For the most part of biology, it is form that follows function. Proteins are a perfect example of this -- they are made of a sequence of amino acids (the protein building units), which are synthesized by the ribosome. Once synthesized, the long strings of amino acids fold up into a particular 3D shape or conformational state. Proteins take less than a thousandth of a second to attain their preferred conformational state (called “native state”) that -- if nothing goes wrong -- ends up being the same for a given sequence. This process is called protein folding. Explaining how a protein finds its folding preference out of all possible ways in such a short time is a longstanding problem in biology.
We are surrounded by phenomena caused by the scattering of light. When enjoying a sunny day at the seaside, like in the photo at the top, why is the sky blue? Blue light scatters more than red light. Why is milk opaque? Protein and fat particles scatter light. If you are reading this with blue eyes, your eye color is due to light scattering. Scientists use the same general scattering principle to study the structure of soft materials using the scattering of well-defined radiation. Scattering measurements reveal structures between an ångström and hundreds of nanometers, an important region for studying soft matter. Just as the color of the sky results from light scattered by air molecules, the scattering of X-rays and neutrons tells us about the size and shape of compounds in soft materials along with their interactions, and I will focus on these two types of radiation.
Look inside a glass of milk. Still, smooth, and white. Now put a drop of that milk under a microscope. See? It’s not so smooth anymore. Fat globules and proteins dance around in random paths surrounded by water. Their dance—a type of movement called Brownian motion—is caused by collisions with water molecules that move around due to the thermal energy. This mixture of dancing particles in water is called a colloid.
In the world of engineering, crafting a material that meets the needs of your application is challenging. Often, a given material may only provide a handful of the required properties for that application. Instead, you may choose to combine two or more materials, forming a composite with all of your desired properties. In this week’s paper, Zhang and coworkers from the University of California at San Diego took a similar approach in the world of biology by combining a biomolecular crystal with a flexible polymer. The crystal provides structure to the composite and the polymer contributes to its flexibility and expandability. They showed that the composite could reversibly expand to nearly 570% of its original volume and unexpectedly found that it was self-healing.
You know how sometimes you tell to yourself things like “life is complicated”? Theoretical physicists are constantly reminded of this fact when studying living organisms. Recently, a new field of physics has emerged, inspired by the observation of living systems. What forces do cells exert during metastasis in cancer? What are the growth dynamics of biofilms of bacteria? How can a school of fish organize itself and move simultaneously? These are questions raised in the physics of active matter. Active matter is an assembly of objects able to move freely and capable of organizing into complex structures by consuming energy from their environment. Active matter can be composed of living or artificial self-propelled particles.
We’ve all been there. We try pouring ketchup onto our fries from the bottle, but it doesn’t come out. So we tap the back of the bottle a few times, and suddenly, the ketchup rushes out and your entire meal is covered with it. Why does the ketchup exhibit such behavior?
The shape of a container can affect the flow of the fluid inside it. Water in a narrow stream flows smoothly, but once the water molecules make their way into a pond, they spread out and no longer flow coherently. If you blow into a long, narrow straw, the air will go straight through. Once the air flows into the large room you are standing in, it slows down as it mixes with the air around it, so someone standing five feet away from you won’t feel a breeze at all.
The above examples show how the shape of a container affect the flow of passive fluids. In today’s study, Kun-Ta Wu and colleagues investigated how the motion of active fluids, fluids that flow using an internal source of energy, is also affected by the shape of their container. They used a system of microtubules, chains of proteins assembled into long, stiff rods. Clusters of a protein called kinesin exert a force on microtubules by “walking” along them. Microtubules interact with each other to form swarms or turbulent-like flows.
Softbites team introduces its official authors. Find here our second post of our series of interviews.
Softbites team introduces its official authors. Find here our first post of our series of interviews.
Cells have to do an awful lot of tasks correctly and on time in a noisy and unpredictable environment. How do they do it? In this post, we look at one particular process, making proteins, and learn how cells operate away from thermodynamic equilibrium in order to make the right protein at the right time over and over again.