Ateneo physics alumnus Dr. Rhonald Lua in Biomedical Computation Review 2006: Knot-detecting algorithm for proteins

Physics alumnus Dr. Rhonald Lua of Ateneo de Manila University (B.S. Physics ’96 and B.S. Computer Engineering ’97) was mentioned in Biomedical Computation Review for his work on knot-finding algorithms for proteins:

Grosberg and his coauthor, postdoc Rhonald Lua, PhD, developed a knot-detecting algorithm that they used to scan 4716 proteins with known shapes from the Protein Data Bank. They found only 19 proteins (0.4 percent) with knots. Bolstering their findings, two other groups (from MIT and Italy) independently arrived at almost the same list of knotted proteins (they missed two of Grosberg’s). Grosberg and Lua next set out to quantify how often proteins would be expected to form knots if only chance was at work. They simulated the shapes of random polymers with chains of equal length, density, and flexibility as proteins using a statistical technique—random walk on a lattice.
Starting at a single point, this algorithm draws a path in three dimensions by randomly moving one unit at a time in one of six possible directions: up, down, forward, backward, right, or left. The end result is a randomly crinkled chain that may or may not contain knots. The proportion of these random polymers with knots trounced that found in real proteins: Simulated polymers at lengths of a typical protein (200-500 amino acids) formed knots 15-60 percent of the time.  (Biomedical Computation Review, Fall 2006)

Dr. Rhonald Lua finished his Ph.D. in Physics in Univesity of Minnesota (2005).  He worked on “The Problem of Knots and Sequence Design in Proteins and Compact Chains” under the supervsion of Dr. Alexander Grosberg”. Check out the You Tube video posted by Dr. Lua entitled, “Intestinal Fortitude – From Flying Spaghetti to Donut.”

Dr. Lua is now a post-doctoral fellow at the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.


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