BIOPHYSICS: A Folding Ruler

The Carpenter’s Ruler Folding Problem

A carpenter’s ruler is a ruler divided into pieces of different lengths which are hinged where the pieces meet, which makes it possible to fold the ruler. The carpenter’s ruler folding problem, originally posed by Hopcroft, Joseph and Whitesides, is to determine the smallest case (or interval on the line) into which the ruler fits when folded. The problem is known to be NP-complete. The best pr...

A Linear Time Approximation Algorithm for Ruler Folding Problem

A chain or n-link is a sequence of n links whose lengths are fixed and are joined together from their endpoints, free to turn about their endpoints, which act as joints. “Ruler Folding Problem”, which is NP-Complete is to find the minimum length of the folded chain. The best linear approximation algorithm for it were proposed by Hopcroft et al. Their algorithm folds any open chain in the interv...

Live discussion: Protein folding and neurodegeneration: biophysics to the rescue?

Live discussion held 30 April 2003 on the Alzheimer Research Forum, featuring David Teplow. http://www.alzforum.org/res/for/journal/teplow/teplow transcript.asp Participants: Nikolay Dokholyan (University of North Carolina, Chapel Hill), Charlie Glabe (University of California, Irvine), Dave Holtzman (Washington University, St. Louis), Alexei Koudinov (Russian Academy of Medical Sciences), Alek...

A single protein redox ruler.

Redox reactions are the heart of function in biological systems. Using a deceptively simple toolbox, consisting largely of first row transition metals and the 20 canonical amino acids, nature has evolved proteins that contain cofactors with reduction potentials (E°′) between +1 V and −1 V. Chemists have long known that ligands to transition metals markedly alter E°′ of the metal, often in a sys...

Biophysics.