
    For discussion purposes, I will ignore dynamic effects like pulses
in the exhaust pipe, and try to paint a useful mental picture.

1.  Unless an engine is supercharged, the pressure available to force
air into the intake tract is _atmospheric_.  At the time the intake
valve is opened, the pressure differential available to move air is only
the difference between the combustion chamber pressure (left over after
the exhaust stroke) and atmospheric.  As the piston decends on the
intake stroke, combustion chamber pressure is decreased, allowing
atmospheric pressure to move more air into the intake tract.  At no time
does the pressure ever become "negative", or even approach a good
vacuum.

2.  At the time of the exhaust valve closing, the pressure in the
combustion chamber is essentially the pressure of the exhaust system up
to the first major flow restriction (the muffler).  Note that the volume
of gas that must flow through the exhaust is much larger than the volume
that must flow through the intake, because of the temperature
difference and the products of combustion.

3.  In the last 6-8 years, the Japanese manufacturers have started
paying attention to exhaust and intake tuning, in pursuit of almighty
horsepower.  At this point in time, on high-performance bikes,
substitution of an aftermarket free-flow air filter will have almost
zero affect on performance, because the stock intake system flows very
well anyway.  Substitution of an aftermarket exhaust system will make
very little difference, unless (in general) the new exhaust system is
_much_ louder than the stocker.

4.  On older bikes,  exhaust back-pressure was the dominating factor.
If free-flowing air filters were substituted, very little difference
was noted, unless a free-flowing exhaust system was installed as well.

5.  In general, an engine can be visualized as an air pump.  At any
given RPM, anything that will cause the engine to pump more air, be it
on the intake or exhaust side, will cause it to produce more horsepower.
Pumping more air will require recalibration (rejetting) of the carburetor.

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