@article{xiao_kuang_burke_chushak_farmer_mirau_naik_hall_2020, title={In Silico Discovery and Validation of Neuropeptide-Y-Binding Peptides for Sensors}, volume={124}, ISSN={["1520-5207"]}, DOI={10.1021/acs.jpcb.9b09439}, abstractNote={Wearable sensors for human health, performance, and state monitoring, which have a linear response to the binding of biomarkers found in sweat, saliva, or urine, are of current interest for many applications. A critical part of any device is a biological recognition element (BRE) that is able to bind a biomarker at the surface of a sensor with a high affinity and selectivity to produce a measurable signal response. In this study, we discover and compare 12-mer peptides that bind to neuropeptide Y (NPY), a stress and human health biomarker, using independent and complimentary experimental and computational approaches. The affinities of the NPY-binding peptides discovered by both methods are equivalent and below the micromolar level, which makes them suitable for application in sensors. The in silico design protocol for peptide-based BREs is low cost, highly efficient, and simple, suggesting its utility for discovering peptide binders to a variety of biomarker targets.}, number={1}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Xiao, Xingqing and Kuang, Zhifeng and Burke, B. J. and Chushak, Yaroslav and Farmer, Barry L. and Mirau, Peter A. and Naik, Rajesh R. and Hall, Carol K.}, year={2020}, month={Jan}, pages={61–68} }
 @article{kim_farmer_yingling_2017, title={Effect of graphene oxidation rate on adsorption of poly-thymine single stranded DNA}, volume={4}, number={8}, journal={Advanced Materials Interfaces}, author={Kim, H. S. and Farmer, B. L. and Yingling, Y. G.}, year={2017} }
 @article{pandey_jacobs_farmer_2017, title={Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation}, volume={146}, ISSN={["1089-7690"]}, DOI={10.1063/1.4983222}, abstractNote={The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ∼ 1.3), random-coil (D ∼ 1.75), and globular (D ∼ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.}, number={19}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Pandey, R. B. and Jacobs, D. J. and Farmer, B. L.}, year={2017}, month={May} }
 @article{pandey_farmer_gerstman_2015, title={Self-assembly dynamics for the transition of a globular aggregate to a fibril network of lysozyme proteins via a coarse-grained Monte Carlo simulation}, volume={5}, ISSN={["2158-3226"]}, DOI={10.1063/1.4921074}, abstractNote={The self-organizing dynamics of lysozymes (an amyloid protein with 148 residues) with different numbers of protein chains, Nc = 1,5,10, and 15 (concentration 0.004 – 0.063) is studied by a coarse-grained Monte Carlo simulation with knowledge-based residue-residue interactions. The dynamics of an isolated lysozyme (Nc = 1) is ultra-slow (quasi-static) at low temperatures and becomes diffusive asymptotically on raising the temperature. In contrast, the presence of interacting proteins leads to concentration induced protein diffusion at low temperatures and concentration-tempering sub-diffusion at high temperatures. Variation of the radius of gyration of the protein with temperature shows a systematic transition from a globular structure (at low T) to a random coil (high T) conformation when the proteins are isolated. The crossover from globular to random coil becomes sharper upon increasing the protein concentration (i.e. with Nc = 5,10), with larger Rg at higher temperatures and concentration; Rg becomes smaller on adding more protein chains (e.g. Nc = 15) a non-monotonic response to protein concentration. Analysis of the structure factor (S(q)) provides an estimate of the effective dimension (D ≥ 3, globular conformation at low temperature, and D ∼ 1.7, random coil, at high temperatures) of the isolated protein. With many interacting proteins, the morphology of the self-assembly varies with scale, i.e. at the low temperature (T = 0.015), D ∼ 2.9 on the scale comparable to the radius of gyration of the protein, and D ∼ 2.3 at the large scale over the entire sample. The global network of fibrils appears at high temperature (T = 0.021) with D ∼ 1.7 (i.e. a random coil morphology at large scale) involving tenuous distribution of micro-globules (at small scales).}, number={9}, journal={AIP ADVANCES}, author={Pandey, R. B. and Farmer, B. L. and Gerstman, Bernard S.}, year={2015}, month={Sep} }
 @article{pandey_farmer_2014, title={Aggregation and network formation in self-assembly of protein (H3.1) by a coarse-grained Monte Carlo simulation}, volume={141}, number={17}, journal={Journal of Chemical Physics}, author={Pandey, R. B. and Farmer, B. L.}, year={2014} }