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A submarine, something a lot smaller, needs a huge power to move. I'm afraid that your system would require a lot more energy than a levitation one. And heat rejection is a problem in Ceres. It would need a web of pipes around the colony to distribute the heat and avoid overheat the surface too much to avoid massive evaporation.

I'm not even consideration a number of colonies so huge. I was thinking about some little colonies to work in it. To live, I suppose that it has more sense space colonies.

In my design, the colony is closed too obviously. It could be usign a dome, or buried deep in the ground, or anything similar. While materials could support the pressure of the zone where is excavated, there is no limit to the place where it could be built, while the align is correct.
It's a design we could adapt to any low mass body, including Mars. With more gravity, more levitation rings are needed, and the perceived slope will be greater, but all others things remain the same.
To have colonies with artificial 1g it could be critical to fetal development and it will be an advantage to greater health for sure.

I don't understand this configuration.
Why stack spheres? which advantage gets over simply using more surface on Ceres?
Or even fragility. I think that not aligned shafts are more robust, even they are buried deep in Ceres, filling the planet.
And we don't know by now how is the deep crust. Perhaps, at some deep, the ice become liquid.

And the water... The water between the sphere and the walls, it's like liquid rails. A lot of friction i think.

Perhaps i'm mistaking the model.

I suggest you use magnetic levitation instead of bearings. Only rails on the base would be used on case of catastrophic stop of the colony.

A configuration of magnetic rings using hall bach arrays like in inductrack configuration should be enough, not only to regulate the rotation but to transfer weight load like in a arc or a cupola, but weight translate through the repulsion of the inner rings (in the rotation section) and outer rings (in the outside part of the tunnel, fixed). With the adecuate magnetic configuration it should be possible.
Because the possibility of stack rings, fixed and rotated sections, the weight can be distributed and it could be build as deep as needed. The stacked rings will be in the outer part of the colony. From inner perspective, "underground" below the perceived floor of the ground level.

That's imply a constant flux of energy, but that would be inevitable on a body with gravity. Magnetic rings or rails, all dissipate energy.
In any case, the environment would be very cold, so energy is a necessity.
I suggest enough redundant configuration in energy source.

In Space, if you try to maximize impulse, you could use the byproduct of fusion (like Helium-4 isotope) as propellent.
But for a SSTO, a lot of mass is required as propellent to reach the high thrust needed to reach orbit, so yes, fusion plasma and propellent are separated.
I suppose that a aneutronic with high energy capture is needed to transfer into the propelent, because using pure thermal transfer, the core would be hotter than propellent, and normal exahust heat is too high for a nuclear wall to resist.
The solution is to capture the energy in usefull (electric) form instead of heat and use fast transfer into propellent. Like a Skylon with extra energy transfer from microwaves usign fusion energy source with high energy capture (to avoid overheat into the nuclear reactor). If the nuclear reactor is enough powerfull, you could even use water in liquid form because the energy of the reactor is enough to avoid the needed of hydrogen and oxygen as in Skylon, and use a more compact design of the spaceship. Or use methane because it has a better hydrogen ratio (you don't need oxygen as oxydizer with a fusion source).

In space, a thermal core is viable, because you can use low thrust and heat rejection.

A rotation structures is completely viable.

http://www.artificial-gravity.com/sw/SpinCalc/

Radius = 207
Rotation = 2 rotations/minute
Speed (tangential) = 156 km/h (a moderate train achieve this)
Gravity (horizontal) = 0,93

(0,93^2+0,376^2)^(1/2)=1,03 g

An structure like that could be rotate using magnetic levitation, using superconductors or permanent magnets like on Inductrack using little energy to compensate air friction and other energy dissipation.

On the sides, the horizontal component of the "gravity" is greater, so people and things would be on almost horizontal. A curved stair could connect with the center. At first, "up" (from inside perspective) is going to the center (from outside perspective). When you goes up from inside, the position of the floor gets more and more parallel to the floor of Mars, and the stairs twist and turns into a ramp and later a corridor to the center.
Another configuration could include a "elevator" from the center to the edges. First, moves to the edges like a car, but tilt at the same time to be parallel to the sum of gravity and centrifugal apparent force, so , from the perspective of the passenger it goes forward at first, and later, goes "down", and when it reach the "bottom" (the side of the rotating structure) reach a 1g "gravity" (the sum of real gravity and centrifugal force by rotation).

For interplanetary, we could use "space jumpers". Electromagnetic cannons, enough large to avoid extreme accelerations.
The cannons would be moved backward, but because it would be more massive, the new orbit could be enough high to avoid reenter on the atmosphere. Then, using a slow but efficient propulsion (solar - ion, magnetic sails...) could return to the original orbit for reuse.
The spaceship could use aerobraking on destination, and ion propulsion for correction after the aerobraking and make a stable low orbit.

My point is that most extremophiles are prokaryotes. Prokaryotes has little margin to create a complex macroorganism, no matter how much we redesign them.
I think that there is more possibilities to build complex organisms that could transform fast the environment, and, although much less endurable at cellular level, is more resilient as a whole organism, because creates a heave skin around it, that ultraresiliant prokaryotes that could only create simple colonies and simple protection because can not create an organism as a common thing.

Of course, if we reach the level of create new artificial life, we could develop extremophiles and multicellular designed from scratch.
Perhaps even in new solvents different from water could allow incredible low temperatures, capable of exists in places like Jupiter and Saturn moons.

