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

Efficient Computational Modeling of Human Ventricular Activation and Its Electrocardiographic Representation: A Sensitivity Study
Johathan P. Cranford, Thomas J. O’Hara, Christopher T. Villongco, Omar M. Hafez, Robert C. Blake, Joseph Loscalzo, Jean-Luc Fattebert, David F. Richards, Xiaohua Zhang, James N. Glosli, Andrew D. McCulloch, David E. Krummen, Felice C. Lightstone, Sergio E. Wong
Cardiovascular Engineering and Technology (2018) 9, Online First.

Development and characterization of a thermophilic, lignin degrading microbiota
Shannon J. Ceballos, Chaowei Yu, Josh T. Claypool, Steven W. Singer, Blake A. Simmons, Michael P. Thelen, Christopher W. Simmons, Jean S. VanderGheynst
Process Biochemistry (2017) 63, 193-203.

Computational lipidomics of the neuronal plasma membrane
Helgi I. Ingólfsson, Timothy S. Carpenter, Harsh Bhatia, Peer-Timo Bremer, Siewert J.Marrink, Felice C. Lightstone
Biophysics Journal (2017) 113 (10), 2271-2280.

The biodistribution and pharmacokinetics of the oxime acetylcholinesterase reactivator RS194B in guinea pigs 
M. A Malfatti, H. A. Enright, N. A. Be, E. A. Kuhn, S. Hok, M. W. NcNerney, V. Lao, T. H. Nguyen, F. C. Lightstone, T. S. Carpenter, B. J. Bennion, C. A. Valdez
Chemico-Biological Interactions (2017) 277, 159-167.

Recovery of Rare Earth Elements from Low-Grade Feedstock Leachates using Engineered Bacteria
Dan M. Park, Aaron Brewer, David W. Reed, Laura N. Lammers, Yongqin Jiao
Environmental Science and Technology (2017) 51 (22), 13471-13480.

Measuring Cyanobacterial Metabolism in Biofilms with NanoSIMS Isotope Imaging and Scanning Electron Microscopy (SEM)
Rhona K. Stuart, Xavier Mayali, Michael P. Thelen, Jennifer Pett-Ridge, and Peter K. Weber
Bio-protocol (2017) 7 (9), e2263.

Simultaneous electrical recording of cardiac electrophysiology and contraction on chip
Fang Qian, Chao Huang, Yi-Dong Lin, Anna N. Ivanovskaya, Thomas J. O'Hara, Ross H. Booth, Cameron J. Creek, Heather A. Enright, David A. Soscia, Anna M. Belle, Ronglih Liao, Felice C. Lightstone, Kristen S. Kulp and Elizabeth K. Wheeler
Lab on a Chip (2017) 17, 1732-1739.

Predicting a Drug’s Membrane Permeability: A Computational Model Validated With In Vitro Permeability Assay Data
Brian J. Bennion, Nicholas A. Be, Margaret Windy McNerney, Victoria Lao, Emma M. Carlson, Carlos A. Valdez, Michael A. Malfatti, Heather A. Enright, Tuan H Nguyen, Felice C Lightstone, and Timothy S Carpenter
J. Phys. Chem. B (2017) 121 (20), 5228-5237.

Re-directing bacterial microcompartment systems to enhance recombinant expression of lysis protein E from bacteriophage ϕX174 in Escherichia coli
Mimi C. Yung, Feliza A. Bourguet, Timothy S. Carpenter and Matthew A. Coleman
Microb. Cell Fact. (2017) 16 (71).

Enhancement of antigen-specific CD4+ and CD8+ T cell responses using a self-assembled biologic nanolipoprotein particle vaccine
Dina Weilhammer, Alexis D. Dunkle, Craig D. Blanchette, Nicholas O. Fischer, Michele Corzett, Doerte Lehman, Tyler Boone, Paul Hoeprich, Adam Driks, Amy Rasley
Vaccine (2017) 35 (11), 1475-1481.

Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus
Dan M. Park, K. Wesley Overton, Megan J. Liou, Yongqin Jiao
Molecular Microbiology (2017) 104(1), 46-64.

A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding Antithrombin
Xiaohua Zhang, Horacio Perez-Sanchez, and Felice C. Lightstone
Current Topics in Medicinal Chemistry (2017) 17, 1-9.

Long-term diffusion of U(VI) in bentonite: Dependence on density
Claudia Joseph, Jens Mibus, Paul Trepte, Christa Müller, Vinzenz Brendler, Dan M. Park, Yongqin Jiao, Annie B. Kersting, Mavrik Zavarin
Sci. Total Environ. (2017) 575, 207–218.

Interactions of Plutonium with Pseudomonas sp. Strain EPS-1W and Its Extracellular Polymeric Substances
M. A. Boggs, Y. Jiao, Z. Dai, M. Zavarin, A. B. Kersting
Appl. Environ. Microbiol. (2016) 82, 7093-7101.

