83 citations · 321 across the 14 of their papers we have counts for
8 papers · 1 filter
On the origin of the unusual behavior in the stretching of single-stranded DNA
Ngo Minh Toan, D. Thirumalai
Force extension curves (FECs), which quantify the response of a variety of biomolecules subject to mechanical force (), are often quantitatively fit using worm-like chain (WLC)…
Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins
S. Vaitheeswaran, Jie Chen, D. Thirumalai
Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the…
Crowding effects on the structural transitions in a flexible helical homopolymer
Alexander Kudlay, Margaret S. Cheung, D. Thirumalai
We elucidate the structural transitions in a helical off-lattice homopolymer induced by crowding agents, as function of the number of monomers () and volume fraction () of…
Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores
S. Vaitheeswaran, G. Reddy, D. Thirumalai
We use Metropolis Monte Carlo and umbrella sampling to calculate the free energies of interaction of two methane molecules and their charged derivatives in cylindrical water-filled…
Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy (FCS): Theory and applications
V. Barsegov, D. Klimov, D. Thirumalai
In the current AFM experiments the distribution of unfolding times, P(t), is measured by applying a constant stretching force f_s from which the apparent unfolding rate is obtained…
Folding in lattice models with side chains
Mai Suan Li, D. K. Klimov, D. Thirumalai
The folding kinetics of three-dimensional lattice Go models with side chains is studied using two different Monte Carlo move sets. A flexible move set based on single, double and t…