Publications

77.  Braun R., M. Tfirn, R. Ford, Listening to life: Sonification for enhancing discovery in biological research. Biotechnol. Bioeng., ESS Open Archive, November 14, 2023, under review.

76.  Kuper, T. J., M. M. Islam, S. M. Peirce-Cottler, J. A. Papin, R. M. Ford. Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment. PLoS Computational Biology, 2024. doi: 10.1371/journal.pcbi.1012031.

75.  Zhao, X. and R. M. Ford, Marine bacteria chemotaxis to crude oil components with opposing effects, bioRxiv, 2022.01.26.477900.

74.  Braun, R., Tfirn, M., and R. M. Ford, Sonification of chemotactic waves of bacteria, 2023 International Conference on Auditory Display, peer-reviewed proceedings https://hdl.handle.net/1853/72885, Awarded best paper for use of sound – academic.

73.  Gao, B., X. Wang and R. M. Ford, Chemotaxis along local chemical gradients enhanced bacteria dispersion and PAH bioavailability in a heterogeneous porous medium, Science of The Total Environment, 2023 859, 160004.

72.  Kuper, T. J., L. Z. Wang, R. K. Prud’homme, S. S. Datta and R. M. Ford, Chemorepellent-loaded nanocarriers promote localized interference of Escherichia coli transport to inhibit biofilm formation, ACS Applied Bio Materials, 2022 5 (11), 5310-5320.

71.  Zhao, X. and R. M. Ford, “Escherichia coli chemotaxis to competing stimuli in a microfluidic device with a constant gradient,” Biotechnol. Bioeng., 2022, 119 (9), 2564-2573. 

70.  Gao, B., E. Taghizadeh, B. D. Wood and R. M. Ford, “Transport of chemotactic bacteria in granular media with randomly distributed chemoattractant-containing NAPL ganglia: Modeling and simulation,” Adv. Wat. Res., 2022, 159, 104065.      

69.  Middlebrooks, S. A., X. Zhao, R. M. Ford, and P. T. Cummings, “A mathematical model for Escherichia coli chemotaxis to competing stimuli,” Biotechnol. Bioeng., 2021, 118 (12) 4678-4686. 

68.  Shim, S., H. A. Stone and R. M. Ford, “Chemotaxis in shear flow: similarity solutions of the steady state chemoattractant and bacterial distributions, AIChE J., 2019, 65 (10) e16713. Designated as Editor’s Choice.

67.  Adadevoh, J. S., C. A. Ramsburg, and R. M. Ford, “Chemotaxis Increases the Irreversible Retention of Bacteria in Porous Media with Residual NAPL Entrapment,” Environ. Sci. Technol., 2018, 52 (13) 7289-7295.

66.  Adadevoh, J. S., S. Ostvar, B. Wood, and R. M. Ford, “Modeling Transport of Chemotactic Bacteria in Granular Media with Distributed Contaminant Sources,” Environ. Sci. Technol., 2017, 51, 14192-14198. 

65.  Janes, K. A, P. L. Chenadran, R. M. Ford, M. J. Lazzara, J. A. Papin, S. M. Peirce, J. J. Saucerman, and D. A. Lauffenburger, “An engineering design approach to systems biology,” Integrative Biology, 2017, 9, 574-583. DOI: 10.1039/c7ib00014f.

64.  Xu, K., X. Wang, R. Ford, and J. Landers, “Self-Partitioned Droplet Array on Laser-Patterned Superhydrophilic Glass Surface for Wall-less Cell Arrays,” Anal. Chem., 2016, 88 (5), 2652–2658.

63.  Adadevoh, J. S., S. C. Triolo, C. A. Ramsburg, and R. M. Ford, “Chemotaxis increases the residence time of bacteria in granular media containing distributed contaminant sources,” Environ. Sci. Technol., 2016, 50 (1), 181-187.

62.  Wang, X., L. Lanning, and R. Ford, “Enhanced Retention of Chemotactic Bacteria in a Pore Network with Residual NAPL Contamination,” Environ. Sci. Technol., 2016, 50 (1), 165-172.

61.  Wang, X., J. Atencia and R. M. Ford, “Quantitative analysis of chemotaxis towards toluene by Pseudomonas putida in a convection-​free microfluidic device,” Biotechnol. Bioeng., 2015, 112 (5): 896-904.

60.  Wang, X., T. Long and R. Ford, “Bacterial chemotaxis toward a NAPL source within a pore-scale microfluidic chamber,” Biotechnol. Bioeng., 2012, 109 (7): 1622-1628. 

59.  Toepfer, J. A., R. 
M. Ford, D.
 Metge, and R.
Harvey, “Impact of Fluorochrome Stains Used to Study Bacterial Transport in Shallow Aquifers on Motility and Chemotaxis of Pseudomonas species,” FEMS Microbiology Ecology, 2012, 81 (1): 163-171.

