Jacob Monroe Email and Phone Number

Shell Research GroupCreated genetic algorithm to optimize thermodynamic or kinetic properties of water near a surface by modifying the functional group arrangement on the surfacePerformed non-equilibrium and equilibrium simulations to determine the scaling of the hydrophobic interaction between peptides of varying hydrophobicity and an extended hydrophobic surfaceMentored undergraduate student in study of helix/hairpin balance for short peptides in recently developed AMBER force fields and implicit solvent models, leading to co-authored paper

Shirts Research GroupSimulations performed to determine free energies of binding for a number of small-molecule host-guest systems to better understand sources of error, such as those introduced by parameterization of atoms, when compared to experimental resultsResults will help develop set of best methods for determining ligand binding behavior and predicting ligand affinities for the cucurbit[7]uril and octa-acid hostsSubmitted results to the SAMPL4 blind free energy prediction competitionPoster presented at 2013 AICHE National Conference in San Francisco won first prize in Computing and Process Control category

Novel Molecules Group, Process BiochemistryDetermined optimal resin and wash and elution buffer compositions for an affinity capture chromatography step for use in a platform process to achieve the purification of a novel biopharmaceutical moleculeAided in the design of a high-throughput automated method for thermodynamically characterizing binding to affinity resins under a variety of bulk solution conditions

Shirts Research GroupAnalyzed HIV-Reverse Transcriptase function and drug-resistant mutations to non-nucleoside reverse transcriptase inhibitors through statistical analysis of computational modeling resultsFound previously unobserved decoupling of the thumb subdomain from the non-nucleoside binding pocket and polymerase-active siteExtensive experience with molecular dynamics simulations of proteins, Principal Component Analysis, Visual Molecular Dynamics software, and scripting in Python, Unix, and Tcl