Dave Thirumalai

Kinematics of the Lever Arm Swing in Myosin VI

This study uses a coarse-grained model to analyze the power stroke mechanism of myosin VI, revealing that the lever arm rotation is largely uncoupled from the motor domain.

Ripping RNA by Force using Gaussian Network Models

This study uses Gaussian network models to analyze RNA unfolding under force, showing qualitative agreement with experimental data but limitations in capturing complex features.

Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension

This study uses simulations to analyze how salt and force affect the structural transitions of an RNA pseudoknot, revealing how these factors influence frameshifting efficiency.

Noise Control In Gene Regulatory Networks With Negative Feedback

The paper applies a noise filtering formalism from communications systems to analyze noise control in gene regulatory networks with negative feedback, showing optimal noise reduction in Hill-like circuits.

Discrete step sizes of molecular motors lead to bimodal non-Gaussian velocity distributions under force

The paper derives a kinetic model to predict velocity and run-length distributions of molecular motors under force, showing bimodal non-Gaussian velocity distributions due to discrete step sizes.

How do metal ions direct ribozyme folding?

This study shows that Mg2+ ions transiently stabilize structural elements of the group I ribozyme but are insufficient for complete folding, which requires higher concentrations and specific metal ligand interactions.

Folding PDZ2 domain using the Molecular Transfer Model

This paper uses the Molecular Transfer Model to simulate urea-dependent folding of the PDZ2 domain, showing the presence of an intermediate state and revealing folding pathways.