58.  Liu, J., R. M. Ford and J. A. Smith, "Idling Time of Motile Bacteria Contributes to Retardation and Dispersion in Sand Porous Medium," Environ. Sci. Technol., 2011, 45 (9): 3945-3951.

57.  Strobel, K. L., S. McGowan, R. D. Bauer, C. Griebler, J. Liu and R. M. Ford, “Chemotaxis Increases Vertical Migration and Apparent Transverse Dispersion of Bacteria in a Bench-Scale Microcosm,” Biotechnol. Bioeng., 2011, 108 (9): 2070-2077.

56.  Wang, M. and R. M. Ford, “Quantitative Analysis of Transverse Bacterial Migration Induced by Chemotaxis in a Packed Column with Structured Physical Heterogeneity,” Environ. Sci. Technol., 44 (2010): 780-786.

55.  Liu, J and R. M. Ford, “Idling Time of Swimming Bacteria near Particulate Surfaces Contributes to Apparent Adsorption Coefficients at the Macroscopic Scale under Static Conditions,” Environ. Sci. Technol., 43 (2009): 8874-8880. 

54.  Valdes-Parada, F. J., M. L. Porter, K. Narayanaswamy, R. M. Ford and B. D. Wood, “Upscaling Microbial Chemotaxis in Porous Media”, Advances in Water Resources, 32 (2009): 1413–1428. 

53.  Wang, M. and R. M. Ford, “Transverse Bacterial Migration Induced by Chemotaxis in a Column with Structured Physical Heterogeneity”, Environ. Sci. Technol., 43 (2009): 5921-5927.

52.  Narayanaswamy, K., R. M. Ford, J. A. Smith, and E. J. Fernandez, “Surface association of motile bacteria and apparent tortuosity values in packed column experiments," Water Resour. Res., 45(2009): W07411. 

51.  Kusy, K. and R. M. Ford, “Surface Association of Motile Bacteria at Granular Porous Media Interfaces,” Environ. Sci. Technol., 2009, 43 (10): 3712–3719. 

50.  Long, T. and R. M. Ford, “Enhanced Transverse Migration of Bacteria by Chemotaxis in a Porous T-Sensor,” Environ. Sci. Technol., 2009, 43 (5): 1546–1552. 

49.  Wang, M., R. M. Ford and R. W. Harvey, “Coupled Effect of Chemotaxis and Growth on Microbial Distributions in Organic-Amended Aquifer Sediments: Observations from Laboratory and Field Studies,” Environ. Sci. Technol., 42:10 (2008), 3556–3562.

48.  Lanning, L., R. M. Ford and T. Long, “Bacterial Chemotaxis Transverse to Axial Flow in a Microfluidic Channel,” Biotechnology & Bioengineering, 100:4 (2008) 653 - 663. 

47.  Kusy, K. and R. M. Ford, “Monte Carlo Simulations Derived from Direct Observations of Individual Bacteria Inform Macroscopic Migration Models at Granular Porous Media Interfaces,” Environ. Sci. Technol., 41 (2007) 6403-6409. 

46.  Wood, B.D. and R.M. Ford, “Biological processes in porous media: From the pore scale to the field,” Advances in Water Resources, 30 (2007) 1387-1391. 

45.  Ford, R.M. and R.W. Harvey, “Role of chemotaxis in the transport of bacteria through porous media,” Advances in Water Resources, 30 (2007) 1608-1617. 

44.  Olson, M.S. R.M. Ford, J.A. Smith and E.J. Fernandez, “Mathematical modeling of chemotactic bacterial transport through a two-dimensional heterogeneous porous medium,” Bioremediation Journal, 10 (2006) 13-23. 

43.  Kohlmeier, S., T.H.M. Smits, R.M. Ford, C. Keel, H. Harms and L.Y. Wick, “Taking the fungal highway: mobilization of pollutant-degrading bacteria by fungi,” Environmental Science & Technology, 39 (2005) 4640-4646.

42. Olson, M.S., J.A. Smith, L. Lanning and E.J. Fernandez, “Analysis of Column Tortuosity for MnCl2 and Bacterial Diffusion Using Magnetic Resonance Imaging (MRI)”, Environmental Science & Technology, 39 (2005) 149-154.

41.  Olson, M.S., R.M. Ford, J.A. Smith and E.J. Fernandez, “Quantification of Bacterial Chemotaxis in Porous Media Using Magnetic Resonance Imaging (MRI)", Environmental Science & Technology, 38 (2004) 3864-3870.

40.  Mills, A. L., J. S. Herman, R. M. Ford, and G. M. Hornberger, “Functional redundancy promotes functional stability in diverse microbial bioreactor communities.” SAE Technical Paper Series No.2003-01-2509.

