Normal modes of Nicolium

Note added 31 January 2013: These animations were constructed 12 October 2007 to illustrate the normal modes of a molecule studied by a Chem-Physics major named Nicole.

REMARK: Go to the Evaluation menu and click on Evaluate Notebook.  To launch the animations, punch the + tab on the right end of the lower slide and hit the start button (▲).

Axial countermotion:

ω=2

frame1[a_,n_]:=Show[Graphics[{{RGBColor[1,1,1],Point[{1.5`,0}]},{RGBColor[1,1,1],Point[{0,1.5`}]},{RGBColor[1,1,1],Point[{-1.5`,0}]},{RGBColor[1,1,1],Point[{0,-1.5`}]},Line[{{1,0},{0,1},{-1,0},{0,-1},{1,0}}],Line[{{-1,0},{1,0}}],Line[{{0,-1},{0,1}}],Circle[{0,0},0.1`],Circle[{0,1},0.1`],Circle[{1,0},0.1`],Circle[{-1,0},0.1`],Circle[{0,-1},0.1`],{RGBColor[1,0,0],Disk[{0,0},0.08`]},{RGBColor[1,0,0],Disk[{1+a Sin[((2 π n)/21)],0},0.08`]},{RGBColor[1,0,0],Disk[{0,1-a Sin[((2 π n)/21)]},0.08`]},{RGBColor[1,0,0],Disk[{-(1+a Sin[((2 π n)/21)]),0},0.08`]},{RGBColor[1,0,0],Disk[{0,-(1-a Sin[((2 π n)/21)])},0.08`]}}],AspectRatio->Automatic]

Manipulate[frame1[.1,n],{n,0,20}]

Rowing 1:

ω=5-(Sqrt[5])//N

frame2[a_,n_]:=Show[Graphics[{{RGBColor[1,1,1],Point[{1.5`,0}]},{RGBColor[1,1,1],Point[{0,1.5`}]},{RGBColor[1,1,1],Point[{-1.5`,0}]},{RGBColor[1,1,1],Point[{0,-1.5`}]},Line[{{1,0},{0,1},{-1,0},{0,-1},{1,0}}],Line[{{-1,0},{1,0}}],Line[{{0,-1},{0,1}}],Circle[{0,0},0.1`],Circle[{0,1},0.1`],Circle[{1,0},0.1`],Circle[{-1,0},0.1`],Circle[{0,-1},0.1`],{RGBColor[1,0,0],Disk[{0,(1+(Sqrt[5])) a Sin[((2 π n)/21)]},0.08`]},{RGBColor[1,0,0],Disk[{1,(-4+(1/2) (5-(Sqrt[5]))) a Sin[((2 π n)/21)]},0.08`]},{RGBColor[1,0,0],Disk[{0,1+a Sin[((2 π n)/21)]},0.08`]},{RGBColor[1,0,0],Disk[{-1,(-4+(1/2) (5-(Sqrt[5]))) a Sin[((2 π n)/21)]},0.08`]},{RGBColor[1,0,0],Disk[{0,-1+a Sin[((2 π n)/21)]},0.08`]}}],AspectRatio->Automatic]

Manipulate[frame2[.1,n],{n,0,20}]

Rowing 2:

ω=5-(Sqrt[5])//N

frame3[a_,n_]:=Show[Graphics[{{RGBColor[1,1,1],Point[{1.5`,0}]},{RGBColor[1,1,1],Point[{0,1.5`}]},{RGBColor[1,1,1],Point[{-1.5`,0}]},{RGBColor[1,1,1],Point[{0,-1.5`}]},Line[{{1,0},{0,1},{-1,0},{0,-1},{1,0}}],Line[{{-1,0},{1,0}}],Line[{{0,-1},{0,1}}],Circle[{0,0},0.1`],Circle[{0,1},0.1`],Circle[{1,0},0.1`],Circle[{-1,0},0.1`],Circle[{0,-1},0.1`],{RGBColor[1,0,0],Disk[{(1+(Sqrt[5])) a Sin[((2 π n)/21)],0},0.08`]},{RGBColor[1,0,0],Disk[{1+a Sin[((2 π n)/21)],0},0.08`]},{RGBColor[1,0,0],Disk[{(-4+(1/2) (5-(Sqrt[5]))) a Sin[((2 π n)/21)],1},0.08`]},{RGBColor[1,0,0],Disk[{-1+a Sin[((2 π n)/21)],0},0.08`]},{RGBColor[1,0,0],Disk[{(-4+(1/2) (5-(Sqrt[5]))) a Sin[((2 π n)/21)],-1},0.08`]}}],AspectRatio->Automatic]

Manipulate[frame3[.1,n],{n,0,20}]

Vertex countermotion:

