The Biochemical and Biophysical Systems Group

The Biochemical and Biophysical Systems Group is formed by experimental and computational biologists who use a wide range of expertise to approach cutting-edge problems in systems biology.  We use multidisciplinary approaches – ranging from molecular biology through proteomics to modeling – to investigate microbes and microbial communities as they respond to different perturbations, including those relevant to emerging issues in bioenergy, bioremediation, and pathogenesis.  In addition to developing computational tools to describe and predict biological systems, we are combining experimental efforts with modeling and simulation methods to design and develop safe and effective therapeutics.  Our principal unifying objective is to gain a predictive understanding of protein-mediated activities that are critical to cells and their interactions in living systems.

Recent Publications

Multiphase Separation of Copper Nanowires
Fang Qian, Pui Ching Lan, Tammy Olson, Cheng Zhu, Eric B. Duoss, Christopher M. Spadaccini, and T. Yong-Jin Han
Chem. Commun.(2016) 52, 11627.

Computational Enzymology and Organophosphorus Degrading Enzymes: Promising Approaches toward Remediation Technologies of Warfare Agents and Pesticides
Teodorico C. Ramalho, Alexandre A. de Castro, Daniela R. Silva, Maria Cristina Silva, Tanos C. C. Franca, Brian J. Bennion and Kamil Kuca
Current Medicinal Chemistry (2016) 23, 1041-1061.

An Electrostatic Funnel in the GABA-Binding Pathway
Timothy S. Carpenter and Felice C. Lightstone
PLoS Comput. Biol. (2016) 12(4): e1004831.

Bioadsorption of Rare Earth Elements through Cell Surface Display of Lanthanide Binding Tags
Dan M. Park, David W. Reed, Mimi C. Yung, Ali Eslamimanesh, Malgorzata M. Lencka, Andrzej Anderko, Yoshiko Fujita, Richard E. Riman, Alexandra Navrotsky, and Yongqin Jiao
Environ Sci Technol. (2016) 50 (5), pp 2735–2742.

Application of a Physiologically-based Pharmacokinetic Model to Study Theophylline Metabolism and Its Interactions with Ciprofloxacin and Caffeine
A. Navid, D. M. Ng, S. E. Wong, F. C. Lightstone
CPT: Pharmacometrics & Systems Pharmacology (2016) 5 (2), 74-81.

Supercapacitors Based on Three-Dimensional Hierarchical Graphene Aerogels with Periodic Macropores
Cheng Zhu, Tianyu Liu, Fang Qian, T. Yong-Jin Han, Eric B. Duoss, Joshua D. Kuntz, Christopher M. Spadaccini, Marcus A. Worsley, and Yat Li
Nano Lett. (2016).

Shock Wave-Induced Damage of a Protein by Void Collapse
Edmond Y. Lau, Max L. Berkowitz, Eric Schwegler
Biophysical Journal (2016) 110(1), 147–156.

Carbonic Anhydrase Mimics for Enhanced CO2 Absorption in an Amine-Based Capture Solvent
Rachael A. Kelsey, David A. Miller, Sean R. Parkin, Kun Liu, Joe E. Remias, Yue Yang, Felice C. Lightstone, Kunlei Liu, Cameron A. Lippert and Susan A. Odom
Dalton Transactions (2016) 45, 324-333.

Cyanobacterial reuse of extracellular organic carbon in microbial mats
Rhona K. Stuart, Xavier Mayali, Jackson Z. Lee, R. Craig Everroad, Mona Hwang, Brad M. Bebout, Peter K. Weber, Jennifer Pett-Ridge, Michael P. Thelen
The ISME J (2015) Advanced online publication 23 October 2015.

Large-scale First-Principles molecular dynamics simulations with electrostatic embedding: application to acetylcholinesterase catalysis
Jean-Luc Fattebert, Edmond Y. Lau, Brian J. Bennion, Patrick Huang, and Felice C. Lightstone
J. Chem. Theory Comput. (2015) 11 (12), 5688–5695.

Do Genome-scale Models Need Exact Solvers or Clearer Standards?
Ali Ebrahim, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P Burgard, Roger L Chang, Andreas Dräger, Iman Famili, Adam M Feist, Ronan MT Fleming, Stephen S Fong, Vassily Hatzimanikatis, Markus J Herrgård, Allen Holder, Michael Hucka, Daniel Hyduke, Neema Jamshidi, Sang Yup Lee, Nicolas Le Novère, Joshua A Lerman, Nathan E Lewis, Ding Ma, Radhakrishnan Mahadevan, Costas Maranas, Harish Nagarajan, Ali Navid, Jens Nielsen, Lars K Nielsen, Juan Nogales, Alberto Noronha, Csaba Pal, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Nathan D Price, Jennifer L Reed, Michael Saunders, Ryan S Senger, Nikolaus Sonnenschein, Yuekai Sun, Ines Thiele
Molecular Systems Biology (2015) 11, 831.

Low-Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography
Geoffrey K. Feld, Michael Heymann, W. Henry Benner, Tommaso Pardini, Ching-Ju Tsai, Sébastien Boutet, Matthew A. Coleman, Mark S. Hunter, Xiaodan Li, Marc Messerschmidt, Achini Opathalage, Bill Pedrini, Garth J. Williams, Bryan A. Krantz, Seth Fraden, Stefan Hau-Riege, James E. Evans, Brent W. Segelke, and Matthias Frank
J. Appl. Cryst. (2015) 48, 1072-1079.

Transposon mutagenesis paired with deep sequencing of Caulobacter crescentus under uranium stress reveals genes essential for detoxification and stress tolerance
Mimi C. Yung, Dan M. Park, K. Wesley Overton, Matthew J. Blow, Cindi A. Hoover, John Smit, Sean R. Murray, Dante P. Ricci, Beat Christen, Grant R. Bowman, Yongqin Jiao
J. Bacteriol. (2015) 197, 3160-72.