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Bioenergy & Defense

Bioenergy & Defense Technologies



Chaudhari, MI; Pratt, LR; and SB Rempe. 2017. Utility of chemical computations in predicting solution free energies of metal ions. Molecular Simulation (invited special issue on Proceedings of the 4th International Conference on Molecular Simulation; submitted).

VanGordon, MR; Gyawali, G; Rick, SW; and SB Rempe. 2017. Atomistic study of intramolecular interactions in the closed-state channelrhodopsin chimera, C1C2. Biophys. J. (in print).


Chambers, M.; Mallory, S.A.; Malone, H.; Gao, Y.; Anthony, S.M.; Yi, Y.; Cacciuto, A.; Yu, Y., Lipid Membrane-Assisted Condensation and Assembly of Amphiphilic Janus Particles. Soft Matter, 2016, 12, 9151-9157.

Collins, A.M.; Timlin, J.A.; Anthony, S.M.; Montano, G.A., Amphiphilic block copolymers as flexible membrane materials generating structural and functional mimics of green bacterial antenna complexes. Nanoscale, 2016, 8, 15056-15063.

Stevens, MJ and SLB Rempe. 2016. Ion specific effects in carboxylate binding. J. Phys. Chem. B 120:12519-12530.

Chaudhari, MI; Pratt, LR; Soto, F; Balbuena, P; and SB Rempe. 2016. Scaling atomic partial charges of carbonate solvents for lithium ion solvation and diffusion. J. Chem. Theory Comput. 12:5709-5718.

La Bauve, S; Vernon, BC; Ye, D; Rogers, DM; Siegrist, CM; Carson, B; Zheng, A; Rempe, SB; Kielian, MC; Shreve, AP; Kent, MS. 2016. New method for measuring the anchoring energy of strongly-bound membrane-associated proteins. BBA: Biomembranes 1858:2753-2762.

Pratt, LR, Chaudhari, MI and SB Rempe. 2016. Statistical analyses of hydrophobic interactions: A mini-review. J. Phys. Chem. B 120:6455-6460 (invited).

You, X; Chaudhari, MI; Rempe, SB; and LR Pratt. 2016. Dielectric relaxation of ethylene carbonate and propylene carbonate from molecular dynamics simulations. J. Phys. Chem. B 120:1849-53 (invited Bruce Garrett Festschrift).

Chaudhari, MI; Rempe, SB; Asthagiri, D; Tan, L; and LR Pratt. 2016. Molecular theory and the effects of solute attractive forces on hydrophobic interactions. J. Phys. Chem. B 120:1864-70 (invited Bruce Garrett Festschrift).


Sanchez, L.; Patton, P.; Anthony, S. M.; Yi, Y.; Yu, Y., Tracking Single-Particle Rotation During Macrophage Uptake. Soft Matter, 2015, 11, 5346-5352.

Anthony, S. M.; Yu, Y., Tracking Single Particle Rotation: Probing Dynamics in Four Dimensions. Analytical Methods. 2015, 7, 7020-7028.

You, X; Chaudhari, MI; Rempe, SB; and LR Pratt. 2015. Dielectric properties of ethylene carbonate and propylene carbonate using molecular dynamics simulations. ECS Trans. 69:107-111.

Anishkin, A; Vanegas, J.; Rogers, DM; Lorenzi, PL; Chan, WK; Purwaha, P; Weinstein, J; Sukharev, S; and SB Rempe. 2015. Catalytic role of the substrate defines specificity of therapeutic L-asparaginase. J. Mol. Bio. 427:2867-85.

Chaudhari, MI; Soniat, M; and SB Rempe. 2015. Octa-coordination and the aqueous Ba2+ ion. J. Phys. Chem. B 119:8746-53.

Soniat, M; Rogers, DM and SB Rempe. 2015. Dispersion- and exchange-corrected density functional theory for sodium ion hydration. J. Chem. Theory Comput. 11:2958-67.

