and cameras and sensors quickly fail. Engineers see only fragments of information: a few sensors at scattered points. It's like trying to grasp a symphony from the sound of three microphones in a vast hall.

For a long time, we only saw proteins in their final form — like photographs of dancers frozen in a beautiful pose. Programs like AlphaFold learned to predict that pose from a chain of carbon links. But the real magic is how a protein finds this shape faster than you can blink, performing a swift dance.

Many chemical transformations resemble assembling furniture in complete darkness: you see the starting parts and the finished cabinet, but the assembly itself remains a mystery. The intermediate states, like awkward positions of the craftsman's hands, vanish too quickly to be discerned.

A time crystal resembles an eternal clock: its atoms spontaneously perform rhythmic movements. In ordinary clocks, a pendulum is driven by a spring or battery, but here the motion arises without an energy supply — the system simply returns to its initial state at regular intervals. This idea was proposed by Frank Wilczek in 2012.

Imagine a factory where hundreds of tiny assembly lines run nonstop. Each line is a molecular motor that converts chemical fuel into motion. To make the motor go faster or in the right direction, an engineer tweaks the settings — the shape of parts, the strength of interactions.

In a benzene molecule, electrons buzz around the nuclei like a swarm of bees around a hive. But this swarm doesn't just hum: it pulses: every 856 attoseconds, the electron cloud completes a full oscillation cycle. The hive itself, the carbon nuclei, rocks more slowly, with a period of 36 femtoseconds.

A tiny gold star melts under the beam of an electron microscope, its points slowly rounding off. In the past, such a process could only be seen in snapshots taken with long pauses, and the probing beam itself would alter the sample.

Superbubbles are cosmic giants, akin to soap bubbles, but instead of soap film, they contain rarefied interstellar gas, and they're inflated not by a breath but by a series of supernova explosions. In computer simulations, they behave like living things: they grow, cool, and move. But until now, we couldn't precisely trace their boundaries.

Plasma is a gas in which electrons are stripped from atoms, behaving like a soup of charged particles. To predict how such a soup flows and heats up, you need to know how particles collide and exchange energy.

Viscoelastic materials — polymers that, like dough, retain a memory of every touch: their response to impact depends on their deformation history. Maxwell and Boltzmann provided the mathematical description long ago.

Modern microscopes see the brain in exquisite detail: not just the synapses themselves, the contact points between neurons, but also the molecules they are made of. Such images are becoming more common and cheaper to produce.

Gold nanoparticles in liquid are like tiny living creatures: they constantly change their internal structure, as if breathing. Scientists managed to peek into this process using an electron microscope that takes snapshots every millisecond, and a neural network that cleans the images from noise.

A seven-metal alloy is like a team where every player is pulling the blanket their own way. Atoms of iron, cobalt, nickel, aluminum, titanium, tantalum, and vanadium can either fall into a strict pattern or scatter into random positions. This determines whether the material will be as strong as steel or as light as aluminum.

The boundary between two liquids is like an invisible skin: it's there, but you can't touch it with your finger. Scientists have found a way to measure its elasticity without touching it. They made a tiny probe oscillate above the surface, and between the probe and the interface lay a thin film of liquid.

Deep inside every hard drive or flash drive lies a material that can 'remember' an electric field. Such a material is called a ferroelectric. When you apply a voltage, tiny regions inside the crystal (domains, like compass needles) flip. Flip the needle one way, you've written a one; flip it back, a zero. But what happens to the atoms at the moment of that flip?

Strike a tuning fork, and it rings with a single pure note. But if the fork is trembling and people are chattering nearby, the sound won't be perfect. Same with molecules: each one absorbs light of a specific color, but due to its own vibrations and the jostling of neighbors, that color gets smeared out. The authors of the paper figured out how to show this to students without complex formulas.

A scanning tunneling microscope probes a molecule with an ultra-fine tip and maps its relief. But the image is flat, while the molecule is three-dimensional. How do you guess a person's pose from their shadow on a wall?

Tearing apart an aluminum cube just a few nanometers wide is like trying to watch a droplet fall in slow motion when the camera itself is firing at machine-gun speed. Atoms inside the metal vibrate trillions of times per second, while real deformation in the lab takes minutes.

Thick honey spreads slowly across a plate. In such a world, where friction suppresses inertia, motion is governed not by force but by viscosity. This is how many soft materials behave: polymer gels, colloidal suspensions, the contents of living cells.

A drop of ink in a glass of water spreads out on its own. But if the ink were made of tiny motors, they wouldn't just spread: they'd crawl, jostle, and cluster into swarms. Such self-propelled particles are called active. You can assemble them into molecules like beads on a bracelet. And here's the surprise: the order of beads on the bracelet changes everything.

A student learned physics from a textbook and is taking an exam. The first two problems are solved brilliantly, but on the third, they err on something not covered in the book. That is roughly what the hybrid atmospheric model NeuralGCM faced when run through three levels of testing: cyclones, El Niño, and anomalous warming.

A chemical bond is like a stretched spring between atoms. When it's snapped, the molecular fragments fly apart, but they don't freeze: they keep vibrating, like a plucked string. That's exactly the vibration a team of researchers caught when they broke a methyl iodide molecule with an ultraviolet laser.

Salt in a glass of water is a crowd of charged particles. When there's plenty of water, each particle floats on its own, wrapped in a thick fur coat of water molecules. But as you keep adding salt, the water runs out for everyone, and the particles start seeking each other out. First, they stick together in pairs, then in larger clumps.

Ultrasound in a liquid is like shaking a bottle of soda vigorously: shake it, and bubbles appear. In science, this is called cavitation, and the bubbles don't just float around: they are born, grow, and collapse with tremendous force.

Our Universe may have arisen from a highly unstable state that physicists call the false vacuum. Imagine a glass of water cooled below its freezing point: the liquid remains liquid only until the first jolt, which instantly triggers crystallization into ice.

Inside a living cell, a tiny carbon spinning top whirls — a molecule billionths of a meter across. An ordinary top falls quickly, but this one behaves differently: it can spin in both directions at once, like a quantum coin perpetually frozen mid-fall. This superposition of motions is key to its strange selectivity.

Six barium ions lined up in a flat hexagon inside a Paul trap, a device that holds charged particles with oscillating electric fields. But a slight change in the shape of the trapping potential made the crystal rearrange: one ion moved to the center, and the other five formed a ring around it.