@article{daubert_afroz_borodin_seo_boyle_henderson_2022, title={Solvate Structures and Computational/Spectroscopic Characterization of LiClO4 Electrolytes}, ISSN={["1932-7455"]}, DOI={10.1021/acs.jpcc.2c03805}, abstractNote={A Raman spectral evaluation of numerous crystalline solvates with lithium perchlorate (LiClO4) has been conducted over a wide temperature range. Two new solvate crystal structures─(PMDETA)1:LiClO4 and (THF)1:LiClO4 with N,N,N′,N″,N″-pentamethyldiethylenetriamine and tetrahydrofuran─have been determined to aid in this study. With a help of density functional theory (DFT) and molecular dynamics (MD) simulations, the spectroscopic data have been correlated with varying modes of ClO4–···Li+ cation coordination within the solvate structures to create a characterization tool to facilitate the Raman band assignments for the determination of ionic association interactions within solid and liquid electrolytes containing LiClO4. This study demonstrates that many of the spectroscopic evaluation conclusions reported in the scientific literature for LiClO4-based electrolytes are inaccurate.}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Daubert, James S. and Afroz, Taliman and Borodin, Oleg and Seo, Daniel M. and Boyle, Paul D. and Henderson, Wesley A.}, year={2022}, month={Aug} }
 @article{beisel_afroz_2016, title={Rethinking the Hierarchy of Sugar Utilization in Bacteria}, volume={198}, ISSN={["1098-5530"]}, DOI={10.1128/jb.00890-15}, abstractNote={ABSTRACT Bacteria are known to consume some sugars over others, although recent work reported by Koirala and colleagues in this issue of the Journal of Bacteriology (S. Koirala, X. Wang, and C. V. Rao, J Bacteriol 198:386–393, 2016, http://dx.doi.org/10.1128/JB.00709-15) revealed that individual cells do not necessarily follow this hierarchy. By studying the preferential consumption of l-arabinose over d-xylose in Escherichia coli, those authors found that subpopulations consume one, the other, or both sugars through cross-repression between utilization pathways. Their findings challenge classic assertions about established hierarchies and can guide efforts to engineer the simultaneous utilization of multiple sugars.}, number={3}, journal={JOURNAL OF BACTERIOLOGY}, author={Beisel, Chase L. and Afroz, Taliman}, year={2016}, month={Feb}, pages={374–376} }
 @article{afroz_luo_beisel_2015, title={Impact of Residual Inducer on Titratable Expression Systems}, volume={10}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0137421}, abstractNote={Inducible expression systems are widely employed for the titratable control of gene expression, yet molecules inadvertently present in the growth medium or synthesized by the host cells can alter the response profile of some of these systems. Here, we explored the quantitative impact of these residual inducers on the apparent response properties of inducible systems. Using a simple mathematical model, we found that the presence of residual inducer shrinks the apparent dynamic range and causes the apparent Hill coefficient to converge to one. We also found that activating systems were more sensitive than repressing systems to the presence of residual inducer and the response parameters were most heavily dependent on the original Hill coefficient. Experimental interrogation of common titratable systems based on an L-arabinose inducible promoter or a thiamine pyrophosphate-repressing riboswitch in Escherichia coli confirmed the predicted trends. We finally found that residual inducer had a distinct effect on “all-or-none” systems, which exhibited increased sensitivity to the added inducer until becoming fully induced. Our findings indicate that residual inducer or repressor alters the quantitative response properties of titratable systems, impacting their utility for scientific discovery and pathway engineering.}, number={9}, journal={PLOS ONE}, author={Afroz, Taliman and Luo, Michelle L. and Beisel, Chase L.}, year={2015}, month={Sep} }
 @article{afroz_seo_han_boyle_henderson_2015, title={Structural Interactions within Lithium Salt Solvates: Acyclic Carbonates and Esters}, volume={119}, ISSN={["1932-7447"]}, DOI={10.1021/acs.jpcc.5b00309}, abstractNote={Solvate crystal structures serve as useful models for the molecular-level interactions within the diverse solvates present in liquid electrolytes. Although acyclic carbonate solvents are widely used for Li-ion battery electrolytes, only three solvate crystal structures with lithium salts are known for these and related solvents. The present work, therefore, reports six lithium salt solvate structures with dimethyl and diethyl carbonate, (DMC)2:LiPF6, (DMC)1:LiCF3SO3, (DMC)1/4:LiBF4, (DEC)2:LiClO4, (DEC)1:LiClO4, and (DEC)1:LiCF3SO3 and four with the structurally related methyl and ethyl acetate, (MA)2:LiClO4, (MA)1:LiBF4, (EA)1:LiClO4, and (EA)1:LiBF4.}, number={13}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Afroz, Taliman and Seo, Daniel M. and Han, Sang-Don and Boyle, Paul D. and Henderson, Wesley A.}, year={2015}, month={Apr}, pages={7022–7027} }
