Soft Matter and Biological Physics
Glasses, gels, grains and other soft materials, and the physics of living systems.
arXiv: cond-mat.soft, physics.bio-ph
24 topics
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Cells copy DNA, build proteins and keep time with error rates far below what chemical equilibrium would allow, by burning fuel such as ATP. Physics asks what minimum fuel cost a given accuracy or timing precision requires, and how close cells come to it.
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Active matter is made of units that each consume energy to move, such as bacteria, cells, birds or chemically driven colloids. Because energy enters at every particle, the usual equilibrium rules fail, and new kinds of order, phase separation and flow appear.
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Glasses, from window glass to metallic glasses and foams, deform permanently through sudden local rearrangements of a few particles. How these rearrangements add up to steady flow, narrow shear bands or brittle cracks is not settled.
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Embryos build their backbone segment by segment, timed by a genetic clock in each cell that ticks about half as fast in human cells as in mouse cells, daily clocks keep a 24-hour period whether warm or cold, and bacteria time their division so that cells stay the same size. How cells set and hold these rhythms against molecular noise and temperature changes is open.
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Cells read their surroundings by counting molecules that bump into receptors on their surface, which is noisy because molecules arrive at random. Physics sets how precise such a measurement can be, and the open questions are how close real cells come to the limit and what they do with the information.
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Chromatin organization and loop extrusion
6 problemsEach human cell packs about 200 cm of DNA into a nucleus about 0.001 cm across, yet keeps genes accessible. Protein motors called cohesin and condensin pull DNA into loops, and how this and other forces organize the genome is still being worked out.
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Flocks of birds, swarms of insects, schools of fish and sheets of migrating cells move as coordinated wholes with no leader issuing commands. Physics asks which simple interaction rules produce this coordination and why groups seem tuned to respond quickly as a whole.
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Cells contain droplets without membranes, called condensates, that form when certain proteins and RNAs separate from the surrounding fluid, much as oil separates from water. Many of these proteins are floppy chains with no fixed shape, and how their sequence sets droplet behavior, and what the droplets do for the cell, are open.
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Ecosystems contain hundreds or thousands of species that eat, compete with and help one another, and physicists model them like disordered materials with random interactions. The models predict when such communities stay stable, fluctuate or collapse, and some of their predictions contradict what is seen in nature.
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Salt water and liquid salts are full of charged ions that shield electric fields, and water squeezed into gaps a few molecules wide behaves differently from ordinary water. Several measurements in these systems disagree with standard theory and with computer simulations.
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Evolution can be pictured as a population moving uphill on a surface whose position is the genome and whose height is reproductive success. The shape of this surface decides whether evolution is predictable, and physicists study it with tools from disordered systems.
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Microscopic origin of friction and wear
4 problemsFriction between solids follows simple rules known for centuries, such as being proportional to the load and not depending on the apparent contact area. How these rules emerge from atoms and from the rough contact between surfaces is not fully explained, and wear is understood even less.
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When many liquids are cooled fast enough they do not crystallize; they become more and more viscous until they are a rigid glass. Nobody knows whether a true phase transition is behind this slowdown or whether it is only a very steep crossover.
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Sand, grain, powders and dense particle suspensions can flow like a liquid or hold weight like a solid. No single set of equations yet describes their flow in all situations the way the Navier-Stokes equations describe water.
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Foams, emulsions, sand and glasses become rigid when their particles are packed tightly enough to block each other, without forming a crystal. The point where this happens and the unusual vibrations of the resulting solid follow scaling laws whose full theory is incomplete.
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Liquid crystals are fluids of rod- or banana-shaped molecules that line up, as in display screens; where the alignment cannot vary smoothly, line and point defects form. Several recently discovered phases, an old phase transition, and the behaviour of defects in three-dimensional active systems remain poorly understood.
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An embryo shapes itself into organs by cells pulling, pushing, growing and moving past each other. How chemical signals and mechanical forces together produce the same shape every time is still largely open.
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The brain's neurons fire in bursts of all sizes, as seen in physical systems balanced at a phase transition, the boundary between two phases such as order and disorder. Whether the brain is really tuned to such a point, and whether that helps it compute, is debated.
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Crystals form when a tiny seed appears by chance in a liquid and then grows; classical nucleation theory (CNT) gives the rate of this from simple bulk properties. Its predictions often miss measured rates by many powers of ten, and some crystals seem to form through intermediate stages the theory leaves out.
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At some point, chemistry on the early Earth produced molecules that could copy themselves and evolve. Life also uses molecules of only one handedness (one of two mirror-image forms), and how either of these came about is unknown.
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Long chain molecules in a melt are tangled with each other, which makes plastics viscous and elastic. The tube model explains much of this, but rings, fast flows and the way chains fold into crystals are still not understood.
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A protein is a chain of amino acids that folds itself into a precise 3D shape, often in well under a second. Computers now predict the final shape well, but not how fast the chain folds, by which route, or why it sometimes misfolds into clumps.
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Quantum effects in biological function
6 problemsSome living processes may use quantum physics, such as electron spins that stay correlated, energy spreading as a wave, or particles passing through energy barriers they classically could not cross. The open question is when these effects actually matter for what the organism does.
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Water behaves unlike almost every other liquid: it is densest at 4 C, and its compressibility and heat capacity rise as it is cooled below freezing. One explanation is that cold water is a mixture of two distinct liquids that separate at a hidden critical point, but rapid ice formation makes the key region hard to reach.