ω=4

frame4[a_,n_]:=Show[Graphics[{{RGBColor[1,1,1],Point[{1.5`,0}]},{RGBColor[1,1,1],Point[{0,1.5`}]},{RGBColor[1,1,1],Point[{-1.5`,0}]},{RGBColor[1,1,1],Point[{0,-1.5`}]},Line[{{1,0},{0,1},{-1,0},{0,-1},{1,0}}],Line[{{-1,0},{1,0}}],Line[{{0,-1},{0,1}}],Circle[{0,0},0.1`],Circle[{0,1},0.1`],Circle[{1,0},0.1`],Circle[{-1,0},0.1`],Circle[{0,-1},0.1`],{RGBColor[1,0,0],Disk[{0,0},0.08`]},{RGBColor[1,0,0],Disk[{1,-a Sin[((2 π n)/21)]},0.08`]},{RGBColor[1,0,0],Disk[{-a Sin[((2 π n)/21)],1},0.08`]},{RGBColor[1,0,0],Disk[{-1,a Sin[((2 π n)/21)]},0.08`]},{RGBColor[1,0,0],Disk[{a Sin[((2 π n)/21)],-1},0.08`]}}],AspectRatio->Automatic]

Manipulate[frame4[.1,n],{n,0,20}]

Breathing mode:

ω=6

frame5[a_,n_]:=Show[Graphics[{{RGBColor[1,1,1],Point[{1.5`,0}]},{RGBColor[1,1,1],Point[{0,1.5`}]},{RGBColor[1,1,1],Point[{-1.5`,0}]},{RGBColor[1,1,1],Point[{0,-1.5`}]},Line[{{1,0},{0,1},{-1,0},{0,-1},{1,0}}],Line[{{-1,0},{1,0}}],Line[{{0,-1},{0,1}}],Circle[{0,0},0.1`],Circle[{0,1},0.1`],Circle[{1,0},0.1`],Circle[{-1,0},0.1`],Circle[{0,-1},0.1`],{RGBColor[1,0,0],Disk[{0,0},0.08`]},{RGBColor[1,0,0],Disk[{0,1+a Sin[((2 π n)/21)]},0.08`]},{RGBColor[1,0,0],Disk[{1+a Sin[((2 π n)/21)],0},0.08`]},{RGBColor[1,0,0],Disk[{-(1+a Sin[((2 π n)/21)]),0},0.08`]},{RGBColor[1,0,0],Disk[{0,-(1+a Sin[((2 π n)/21)])},0.08`]}}],AspectRatio->Automatic]

Manipulate[frame5[.1,n],{n,0,20}]

Jumping jack 1:

ω=5+(Sqrt[5])//N

frame6[a_,n_]:=Show[Graphics[{{RGBColor[1,1,1],Point[{1.5`,0}]},{RGBColor[1,1,1],Point[{0,1.5`}]},{RGBColor[1,1,1],Point[{-1.5`,0}]},{RGBColor[1,1,1],Point[{0,-1.5`}]},Line[{{1,0},{0,1},{-1,0},{0,-1},{1,0}}],Line[{{-1,0},{1,0}}],Line[{{0,-1},{0,1}}],Circle[{0,0},0.1`],Circle[{0,1},0.1`],Circle[{1,0},0.1`],Circle[{-1,0},0.1`],Circle[{0,-1},0.1`],{RGBColor[1,0,0],Disk[{0,(1-(Sqrt[5])) a Sin[((2 π n)/21)]},0.08`]},{RGBColor[1,0,0],Disk[{1,(-4+(1/2) (5+(Sqrt[5]))) a Sin[((2 π n)/21)]},0.08`]},{RGBColor[1,0,0],Disk[{0,1+a Sin[((2 π n)/21)]},0.08`]},{RGBColor[1,0,0],Disk[{-1,(-4+(1/2) (5+(Sqrt[5]))) a Sin[((2 π n)/21)]},0.08`]},{RGBColor[1,0,0],Disk[{0,-1+a Sin[((2 π n)/21)]},0.08`]}}],AspectRatio->Automatic]

Manipulate[frame6[.1,n],{n,0,20}]

Jumping jack 2:

ω=5+(Sqrt[5])//N

frame7[a_,n_]:=Show[Graphics[{{RGBColor[1,1,1],Point[{1.5`,0}]},{RGBColor[1,1,1],Point[{0,1.5`}]},{RGBColor[1,1,1],Point[{-1.5`,0}]},{RGBColor[1,1,1],Point[{0,-1.5`}]},Line[{{1,0},{0,1},{-1,0},{0,-1},{1,0}}],Line[{{-1,0},{1,0}}],Line[{{0,-1},{0,1}}],Circle[{0,0},0.1`],Circle[{0,1},0.1`],Circle[{1,0},0.1`],Circle[{-1,0},0.1`],Circle[{0,-1},0.1`],{RGBColor[1,0,0],Disk[{(1-(Sqrt[5])) a Sin[((2 π n)/21)],0},0.08`]},{RGBColor[1,0,0],Disk[{1+a Sin[((2 π n)/21)],0},0.08`]},{RGBColor[1,0,0],Disk[{(-4+(1/2) (5+(Sqrt[5]))) a Sin[((2 π n)/21)],1},0.08`]},{RGBColor[1,0,0],Disk[{-1+a Sin[((2 π n)/21)],0},0.08`]},{RGBColor[1,0,0],Disk[{(-4+(1/2) (5+(Sqrt[5]))) a Sin[((2 π n)/21)],-1},0.08`]}}],AspectRatio->Automatic]

Manipulate[frame7[.1,n],{n,0,20}]