Leung, K; Chaudhari, MI; Rempe, SB; Fenton, KR; Pratt, HD; Staiger, CL: and G. Nagasubramanian. 2015. Density functional theory and conductivity studies of boron-based anion receptors. J. Electrochem. Soc. 162:A1927-34.

Mason, PE; Ansell, S; Neilson, GW; and SB Rempe. 2015. Neutron scattering studies of the hydration structure of Li+(aq). J Phys Chem B. 119:2003-9.

Rogers, DM; Kent, M; and SB Rempe. 2015. Molecular basis of host-membrane association for the Dengue virus envelope protein. Biochim. Biophys. Acta-Biomembranes 1848:1041-52.


Ruffing AM and Trahan CA. Biofuel toxicity and mechanisms of biofuel tolerance in three model cyanobacteria. Algal Research. 2014. 5:121-132.

Chen, B.; Jia, Y.; Gao, Y.; Sanchez, L.; Anthony, S.M.; Yu, Y., Janus particles as artificial antigen-presenting cells for T cell Activation. ACS Applied Materials & Interfaces. 2014, 6, 18435.

Collins AM, Jones HDT, McBride RC, Behnke, CA, Timlin JA, "Host cell pigmentation in Scenedesmus dimorphus as a beacon for nascent parasite infection," Biotechnology and Bioengineering, 2014, 111:9, 1748-1757.

Hanson DT, Collins AM, Jones HDT, Roesgen J, Lopez-Nieves S, Timlin JA, "On-line stable isotope gas exchange reveals an inducible but leaky carbon concentrating mechanism in Nannochloropsis salina," Photosynthesis Research, 2014, 121:311-322.

Chen, K.; Anthony, S. M.; Granick, S., Extending Particle Tracking Capability with Delaunay Triangulation. Langmuir 2014, 30, 4760-4766.

Reichardt TA, Collins AM, McBride RC, Behnke, CA, Timlin, JA, "Spectroradiometric monitoring for open outdoor culturing of algae and cyanobacteria," Applied Optics, 2014, 53:24, F31-F45.

Ruffing AM. Improved free fatty acid production in cyanobacteria with Synechococcus sp. PCC 7002 as host. Frontiers in Bioengineering and Biotechnology. 2014.2:17.

Jiang, S.; Yan, J.; Whitmer, J. K.; Anthony, S. M.; Luijten, E.; Granick, S., Orientationally Glassy Crystals of Janus Spheres. Physical Review Letters 2014, 112, 218301.


Chen W, Han D, Li Y, Jones HDT, Timlin JA, Hu Q, Semi-Quantitative and Absolute Quantitative Analyses of Biochemical Composition of Microalgae. In Handbook of Microalgal Cultures - Second Edition. Hu R, (Ed.), Wiley-Blackwell, 2013 - in press.

Davis RW, Jones HDT, Collins AM, Ricken JB, Sinclair MB, Timlin JA and Singh S. "Label-free measurement of algal triacylglyceride production using fluorescence hyperspectral imaging," Algal Research, 2013, in press.

Kilcrease, JA, Collins, AM, Richins, RD, Timlin, JA and O'Connell, MA, "Multiple microscopic approaches demonstrate linkage between chromoplast architecture and carotenoid composition in diverse capsicum annum fruit," The Plant Journal, 2013, 76:6, 1074-1083.

Liberton M, Collins A, Page L, O'Dell W, O'Neill H, Urban V, Timlin JA, Pakrasi, HB, "Probing the consequences of antenna modification in cyanobacteria," Photosynthesis Research, 2013, 1-8.

Ruffing AM. RNA-Seq analysis and targeted mutagenesis for improved free fatty acid production in an engineered cyanobacterium. Biotechnology for Biofuels. 2013. 6:113.

