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Nanoscale pores have proved useful as a means to assay DNA and are actively being developed as the basis of genome sequencing methods. Hairpin DNA (hpDNA), having both double-helical and overhanging coil portions, can be trapped in a nanopore, giving ample time to execute a sequence measurement. In this article, we provide a detailed account of hpDNA… (More)

- Jehanzeb Hameed Chaudhry, Jeffrey Comer, Aleksei Aksimentiev, Luke N Olson, Bo Li, J H Chaudhry +1 other
- 2013

The conventional Poisson-Nernst-Planck equations do not account for the finite size of ions explicitly. This leads to solutions featuring unrealistically high ionic concentrations in the regions subject to external potentials, in particular, near highly charged surfaces. A modified form of the Poisson-Nernst-Planck equations accounts for steric effects and… (More)

- Horacio Poblete, Ingrid Oyarzún, Pablo Olivero, Jeffrey Comer, Matías Zuñiga, Romina V Sepulveda +4 others
- The Journal of biological chemistry
- 2015

Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) has been recognized as an important activator of certain transient receptor potential (TRP) channels. More specifically, TRPV1 is a pain receptor activated by a wide range of stimuli. However, whether or not PI(4,5)P2 is a TRPV1 agonist remains open to debate. Utilizing a combined approach of mutagenesis and… (More)

- Jeffrey Comer, James C. Gumbart, Jérôme Hénin, Tony Lelièvre, Andrew Pohorille, Christophe Chipot
- The journal of physical chemistry. B
- 2015

In the host of numerical schemes devised to calculate free energy differences by way of geometric transformations, the adaptive biasing force algorithm has emerged as a promising route to map complex free-energy landscapes. It relies upon the simple concept that as a simulation progresses, a continuously updated biasing force is added to the equations of… (More)

- Bala Murali Venkatesan, James Polans, Jeffrey Comer, Supriya Sridhar, David Wendell, Aleksei Aksimentiev +1 other
- Biomedical microdevices
- 2011

Solid-state nanopore sensors are highly versatile platforms for the rapid, label-free electrical detection and analysis of single molecules, applicable to next generation DNA sequencing. The versatility of this technology allows for both large scale device integration and interfacing with biological systems. Here we report on the development of a hybrid… (More)

Calculations of lipid bilayer permeabilities from first principles, using molecular simulations, would be valuable to rapidly assess the bioavailability of drug candidates, as well as to decipher, at the atomic level, the mechanisms that underlie the translocation of permeants. The most common theoretical approach, the solubility-diffusion model, requires… (More)

- Valeria Márquez-Miranda, Ingrid Araya-Durán, María Belén Camarada, Jeffrey Comer, Jesús A. Valencia-Gallegos, Fernando Danilo González-Nilo
- Scientific reports
- 2016

An ideal nucleic-acid transfection system should combine the physical and chemical characteristics of cationic lipids and linear polymers to decrease cytotoxicity and uptake limitations. Previous research described new types of carriers termed amphiphilic dendrimers (ADs), which are based on polyamidoamine dendrimers (PAMAM). These ADs display the cell… (More)

Predicting the rate of nonfacilitated permeation of solutes across lipid bilayers is important to drug design, toxicology, and signaling. These rates can be estimated using molecular dynamics simulations combined with the inhomogeneous solubility-diffusion model, which requires calculation of the potential of mean force and position-dependent diffusivity of… (More)

Accurate calculation of permeabilities from first-principles has been a long-standing challenge for computer simulations, notably in the context of drug discovery, as a route to predict the propensity of small, organic molecules to spontaneously translocate biological membranes. Of equal importance is the understanding of the permeation process and the… (More)

- Jeffrey Comer, Christophe Chipot, Fernando D González-Nilo
- Journal of chemical theory and computation
- 2013

Calculating transition rates and other kinetic quantities from molecular simulations requires knowledge not only of the free energy along the relevant coordinate but also the diffusivity as a function of that coordinate. A variety of methods are currently used to map the free-energy landscape in molecular simulations; however, simultaneous calculation of… (More)

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