When considered from a broad perspective, many events that appear to occur at random, such as weather, are in fact part of recurring patterns subject to mathematical principles. Libchaber applies a type of mathematics called nonlinear dynamics to biological systems in order to understand how an object and its surrounding environment act on one another to produce a specific result.
Libchaber studies mathematical patterns in biology at the organismal, cellular, and molecular levels. His work examines the interactions and dynamics between organism and environment, including the effects of moving boundary conditions on fluid flow. A moving fish, for example, involves a complicated interaction of a dynamic object with the surrounding fluid, with forces by both elements acting on one another. Additionally, Libchaber has shown how temperature and oxygen gradients as well as bacterial concentrations finely tune and control the bacteria’s motility and genetics. The research firmly established that an organism’s environment affects its genes and behavior.
Libchaber’s lab has also undertaken experiments at the single-molecule level to define the minimal conditions needed to produce an artificial cell. Within a phospholipid vesicle, which mimics a cell membrane, he places DNA containing the necessary genes and their regulatory sequences. This cell, which is in contact with a feeding solution through its semipermeable membrane pores, is then the environment for testing different gene networks and elementary logic circuits for their ability to reproduce essential events in a cell’s life, such as producing proteins and transporting them to the cell’s surface. The research may hold clues to the origin of life: the ultimate aim is to produce an artificial cell that reproduces itself following a genetic program.
Another important concept concerning the origin of life is the development of a genetic code that relates the 20-amino acid world to the four-nucleotide one. Libchaber has shown that an RNA molecule of a stem-loop structure, acting as a ribozyme, can load an amino acid to its 3′ end. This amino acid corresponds to the anticodon in the loop, and this whole process can be done without enzymes.
Past research in Libchaber’s lab has elucidated the effects of temperature on DNA. In a detailed study on the effects of thermophoresis on DNA in solution, they found that when far infrared lights are focused on the center of a chamber, DNA moves from a hot region to a cold one. As the heat is increased, however, convection sets in and causes the opposite occurrence: the DNA collects and accumulates at the bottom center of the chamber. Because this phenomenon could be used to sustain very high concentrations of DNA or proteins, it sheds light on how critical concentrations of DNA may have been reached amid early primordial-soup chain reactions. The laboratory then showed that DNA amplification by polymerase chain reaction is essentially a thermal convection process.
Currently, Libchaber’s work focuses on subsurface microbial ecosystems. Mud, a porous medium, contains a high density of diverse organisms. Despite this complexity, microbes in nature self-organize into simple reproducible patterns. His lab is conducting experiments in which the dynamics of natural mud coming to a steady state are observed and modeled.