Reyes-Ortiz V, Heins RA, Cheng G, Kim EY, Vernon BC, Elandt RB, Adams PD, Sale KL, Hadi MZ, Simmons BA, Kent MS, and Tullman-Erck D. Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrate. Biotechnology for Biofuels. 2013. Accepted.

Ruffing AM. Borrowing genes from Chlamydomonas reinhardtii for free fatty acid produciton in engineered cyanobacteria. J. Appl. Phycol. 2013. DOI 10.1007/s10811-013-9993-7.

Ruffing AM. Metabolic Engineering of Hydrocarbon Biosynthesis for Biofuel Production. Book chapter in Liquid, Gaseous and Solid Biofuels - Conversion Techniques. Fang Z (ed). InTech. 2013. ISBN 978-953-51-1050-7.


Laurens LM, Dempster TA, Jones HDT, Wolfrum EJ, Van Wychen S, McAllister JSP, Rencenberger M, Parchert KJ, Gloe LM. Algae biomass constituent analysis: Method uncertainties and investigation of the underlying measuring chemistries. Analytical Chemistry. 2012.84:1879-1887.

Powell AJ, Parchert KJ, Bustamante J, Ricken JB, Hutchinson M, and Natvig DO. Thermophilic fungi in an aridland ecosystem. Mycologia. 2012. 104: 813-825.

Harper JC, Brozik SM, Brinker CJ, Kaehr B. Biocompatible microfabrication of 3D isolation chambers for targeted confinement of individual cells and their progeny. Anal. Chem. 2012. 84, 8985-8989.

Achyuthan KE, Allen A, Arango DC, Harper JC, Whitten DG, Brozik SM. High-throughput screening of transglutaminase activity using plasmonic fluorescent nanocomposites. Anal. Sci. 2012. 28, 905-910.

Harper JC, Edwards TL, Savage T, Harbaugh S, Kelley-Loughnane N, Stone MO, Brinker CJ, Brozik SM. Orthogonal cell-based biosensing: Fluorescent, electrochemical, and colorimetric detection with silica-immobilized cellular communities integrated with an ITO/plastic laminate cartridge. Small. 2012. 8, 2743-2751. FRONT COVER.

Holland TD, Harper JC, Dolan PL, Manginell MM, Arango DC, Rawlings JA, Apblett CA, Brozik SM. Rational redesign of glucose oxidase for improved function in biological fuel cells. PLoS ONE. 2012. 7, e37924.

Cheng G, Datta S, Liu Z, Wang C ,Murton JK, Brown P, Jablin MS, Dubey M, Majewski J, Halbert C, Browning J, Esker A, Watson BJ, Zhang H, Hutcheson SW, Huber D, Sale KL, Simmons BA, Kent MS. Interactions of endoglucanases with amorphous cellulose films resolved by neutron reflectometry and quartz crystal microbalance with dissipation monitoring. Langmuir. 2012. In press.

Ruffing AM and Jones HDT. Physiological effects of free fatty acid production in genetically engineered Synechococcus elongatus PCC 7942. Biotechnology and Bioengineering. 2012. 109(9): 2190-2199.

Aaron JS, Carson BD & Timlin JA. Characterization of differential toll-like receptor responses below the optical diffraction limit. Small. 2012. 8(19): 3041-3049.

Aaron JS, Timlin JA. Advanced Optical Imaging of Endocytosis in Molecular Regulation of Endocytosis. Ed: Brian Ceresa. 2012. ISBN: 978-953-51-0662-3, InTech.

Collins AM, Liberton M, Garcia OF, Jones HDT, Pakrasi HB, and Timlin JA. Photosynthetic pigment localization and thylakoid membrane morphology are altered in Synechocystis 6803 phycobilisome mutants. Plant Phys. 2012.158: 1600-1609.

Reichardt TA, Garcia OF, Collins AM, Jones HDT, Ruffing AM, and Timlin TA. Spectroradiometric monitoring of Nannochloropsis salina growth. Algal Research 2012. 1(1): 22-31.

