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Simulating how molecules move.



A complex molecule, whether a fullerene fullerene, any of a class of carbon molecules in which the carbon atoms are arranged into 12 pentagonal faces and 2 or more hexagonal faces to form a hollow sphere, cylinder, or similar figure. , protein, or strand of DNA DNA: see nucleic acid.
DNA
 or deoxyribonucleic acid

One of two types of nucleic acid (the other is RNA); a complex organic compound found in all living cells and many viruses. It is the chemical substance of genes.
, is an unwieldy object to describe. Though a stick-and-ball model can reveal its structure, one, can only guess how such an entity will move when it flexes and folds.

Biochemists have now joined with mathematicians to make computer programs that show how complicated molecules -- sometimes composed of thousands of atoms -- move.

Benedict J. Leimkuhler and Eric J. Barth, both mathematicians at the University of Kansas The University of Kansas (often referred to as KU or just Kansas) is an institution of higher learning in Lawrence, Kansas. The main campus resides atop Mount Oread.  in Lawrence, report devising a model that simulates the interactive motions of a large molecule. Their algorithm, which illustrates "constrained molecular dynamics," not only captures the movements within complex molecules, it also speeds up such simulations.

"The problem we're addressing as mathematicians is to improve the algorithms used to model biomolecules This page aims to list articles on Wikipedia that describe particular biomolecules or types of biomolecules.

This list is not necessarily complete or up to date - if you see an article that should be here but isn't (or one that shouldn't be here but is), please update the page
," explains Leimkuhler. "The models treat molecules as a collection of point masses connected by forces. Our goal is to make those algorithms more efficient for ... more powerful simulations."

To mimic motion in a protein with 10,000 atoms, the algorithm breaks up the molecule's twisting into discrete units. "It determines the state of the molecule at each time step. At any moment, the algorithm knows where the molecule has been and then predicts where it is going," says Leimkuhler.

In a stepwise stepwise

incremental; additional information is added at each step.


stepwise multiple regression
used when a large number of possible explanatory variables are available and there is difficulty interpreting the partial regression
 fashion, the program shows how a molecule's components interact with and affect one another. "The goal is to make an algorithm efficient so it can show realistic motions over a reasonable span of time," says Leimkuhler. "Right now we're working in femtosecond, or 10-15, increments. Ultimately, we want to show how proteins fold, or how nylon stretches, or how buckyballs lubricate lu·bri·cate  
v. lu·bri·cat·ed, lu·bri·cat·ing, lu·bri·cates

v.tr.
1. To apply a lubricant to.

2. To make slippery or smooth.

v.intr.
To act as a lubricant.
 a surface. These actions take place over 1 or more seconds, so we have a long way to go."
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Title Annotation:mathematicians improve algorithm used to model molecule movement
Author:Lipkin, Richard
Publication:Science News
Article Type:Brief Article
Date:Aug 6, 1994
Words:289
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