I'm not so sure that we could build extremophiles that could thrive on Mars. There is extremophile that tolerates radiation, that tolerates very dry enviroments, very cold ones... but, all the same time, in the most extremes, and not only survive but thrive?
Too much.

Instead, I think that we could design, in some decades when we have the advancements in artificial life, multicellular organisms enough complex to create a "bubble", a "microscopic paraterraformation". Think, for example, in a organism capable to build a crystalline, similar to glass, sufficiently thick to contain some internal pressure and moist, and a black porous life, sustance inside, to retain heat. A very active "plant" capable of efficient energy capture, and generate heat inside while the whether cold. The porous material allow to retain easily the heat.
A biological design similar to a solar thermal plant with heat and chemical accumulation.
And roots that could penetrate in the "soil" (very cold) using some chemicals to break it even at these temperatures.

No. Half life means that in that time, it would be half neutrons. So, some neutrons always hit.

I think that if the body is so small that any open terraformation is impractical, then underground colonies could be a better alternative.
With time, the underground colonies could be so big and cover so much surface than it could be considered paraterraforming with opaque roof.

If caves was big enough and well connected, even a common biosphere is possible.

Gigant stable caves are possible when gravity is so small.

Titan has a thick atmosphere, as dense as Earth, and it not lose it.
What is the key? It is very cold and it has molecules too heavy to reach escape velocity at that temperature.

Could we have a moon at the Titan's atmosphere pressure but at Earth temperatures and breathable?

To the question of temperature, some methods could been proposed, like the active towers. The Earth's temperature is required in the layers near the ground, where they are living beings, while the loss of the atmosphere occurs in the outer layer, where the molecules are unlikely to collide with each other, and it could get up escape velocity and lost forever.

This issue can become so deep that it could lead to the development of a future branch of geoengineering. About how the heat is distributed by the layers of the atmosphere, and as radiation, convection and conduction between the gas creates the gradient.

Assume for a moment that this is not a problem. Ganymede dense atmosphere, for example, would isolate the heat generated by light from artificial fusion reactors. Escaping most as radiant heat, the last layer being the more "transparent" to these, so that the heat escape transparently maintaining very cold the upper.

The second is more complicated. Molecules? Heavy? A "unsolvable" problem occurs. Heavy molecules tend to be lower in the atmosphere, so that would probably unbearable for earthlings. And the necessary O2 and N2 would remain light, rising up and losing equally.

Here is an idea that has been haunting me. What if we make very large molecules ... heavy, but simultaneously form a very light gas?
Is that possible?

The first question you must understand is that the gas density depends on the space between molecules, not only of these. These molecules are separated from one another by various fundamental forces, creating a "rejection space". Is your weight, divided into the space, which will form the density. Another thing is that the molecules usually tend to create a similar space, since the effective space is much larger than the molecule, so they tend to create similar areas. So, normally, we could considerate that density depends only of molecular weight.

But this need not be so.

Imagine a sphere totally made of graphene. The area would be very small. I'm talking about hundreds of thousands of carbon atoms, not more. Inside, just empty space. Its effective space is huge, because they are areas "impenetrable". The number of carbon atoms grow with surface. The effective space of the "molecule" with the volume. With an area of sufficient size, density would be lower even than the less dense molecule ... hydrogen.
Yet this "molecules" would be very heavy! With lots of atoms.

So, these molecules tends to be at the top of atmosphere, but at the same time, it would be too heavy to reach scape speed. It could be a wonderful tool to make dense atmosphere relative stable in time. When a "molecule" of this kind breaks, it probably turns into a broken ball more dense and drops to the low atmosphere.

It may have defects. It is possible that the material proposed (graphene) did not have the right properties. For example, you may not be able to sustain its vacuum state for long because other molecules could pass through the graphene using tunnel effect. But it is possible that may exist other alternatives for the same purpose. For example, with larger areas, although some molecules enter the density molecules take longer to go down. The issue is not that they are always empty, but its state of lighter molecules that hydrogen could be sustained long enough. The location of a graphene layer could perhaps use a multilayer model with some technology that would allow these layers remain in a stable state.
The question would be to have these "balls" lighter than hydrogen stable long enough to need little repleshing.

I think that you are very optimist. Passive or "medium passive" methods like use special gasses on little quantities to generate a possitive feedback that could need centuries only to wait to get the correct temperature. But generete an little percent of gas ammount into an atmosphere, is huge for us. For example, change the CO2 in Earth Atmosphere to change the little quantity of CO2 that out atmosphere contains have required a century, massive process of burning carbons that is easy because generate energy, don't consume it and don't require advanced technology.

And it was burning is all our machines, the machines that work for a population of billions of humans.

Although CO2 have been generated as a waste it could show us, how difficult is any kind of planetary engineering that is some orders of magnitude bigger that change a little the composition of out atmosphere.

With current technology, it could require from thousands to hundred of thousands years to complete a terraforming. Perhaps Mars could be an exception and, if all is in the better case, it could be completed in some hundred of years. We need more investigation to check it.

But things like remove all carbon from venus atmospheres is a lot more complicated.

I think that future technologies could change that, but bring this technologies to reality need time. Only make fusion energy feasible requires now decades, and fusion will be necessary only to make a serius colonization in centuries instead millennia. So terraforming is far, far away.
Perhaps, future technologies like selfreplication machines could change some orders of magnitude to make terraforming feasible. I hope it. But the numbers are really big in any case.