automaton cartoon

Multiple pattern matching: A Markov chain approach

July 31, 2007

RNA motifs typically consist of short, modular patterns that include base pairs formed within and between modules. Estimating the abundance of these patterns is of fundamental importance.

Model cartoon

Entropic elasticity of DNA with a permanent kink

Dec. 31, 2006

Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA, using relatively short DNA molecules with a single, well-defined bend site. We developed a simple, theoretical description of the effect of a single bend.

Model cartoon

Systems theory of SMAD signaling

Nov. 30, 2006

To investigate the mechanisms of Smad nuclear accumulation, we developed a simple mathematical model of canonical Smad signalling.

Substitution matrix schematic

Using the nucleotide substitution rate matrix to detect horizontal gene transfer

Oct. 26, 2006

Horizontal gene transfer has allowed bacteria to evolve many new capabilities. We introduce a new class of methods for detecting HGT based on the changes in nucleotide substitution rates.

Reaction schematic

Incorporating expression data in metabolic modeling: A case study of lactate dehydrogenase

March 30, 2006

We use data from mRNA expression arrays and chemical kinetics to formulate a metabolic model relevant to K562 erythroleukemia cells.


Controlled irradiative formation of penitentes

March 10, 2006

Spike-shaped structures are produced by light-driven ablation in very different contexts. We report the first laboratory generation of centimeter-scale snow and ice penitentes.

Model cartoon

Opening of nucleic-acid double strands by helicases: Active versus passive opening

Jan. 19, 2005

his paper presents a theoretical study of the coupling between helicase translocation and nucleic acid unwinding.

cylinder plot

Collapsing bacterial cylinders

Dec. 31, 2001

Under special conditions bacteria excrete an attractant and aggregate. The high density regions initially collapse into cylindrical structures, which subsequently destabilize and break up into spherical aggregates.

dirt cartoon

Formation of structure in snowfields motivated by penitentes, suncups, and dirt cones

Nov. 30, 2001

Penitentes and suncups are structures formed as snow melts, typically high in the mountains. When the snow is dirty, dirt cones and other structures can form instead.