Chain parameters

This is where the basic properties of the polymer segment in question are set. Each of these properties can be specified in different units, specified in the menus to the right of each field.

1. Contour length: the length of polymer between the two ends that are being measured, measured along the contour of the polymer (i.e. not just the displacement of the two ends). This may be given in the following units:
   
   
   • Lp: persistence lengths (the bend persistence length given in the second field)
   • nm: nanometers
   • A: Angstroms
   • bp DNA: DNA base pairs at 0.3 nm each
   • kb DNA: kilobases of DNA; 1 kb = 300 nm
   
   
2. Bend persistence length: gives the typical lengths scale over which the polymer bends. (For a better explanation see the Wikipedia entry.) Unless otherwise indicated, the term 'persistence length' usually refers to the bending persistence length. The units in which this can be given are:
   
   
   • Lp: multiples of the bending persistence length of naked DNA. Thus if we are modeling DNA we can enter '1' and select this unit. The persistence length of DNA is taken to be 50 nm.
   • nm: nanometers
   • A: Angstroms
   • bp DNA: DNA base pairs, 0.3 nm each
   • kb DNA: kilobases of DNA, 300 nm per kilobase
   
   
3. Twist persistence length: the typical lengths scale over which the polymer twists. This is defined analogously to the bending persistence length, except that it measures the twisting stiffness. Measured in the following units:
   
   
   • Lp: the bending persistence length given in the previous field.
   • Lp: multiples of the measured twist persistence length of naked DNA, taken to be 100 nm. We can model DNA by selecting these units and entering '1' in the corresponding field.
   • nm: nanometers
   • A: Angstroms
   • bp DNA: DNA base pairs, 0.3 nm each
   • kb DNA: kilobases of DNA, 300 nm per kilobase
   
   
4. Intrinsic twist: the rate of at which the polymer naturally twists in a completely relaxed state. All angles are given in radians, where pi radians = 180 degrees. The intrinsic twist can be specified in the following units:
   
   
   • rad/lp: radians per bending persistence length given in the 2nd field.
   • T DNA: the intrinsic twist of naked DNA, taken at 98 radians (approximately 15.5 full twists) per every 50 nm. To model DNA, select these units and entering '1' in the corresponding field.
   • rad/nm: radians of twist per nanometer
   • rad/A: radians of twist per Angstrom
   • rad/bp DNA: radians of twist per 0.3 nm (the length of one DNA base pair)
   • rad/kb DNA: radians of twist per 300 nm (the length of one DNA kilobase)

   In order to specify the twist in degrees instead of radians, one must perform the conversion manually inside the twist field by multiplying by (pi / 180). ('pi', all lowercase, is a predefined variable in this calculator.) For example, a twist of 100 degrees would be entered:

   • 100 * pi / 180