39.  Chen, K. C., R. M. Ford and P. T. Cummings, “Cell balance equation for chemotactic bacteria with a biphasic tumbling frequency," J. Mathematical Biology, 47 (2003) 518-546.

38.  Jin, M., R. M. Ford and P. T. Cummings, “A numerical method for solving a scalar advection-dominated transport equation with concentration-dependent sources,” Computers & Chemical Engineering, 27 (2003) 1405-1419.

37.  Sherwood, J. L., J. C. Sung, R. M. Ford, E. J. Fernandez, J.E. Maneval and J. A. Smith, "Analysis of Bacterial Random Motility in a Porous Medium Using Magnetic Resonance Imaging and Immunomagnetic Labeling," Environmental Science & Technology, 37 (2003) 781-785.

36.  Smith, L.V., L. K. Tamm and R. M. Ford, "Explaining non-zero separation distances between attached bacteria and surfaces measured by total internal relection aqueous fluorescence microscopy," Langmuir, 18 (2002) 5247-5255.

35.  Vigeant, M. A. S., R. M. Ford, M. Wagner and L. K. Tamm "Reversible and irreversible adhesion of motile E. coli bacteria analyzed by TIRAF microscopy," Appl. Environ. Microbiol., 68 (2002) 2794-2801 

34.  Lanning, L. M. and R. M. Ford, "Glass Micromodel Study of Bacterial Dispersion in Spatially Periodic Porous Networks," Biotechnology & Bioengineering, 78 (2002) 556-566.

33.  McClaine, J. W. and R. M. Ford, "Reversal of flagellar rotation is important in initial attachment of Escherichia coli to glass in a dynamic system in high- and low-ionic-strength buffers," Appl.Environ. Microbiol., 68 (2002) 1280-1289.

32.  McClaine, J. W. and R. M. Ford, "Characterizing the Adhesion of Motile and Nonmotile Escherichia coli to a Glass Surface Using a Parallel Plate Flow Chamber," Biotechnology & Bioengineering, 78 (2002) 179-189.

31.  Lewus, P. and R. M. Ford, “Quantification of Random Motility and Chemotaxis Bacterial Transport Coefficients using Individual-Cell and Population-Scale Assays,” Biotechnol. Bioeng, 75 (2001) 292-304.

30.  Greenbaum, E., S. L. Blankinship, J. W. Lee and R. M. Ford, "Solar Photobiochemistry: Simultaneous Photoproduction of Hydrogen and Oxygen in a Confined Bioreactor," J. Phys. Chem B, 105 (2001) 3605-3609.

29.  Vigeant, M. A.-S., M. Wagner, L. K. Tamm and R. M. Ford, "Nanometer Distances Between Swimming Bacteria and Surfaces Measured by TIRAF Microscopy," Langmuir, 17 (2001) 2235-2242.

28.  Armitage, J., T. Pitta, M. Vigeant, H. Packer and R. Ford, “Transformations in Flagellar Structure in Rhodobacter sphaeroides and their Possible Relationship to Changes in Swimming Speed.” J. Bacteriol., 181 (1999) 4825-4833.

27.  Lewus, P. and R. M. Ford, “Temperature-Sensitive Motility of Sulfolobus acidocaldarious Influences Population Distribution in Extreme Environments,” J. Bacteriol., 181 (1999) 4020-4025.

26.  Chen, K. C., R. M. Ford and P. T. Cummings, “Spatial Effect of Tumbling Frequencies for Motile Bacteria on Cell Balance Equations,” Chem. Eng. Sci., 54 (1999) 593-617.

25.  Chen, K. C., R. M. Ford and P. T. Cummings, “Perturbation Expansion of Alt’s Cell Balance Equations Reduces to Segel’s 1D Equations for Shallow Chemoattractant Gradients,” SIAM J. Appl. Math., 59 (1998) 35-57. 

24.  Chen, K. C., R. M. Ford and P. T. Cummings, “Mathematical Models for Motile Bacterial Transport in Cylindrical Tubes,” J. theor. Biol., 195 (1998) 481-504.

23.  Chen, K. C., R. M. Ford and P. T. Cummings, “The Global Turning Probability Density Function for Motile Bacteria and Its Applications," J. Theor. Biol., 195 (1998) 139-155.

22.  Duffy, K. J., R. M. Ford and P. T. Cummings, “Residence Time Calculation for Chemotactic Bacteria within Porous Media,” Biophys. J., 73 (1997) 2930-2936.

21.  Vigeant, M. A. S. and R. M. Ford, “Interactions Between Motile E. coli and Glass with Varying Ionic Strength, as Observed with a Three-dimensional Tracking Microscope,” Appl. Environ. Microbiol., 63 (1997) 3474-3479.

