Electronic – What expression can I use in matlab to remove the negative component of a sine wave so it can look like the picture below

If you apply power at +5V0 and you have some sort of an overvoltage condition (if the source loses control, or is inadvertently swapped for a 12V supply, etc), the current that will be drawn when the TVS clamps will not pass through the 1.1A fuse. The TVS may survive forever, or for a while, or for a few milliseconds. Once it gives up there's no line of protection left to prevent your downstream components and capacitors.

If you apply power at VBUS and get an overvoltage condition, the TVS clamp current will pass through the fuse. If the TVS, fuse, and source power supply are rated 'correctly', the TVS should be able to draw enough current (and the power supply should be able to provide enough current) to clear the fuse and safely isolate the supply from the load.

Properly placed caps should be close to where they're needed. Small decoupling caps should be near the ICs that need decoupling. Your power connection should 'see' the \$220 \mu F\$ cap before 'seeing' the load in terms of PCB geometry, but this really depends on how the board is laid out.

I would approach this as a mechanical problem, not a servo-selection problem. Design a mechanism which can take a hit and keep the servo isolated, then you only need a normally rated servo (one that can move the object, rather than being strong enough to cut a dog in half).

I would look at adding some spring, rubber, a cush-drive, overload or slip clutch (or dog clutch, ha ha!), or just slack in the mechanism to allow the movement/impact.

Personally I'd look closely at other actuation methods, for example small pneumatic cylinders are easily actuated with solenoid valves and a £5 12v car tyre inflator can provide enough air, and being pneumatic they will take having their pistons moved by force and return naturally to where they're set.