network cartoon

Activating and inhibiting connections in biological network dynamics

Dec. 4, 2008

The balance between activating and inhibiting connections is important in determining whether network dynamics reach steady state or oscillate.

experimental schematic

Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 micrometers

Dec. 31, 2007

The wormlike chain (WLC) model currently provides the best description of double-stranded DNA elasticity for micron-sized molecules.

TFIIA structural model

TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability

Dec. 31, 2007

TFIIA induces a conformational change within the TBP/TATA complex that enhances its stability under both in vitro and physiological salt conditions. We present a refined model for the effect that TFIIA has on DNA conformation that takes into account potential changes in bend angle as well as twist angle.

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.