20.  Duffy, K. J. and R. M. Ford, “Turn Angle and Run Time Distributions Characterize Swimming Behavior for Pseudomonas putida,” J. Bacteriol., 179 (1997) 1428-1430.

19.  Frymier, P. D. and R. M. Ford “Analysis of Bacterial Swimming Speed Approaching a Solid-Liquid Interface,” AIChE Journal, 43 (1997) 1341-1347.

18.  Barton, J. W. and R. M. Ford, “Mathematical Model for Characterization of Bacterial Migration Through Sand Cores,” Biotechnol. Bioeng., 53 (1997) 487-496.

17.  Brosilow, B. J., R. M. Ford, S. S. Sarman, and P. T. Cummings, “Numerical Solution of Transport Equations for Bacterial Chemotaxis,” SIAM J. Appl. Math., 56 (1996) 1639-1663.

16.  Reddy, H. L. and R. M. Ford, “Analysis of Biodegradation and Bacterial Transport: Comparison of Models with Kinetic and Equilibrium Bacterial Adsorption,” J. Contam. Hydrol, 22 (1996) 271-287.

15.  Barton, J. W. and R. M. Ford, “Determination of Effective Random Motility Coefficient for Bacterial Migration through Sand Cores” Appl. Environ. Microbiol., 61 (1995) 3329-3335.

14.  Frymier, P. D., R. M. Ford, H. C. Berg and P. T. Cummings, “Three-dimensional tracking of motile bacteria near a solid planar surface,” Proc. Natl. Acad. Sci USA, 92 (1995) 6195-6199.

13.  Duffy, K. J., P. T. Cummings and R. M. Ford, “Random Walk Calculations for Bacterial Migration in Porous Media,” Biophys. J., 68 (1995) 800-806.

12.  Strauss, I., P. D. Frymier, C. M. Hahn and R. M. Ford “Analysis of Bacterial Migration: II. Studies of Multiple Attractant Gradients,” AIChE Journal 41 (1995) 402-414.

11.  Frymier, P. D., R. M. Ford and P. T. Cummings, “Analysis of Bacterial Migration: I. Numerical Solution of Balance Equation,” AIChE Journal  40 (1994) 704-715.

10.  Mercer, J. R., R. M. Ford, J. L. Stitz and C. Bradbeer, “Growth Rate Effects on Fundamental Transport Properties of Bacterial Populations,” Biotechnol. Bioeng. 42 (1993) 1277-1286.

9.    Frymier, P. D., R. M. Ford and P. T. Cummings, “Cellular Dynamics Simulations of Bacterial Chemotaxis,” Chem. Eng. Sci. 48 (1993) 687-699.

8.    Ford, R. M. and P. T. Cummings, “On the Relationship Between Cell Balance Equations for Chemotactic Cell Populations,” SIAM J. Appl. Math. 52 (1992) 1426-1441.

7.    Ford, R. M. and D. A. Lauffenburger, “A Simple Expression for Quantifying Bacterial Chemotaxis Using Capillary Assay Data:  Application to the Analysis of Enhanced Chemotactic Responses from Growth-Limited Cultures,” Math. Biosci. 109 (1992) 127-149.

6.    Ford, R. M., B. R. Phillips, J. A. Quinn, and D. A. Lauffenburger, “Stopped-Flow Chamber and Image Analysis System for Quantitative Characterization of Bacterial Population Migration:  Motility and Chemotaxis of E. coli K12 to Fucose,” Microbial Ecology 22 (1991) 127-138.

5.    Ford, R. M. and D. A. Lauffenburger, “Analysis of Chemotactic Bacterial Distributions in Population Migration Assays Using a Mathematical Model Applicable to Steep or Shallow Attractant Gradients,” Bull. Math. Biol. 53 (1991) 721-749.

4.    Ford, R. M. and D. A. Lauffenburger, “Measurement of Bacterial Random Motility and Chemotaxis Coefficients:  II. Application of Individual Cell-Based Mathematical Model,” Biotechnol. Bioeng. 37 (1991) 661-672.

3.    Ford, R. M., B. R. Phillips, J. A. Quinn, and D. A. Lauffenburger, “Measurement of Bacterial Random Motility and Chemotaxis Coefficients:  I. Stopped-Flow Diffusion Chamber Assay,” Biotechnol. Bioeng. 37 (1991) 647-660.

2.    Lauffenburger, D. A., M. Rivero, F. Kelly, R. Ford, and J. DiRienzo, “Bacterial Chemotaxis - Cell Flux Model, Parameter Measurement, Population Dynamics, and Genetic Manipulation,” Ann. N.Y. Acad. Sci. 506 (1987) 281-295.

1.    Givler, R. M., P. Dhurjati, and M. T. Klein, “A Model Compound Study of a Strategy for the Selective Microbial Pretreatment of Lignin,” Chem. Eng. J. 30 (1985) B37-B41.