Two outer membrane proteins contribute to Caulobacter crescentus cellular fitness by preventing intracellular S-layer protein accumulation
K. Wes Overton, Dan Park, Mimi Yung, Alice Dohnalkova, John Smit, Yongqin Jiao
Appl Environ Microbiol (2016) 82:6961–6972.

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.

Permanent Draft Genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria
R. Craig Everroad, Rhona K. Stuart, Brad M. Bebout, Angela M. Detweiler, Jackson Z. Lee, Dagmar Woebken, Leslie Prufert-Bebout, Jennifer Pett-Ridge
Standards in Genomic Sciences (2016) 11:53, 1-8.

Bioleaching of Rare Earth Elements from Waste Phosphors and Cracking Catalysts
D. W. Reed, Y. Fujita, D. L. Daubaras, Y. Jiao, V. S. Thompson
Hydrometallurgy (2016) 166, 34–40.

The Free Energy of Small Solute Permeation through the Escherichia coli Outer Membrane Has a Distinctly Asymmetric Profile
Tim Carpenter, Jamie Parkin, and Syma Khalid
J. Phys. Chem. Lett. (2016) 7(17): p. 3446-3451.

Microbial mercury methylation in Antarctic sea ice
C. M. Gionfriddo, M. T. Tate, R. R. Wick, M. B. Schultz, A. Zemla, M. P. Thelen, R. Schofield, D. P. Krabbenhoft, K. E. Holt, J. W. Moreau
Nature Microbiology. (2016) 1, 16127.

Lipid crosslinking of nanolipoprotein particles substantially enhances serum stability and cellular uptake
Sean F. Gilmore, Craig D. Blanchette, Tiffany M. Scharadin, Greg L. Hura, Amy Rasley, Michele Corzett, Chong-xian Pan, Nicholas O. Fischer, Paul T. Henderson
ACS Applied Materials and Interfaces. (2016) 8, 20549-20557.

Long-term non-invasive interrogation of human dorsal root ganglion neuronal cultures on an integrated microfluidic multielectrode array platform
Heather E. Enright, Sarah H. Felix, Nicholas O. Fischer, Erik Mukerjee, David Soscia, Margerat Mcnerney, Kris Kulp, Jingming Zhang, G. Page, Paul Miller, Andre Ghetti, Elizabeth K. Wheeler, Satinderpall Pannu
Analyst. (2016) 141, 5346-5357.

Light regimes shape utilization of extracellular organic C and N in a cyanobacterial biofilm
Rhona K. Stuart, Xavier Mayali, Amy A. Boaro, Adam Zemla, R. Craig Everroad, Daniel Nilson, Peter K. Weber, Mary Lipton, Brad M. Bebout, Jennifer Pett-Ridge, Michael P. Thelen
mBio (2016) 7: e00650-00616.

Ion Intercalation Induced Capacitance Improvement for Graphene-based Supercapacitor Electrodes
Tianyu Liu, Cheng Zhu, Tianyi Kou, Marcus A. Worsley, Fang Qian, Cecilia Condes, Eric B. Duoss, Christopher M. Spadaccini, Yat Li
ChemNanoMat (2016) 2, 635-641.

Behavior of P85 and P188 Poloxamer Molecules: Computer Simulations Using United-Atom Force-Field
Ardeshir Goliaei, Edmond Y. Lau, Upendra Adhikari, Eric Schwegler, and Max L. Berkowitz
Journal of Physical Chemistry B (2016) 120(33), 8631-8641.

Molecular dynamics simulations reveal the conformational flexibility of Lipid II and its loose association with the defensin plectasin in the Staphylococcus aureus membrane
Sarah Witzke, Michael Petersen, Tim Carpenter, Syma Khalid
Biochemistry (2016) 55(23): 3303-3314.

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.

Expression and Association of the Yersinia pestis Translocon Proteins, YopB and YopD, Are Facilitated by Nanolipoprotein Particles
Matthew A. Coleman, Jenny A. Cappuccio, Craig D. Blanchette, Tingjuan Gao, Erin S. Arroyo, Anegela K. Hinz, Feliza A. Bourguet, Brent Segelke, Paul D. Hoeprich, Thomas Huser, Ted A. Laurence, Vladimir L. Motin, Brett A. Chromy
PLoS ONE (2016) 11(3), e0150166.

Salt Solutions in Carbon Nanotubes: The Role of Cation−π Interactions
Tuan Anh Pham, S. M. Golam Mortuza, Brandon C. Wood, Edmond Y. Lau, Tadashi Ogitsu, Steven F. Buchsbaum, Zuzanna S. Siwy, Francesco Fornasiero, and Eric Schwegler
Journal of Physical Chemistry C (2016) 120 (13), 7332–7338.

Solution-State Structure and Affinities of Cyclodextrin:Fentanyl Complexes by Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation
Brian P. Mayer, Daniel J. Kennedy, Edmond Y. Lau, Carlos A. Valdez
Journal of Physical Chemistry B (2016) 120(9), 2423-2433.

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) 16 (6), 3448-3456.

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.