 @article{afroz_biliouris_boykin_kaznessis_beisel_2015, title={Trade-offs in Engineering Sugar Utilization Pathways for Titratable Control}, volume={4}, ISSN={["2161-5063"]}, DOI={10.1021/sb400162z}, abstractNote={Titratable systems are common tools in metabolic engineering to tune the levels of enzymes and cellular components as part of pathway optimization. For nonmodel microorganisms with limited genetic tools, inducible sugar utilization pathways offer built-in titratable systems. However, these pathways can exhibit undesirable single-cell behaviors that hamper the uniform and tunable control of gene expression. Here, we applied mathematical modeling and single-cell measurements of l-arabinose utilization in Escherichia coli to systematically explore how sugar utilization pathways can be altered to achieve desirable inducible properties. We found that different pathway alterations, such as the removal of catabolism, constitutive expression of high-affinity or low-affinity transporters, or further deletion of the other transporters, came with trade-offs specific to each alteration. For instance, sugar catabolism improved the uniformity and linearity of the response at the cost of requiring higher sugar concentrations to induce the pathway. Within these alterations, we also found that a uniform and linear response could be achieved with a single alteration: constitutively expressing the high-affinity transporter. Equivalent modifications to the d-xylose utilization pathway yielded similar responses, demonstrating the applicability of our observations. Overall, our findings indicate that there is no ideal set of typical alterations when co-opting natural utilization pathways for titratable control and suggest design rules for manipulating these pathways to advance basic genetic studies and the metabolic engineering of microorganisms for optimized chemical production.}, number={2}, journal={ACS SYNTHETIC BIOLOGY}, author={Afroz, Taliman and Biliouris, Konstantinos and Boykin, Kelsey E. and Kaznessis, Yiannis and Beisel, Chase L.}, year={2015}, month={Feb}, pages={141–149} }
 @article{afroz_biliouris_kaznessis_beisel_2014, title={Bacterial sugar utilization gives rise to distinct single-cell behaviours}, volume={93}, ISSN={["1365-2958"]}, DOI={10.1111/mmi.12695}, abstractNote={Inducible utilization pathways reflect widespread microbial strategies to uptake and consume sugars from the environment. Despite their broad importance and extensive characterization, little is known how these pathways naturally respond to their inducing sugar in individual cells. Here, we performed single‐cell analyses to probe the behaviour of representative pathways in the model bacterium Escherichia coli. We observed diverse single‐cell behaviours, including uniform responses (d‐lactose, d‐galactose, N‐acetylglucosamine, N‐acetylneuraminic acid), ‘all‐or‐none’ responses (d‐xylose, l‐rhamnose) and complex combinations thereof (l‐arabinose, d‐gluconate). Mathematical modelling and probing of genetically modified pathways revealed that the simple framework underlying these pathways – inducible transport and inducible catabolism – could give rise to most of these behaviours. Sugar catabolism was also an important feature, as disruption of catabolism eliminated tunable induction as well as enhanced memory of previous conditions. For instance, disruption of catabolism in pathways that respond to endogenously synthesized sugars led to full pathway induction even in the absence of exogenous sugar. Our findings demonstrate the remarkable flexibility of this simple biological framework, with direct implications for environmental adaptation and the engineering of synthetic utilization pathways as titratable expression systems and for metabolic engineering.}, number={6}, journal={MOLECULAR MICROBIOLOGY}, author={Afroz, Taliman and Biliouris, Konstantinos and Kaznessis, Yiannis and Beisel, Chase L.}, year={2014}, month={Sep}, pages={1093–1103} }
 @article{afroz_beisel_2013, title={Understanding and exploiting feedback in synthetic biology}, volume={103}, ISSN={["1873-4405"]}, DOI={10.1016/j.ces.2013.02.017}, abstractNote={Synthetic biology employs traditional engineering concepts in the construction of cells and organisms. One of the most fundamental concepts is feedback, where the activity of a system is influenced by its output. Feedback can imbue the system with a range of desirable properties such as reducing the rise time or exhibiting an ultrasensitive response. Feedback is also commonly found in nature, further supporting the incorporation of feedback into synthetic biological systems. In this review, we discuss the common attributes of negative and positive feedback loops in gene regulatory networks, whether alone or in combination, and describe recent applications of feedback in metabolic engineering, population control, and the development of advanced biosensors. The examples principally come from synthetic systems in the bacterium Escherichia coli and in the budding yeast Saccharomyces cerevisiae, the two major workhorses of synthetic biology. Through this review, we argue that biological feedback represents a powerful yet underutilized tool that can advance the construction of biological systems.}, journal={CHEMICAL ENGINEERING SCIENCE}, author={Afroz, Taliman and Beisel, Chase L.}, year={2013}, month={Nov}, pages={79–90} }
 @inproceedings{seo_afroz_ly_o'connell_boyle_henderson_2012, title={A "Looking Glass" into electrolyte properties: Cyclic carbonate and ester-LiClO4 mixtures}, volume={41}, number={41}, booktitle={Rechargeable lithium and lithium ion batteries}, author={Seo, D. M. and Afroz, T. and Ly, Q. and O'Connell, M. and Boyle, P. D. and Henderson, W. A.}, year={2012}, pages={11–15} }