I really don't know what to say.  Some people here have machines with 8 cores
and insane amounts of RAM, while I just go by with an "ancient" P4 2.66 and
512MB.

With full AA and full quality and just a lower resolution than yours:
povray +q9 +W320 +H240 +A0.02 +AM2 test.pov

I get a 2 secs render.  and with no AA and no area_lights or shadows:
povray +q2 +W320 +H240 -A0.02 -AM2 test.pov

time is so negligible it goes below 0 secs.  If you need more than that, you
could try lowering parsing time by having a less things to parse.  For
instance, all those finish look pretty much the same.  You could try getting
the equal values inside a default expression, as in:
#default {finish {specular 0.9 roughness 0.001}}

I improvised a bit upon your test scene in order to get a lot more spheres:



#include "colors.inc"
#include "textures.inc"

#declare ATM_FINISH = finish {specular 0.9 roughness 0.001 ambient rgb
<0.3,0.3,0.3> metallic}
#declare RIBBON_FINISH = finish {specular 0.9 roughness 0.001 ambient rgb
<0.3,0.3,0.3>}
#declare SURF_FINISH = finish {specular 0.9 roughness 0.001 ambient rgb
<0.3,0.3,0.3>}
#declare N_tex = texture { pigment { colour red 0.231 green 0.318 blue 1.000 }
finish{ ATM_FINISH }}
#declare C_tex = texture { pigment { colour red 0.100 green 0.100 blue 0.100 }
finish{ ATM_FINISH }}
#declare O_tex = texture { pigment { colour red 0.700 green 0.000 blue 0.000 }
finish{ ATM_FINISH }}
//************ CAMERA *********

#declare zoom = 15;

// Define Camera Positions
#declare xtopview = camera {orthographic direction <1, 0, 0> sky <0, 0, 1> up
<0, 0, zoom> right<zoom*4/3,0,0> rotate <0,0,180> location <0, 0, 20> look_at
<0, 0, 0>}
#declare xfrontview = camera {orthographic location  <0, -20, 0> direction <1,0,
0> sky <0, 0, 1> up <0, 0, zoom> right<zoom*4/3,0>
 look_at <0, 0,0>}


//************ LIGHTS *********

#declare Intensity = 1.7;

light_source
{
  0*z // light's position (translated below)
  color rgb 1.7  // light's color
  // <widthVector> <heightVector> nLightsWide mLightsHigh
  area_light
  <12, 0, 0> <0, 0, 12> // lights spread out across this distance (x * z)
  4, 4                // total number of lights in grid (4x*4z = 16 lights)
  adaptive 0          // 0,1,2,3...
  jitter              // adds random softening of light
  translate <30, -60, 40>   // <x y z> position of light
  shadowless
}
light_source
{
  0*z // light's position (translated below)
  color rgb 1  // light's color
  // <widthVector> <heightVector> nLightsWide mLightsHigh
  area_light
  <12, 0, 0> <0, 12, 0> // lights spread out across this distance (x * z)
  6, 6                // total number of lights in grid (4x*4z = 16 lights)
  adaptive 0          // 0,1,2,3...
  jitter              // adds random softening of light
  translate <7.5, 4, 20>   // <x y z> position of light
  shadowless
}
//************ Simulation Box ******

background { color rgb < 1.000, 1.000, 1.000 >}


//********** CAMERA *************

camera { xfrontview }

//********** ATOMS *************

#declare atoms = union {
sphere   { <1.34073,2.44067,2.09778>,  0.77 texture{C_tex}}
sphere   { <0.22055,2.50846,2.75588>,  0.73 texture{O_tex}}
sphere   { <2.20820,2.40215,2.77242>,  0.32 texture{N_tex}}
sphere   { <-0.54093,2.52909,2.04946>,  0.32 texture{N_tex}}
sphere   { <0.07183,-0.04000,-0.02136>,  1.3 texture{C_tex}}
sphere   { <2.90433,-0.03858,-0.02034>,  1.3 texture{C_tex}}
sphere   { <1.50770,2.40207,0.19218>,  1.3 texture{C_tex}}
} // End atom union

#declare atoms = union {
 #local i = 0; #while (i<40)
 object {atoms translate x*.6*i}
 #declare i = i + 1; #end
} // End atom union

object {atoms rotate <0,0,0> translate <-7.50771, -4.47073, 2.07789> scale
0.775927395422}

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