Coray M Colina

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The viral RNA-dependent RNA polymerase (RdRp) is essential for multiplication of all RNA viruses. The sequence diversity of an RNA virus population contributes to its ability to infect the host. This diversity emanates from errors made by the RdRp during RNA synthesis. The physical basis for RdRp fidelity is unclear but is linked to conformational changes(More)
RNA viruses encoding high- or low-fidelity RNA-dependent RNA polymerases (RdRp) are attenuated. The ability to predict residues of the RdRp required for faithful incorporation of nucleotides represents an essential step in any pipeline intended to exploit perturbed fidelity as the basis for rational design of vaccine candidates. We used x-ray(More)
BACKGROUND 'Idling' or ongoing low-level activity of the tissue factor (TF) pathway is a postulated mechanism by which the coagulation process can become active without a lag period at sites of injury. OBJECTIVE To determine whether TF around cutaneous vessels has bound factor VIIa in the absence of injury, and thus could participate in the idling(More)
Explicit water atomistic molecular dynamics simulations (200 ns, ∼330,000 atoms) were performed to study the effects of galactosylation in the Fc domain of immunoglobulin G1. Two glycoforms were simulated to observe changes in protein-carbohydrate interactions and carbohydrate structure. A high degree of flexibility was observed in the small hinge region of(More)
Polymers of intrinsic microporosity (PIMs) are a promising alternative in gas separation applications; however, their industrial applicability is greatly reduced by their susceptibility toward sorption-induced plasticization. In this study, the effects of swelling during nitrogen adsorption isotherms at 77 K for five PIMs (PIM-1, PIM-1c, PIM-SBF,(More)
This work presents the predictive molecular simulations of a functionalized polymer of intrinsic microporosity (PIM) with an ionic backbone (carboxylate) and extra-framework counterions (Na(+)) for CO2 gas storage and separation applications. The CO2-philic carboxylate-functionalized polymers are predicted to contain similar degrees of free volume to PIM-1,(More)
Because of the complex connectivity of cross-linked polymers, generating structures for molecular simulations is a nontrivial task. In this work, a general methodology is presented for constructing post-cross-linked polymers by a new two-stage implementation of the Polymatic simulated polymerization algorithm, where linear polymers are first polymerized and(More)
Deep eutectic solvents, considered ionic liquid (IL) analogues, show promise for many material science and engineering applications over typical ILs because they are readily available and relatively inexpensive. Atomistic molecular dynamics simulations have been performed over a range of temperatures on one eutectic mixture, 1:2 choline chloride/urea, using(More)
We study the permeation dynamics of helium and carbon dioxide through an atomistically detailed model of a polymer of intrinsic microporosity, PIM-1, via non-equilibrium molecular dynamics (NEMD) simulations. This work presents the first explicit molecular modeling of gas permeation through a high free-volume polymer sample, and it demonstrates how(More)