Jones HDT, Haaland DM, Sinclair MB, Melgaard DK, Collins AM, and Timlin JA. Preprocessing strategies to improve MCR analyses of hyperspectral images. Chemom. Intell. Lab. Syst. 2012. 117: 149-158.

Zarzar LD, Swartzentruber BS, Harper JC, Dunphy DR, Brinker CJ, Aizenberg J, Kaehr B. Multiphoton lithography of nanocrystalline platinum and palladium for site-specific catalysis in 3D microenvironments. J. Am. Chem. Soc. 2012. 134: 4007-4010.

Achyuthan KE, Achyuthan AM, Brozik SM, Dirk SM, Lujan T, Romero J, Whitten DG, Harper JC. Plasmonic fluorescent nanocomposites of cyanines self-assembled upon gold nanoparticle scaffolds. 2012. Anal. Sci. 2012. 28: 433-438.


Aaron JS, Greene A, Kotula PG, Bachand GD, Timlin JA. Advanced optical imaging reveals dependence of particle geometry on interactions between CdSe quantum dots and immune cells. Small 2011. 7(3): 334-341.

Collins AM, Jones HDT, Han D, Hu Q, Beechem TE, Timlin JA. Carotenoid distribution in living cells of Haematococcus pluvialis (Chlorophyceae). PLoS ONE. 2011. 6(9): e24302.

Ruffing AM. Engineered Cyanobacteria: Teaching an old bug new tricks. Bioengineered Bugs. 2011. 2(3).

Cheng G, Liu ZL, Murton JK, Brown P, Jablin M, Dubey M, Majewshi J, Halbert C, Browning J, Ankner J, Akgun B, Wang C, Esker AR, Sale KL, Simmons BA, Kent MS. Neutron reflectometry and QCM-D study of the interaction of cellulases with films of amporphous cellulose. Biomacromolecules. 2011. 12(6): 2216-2224.

Cheng G, Varanasi P, Li C, Liu H, Melnichenko YB, Simmons BA, Kent MS, Singh S. Transition of cellulose crystalline structure and surface morphology of biomass as a function of ionic liquid pretreatment and its relation to enzymatic hydrolysis. Biomacromolecules. 2011. 12(4): 933-941.


Davis RW, Timlin JA, Noek R, Kaiser JN, Jones HDT, Lane TW. Accurate detection of low levels of fluorescence emission in autofluorescent background: Francisella-infected macrophage cells. Microscopy & Microanalysis. 2010. 16:478.

Spendier K, Carroll-Portillo A, Lidke KA, Wilson BS, Timlin JA, Thomas JL. Distribution and dynamics of rat basophilic leukemia immunoglobulin E receptors (FcεRI) on planar ligand-presenting surfaces. Biophysical Journal. 2010. 99:388.

Carroll-Portillo A, Spendier K, Lidke K, Pfeiffer J, Lidke D, Thomas J, Wilson B, Timlin JA. Formation of a mast cell synapse: FcεRI membrane dynamics upon binding mobile or immobilized ligands on surfaces. Journal of Immunology. 2010.184:1328.

Kent MS, Yim H, Murton JK, Sasaki DY, Satija S, Akgun B, Nanda H, Curtis JE, Majewski J, Morgan CR, Engen JR. A study of the conformation of HIV Nef bound to lipid membranes by neutron reflectometry. Biophysical Journal. 2010.

Kent MS, Cheng G, Carles EL, Dibble DC, Zendejas F, Rodriguez MA, Tran H, Holmes B, Simmons BA, Knierim B, Auer M, Banuelos JL, Urquidi J, Hjelm RP. Study of enzymatic digestion of cellulose by small angle neutron scattering. Biomacromolecules. 2010. 11:357.

Pedroso MC, Sinclair MB, Jones HDT, Haaland DM. Hyperspectral confocal fluorescence microscope: A new look into the cell. Microscopy Today. 2010. 18(05): 14-18.


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