My idea is that, when shaking, all pieces try to move. Big pieces can only go upwards, while small pieces can go sideways (and take the space that was previously taken by a big piece). This ends up with the effect of big pieces floating to the top
No. If you have a system with a well-defined energy/entropy exchange rate (temperature) you can use it to put entropy in units of energy, add it to your energy term, and model the combined system behavior on the basis of this "free energy." The free energy is not a fundamental quantity, though, and it doesn't define entropy. That's why the first two laws of thermodynamics are "Energy is Conserved" and "Entropy Increases," not "Free Energy decreases."
No. I’m not really sure how you’re trying to define entropy, but you’ll probably have quite a bit of difficulty with endothermic processes if you try to think about entropy like this. For example, if you sprinkle sodium acetate in water, the sodium acetate dissolves, and the solution absorbs heat in the process, thus increasing the energy of the system.
In general, entropy increases but energy just moves around.
That said, things I've worked on include: classifiers to identify genes in DNA, molecular dynamics simulations of proteins and nucleic acids, methods to discover new drugs, analysis of protein function from an evolutionary perspective, protein design.
My wife got this gift recently, that at first looks like a snowglobe, but actually has fine sand and seashells inside. You can kind of shake it or rotate it about, and the seashells that "rise" to the top on the sand change as you do it.
For some reason, that got me thinking about this topic. Then I see it on HN...
