Publications

You can also find my articles on Google Scholar and PubMed.

Note that Conradi Smith GD = Smith GD (my name changed in 2017). *These authors contributed equally.

Books

Conradi Smith GD. Cellular Biophysics and Modeling: The Computational Biology of Excitable Cells. Cambridge University Press. March 2019. 394 pages. [doi:10.1017/9780511793905] [Amazon]

Conradi Smith GD. Receptor Modeling Jupyter Book. 2025. Jupyter Book An unrefereed deliverable supported by NSF DMS grant #1951646, Cycle representations of receptor complex signal transduction.

Research Articles

Sakly S, Conradi Smith GD. Phase separation dynamics of SynGAP & PSD-95 in post-synaptic densities. In preparation.

Kalajian EJ, Stettler MK, Conradi Smith GD, Del Negro CA. μ-opioid receptor signaling enhances Kir3 currents in glutamatergic preBötzinger complex neurons. Under review at J. Physiol.

Cooley AM, Schlutius C, Matthews M, Simmons E, Zheng X, Thomas D, Edger PP, Platts AE, LaFountain A, George L, Williams A, Hundley D, Conradi Smith GD, Yuan Y-W, Twyford A and Puzey JR. Genetic architectures of floral pigment and patterning in hybrid monkeyflowers. Under review at Genetics.

Borrus DS, Stettler MK, Grover CJ, Kalajian EJ, Gu J, Conradi Smith GD*, Del Negro CA*. Inspiratory and sigh breathing rhythms depend on distinct cellular signaling mechanisms in the preBötzinger complex. The Journal of Physiology (London) 602:809-834, 2024. [10.1113/JP285582] *Contributed equally.

Simmons ESG, Cooley AM, Puzey JR, Conradi Smith GD. A multigenerational Turing model reproduces transgressive petal spot phenotypes in hybrid Mimulus. Bulletin of Mathematical Biology 85:120, 2023. [10.1007/s11538-023-01223-7]

David CK, Sugimura YK, Kallurkar PS, Picardo MCD, Saha MS, Conradi Smith GD, Del Negro CA. Single cell transcriptome sequencing of inspiratory neurons of the preBötzinger complex in neonatal mice. Scientific Data 9:457, 2022. [10.1038/s41597-022-01569-y]

Smith RD, Puzey JR, Conradi Smith GD. Population genetics of transposable element load: a mechanistic account of observed overdispersion. PLOS ONE 17(7):e0270839, 2022. [10.1371/journal.pone.0270839]

Kallurkar PS, Picardo MCD, Sugimura YK, Saha MS, Conradi Smith GD, Del Negro CA. Transcriptomes of electrophysiologically recorded Dbx1-derived respiratory neurons of the preBötzinger complex in neonatal mice. Scientific Reports 12:2923, 2022. [10.1038/s41598-022-06834-z]

Kinser TJ, Smith RD, Lawrence AH, Cooley AM, Vallejo-Marin M, Conradi Smith GD, and Puzey JR. Endosperm-based incompatibilities in hybrid monkeyflowers. The Plant Cell, koab117, 2021. [10.1093/plcell/koab117]

Zheng X, Om K, Stanton KA, Thomas D, Schlutius C, Cheng PA, Eggert A, Simmons E, Yuan Y-W, Conradi Smith GD, Puzey JR*, Cooley AM*. The regulatory network for petal anthocyanin pigmentation is shaped by the MYB5a/NEGAN transcription factor in Mimulus. Genetics 217(2), iyaa036, 2021. [10.1093/genetics/iyaa036]

Borrus D, Conradi Smith GD, Del Negro CA. Role of synaptic inhibition in the coupling of the respiratory rhythms that underlie eupnea and sigh behaviors. eNeuro, 7(3):1-20, 2020. [10.1523/ENEURO.0302-19.2020] [PMID:32393585]

Conradi Smith GD. Allostery in oligomeric receptor models. Mathematical Medicine and Biology: A Journal of the IMA. 37:313-333, 2020. [10.1093/imammb/dqz016] [PMID:31822901] [BioRxiv preprint]

Smith RD, Kinser TJ, Conradi Smith GD and Puzey JR. A likelihood ratio test for changes in homeolog expression bias. BMC Bioinformatics. 20:149, 2019. [doi:10.1186/s12859-019-2709-5] [PMID:30894122] [BioRxiv preprint]

Edger PP, Smith RD, McKain MR, Cooley AM, Vallejo-Marin M, Yuan Y, Bewick AJ, Ji L, Platts AE, Bowman MJ, Childs KL, Schmitz RJ, Smith GD, Pires JC, Puzey JR. Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower. The Plant Cell. 29(9):2150-2167, 2017. [doi:10.1105/tpc.17.00010] [PMID:28814644]

Hayes JA, Kottick A, Picardo MCD, Halleran AD, Smith RD, Smith GD, Saha MS, Del Negro CA. Transcriptome of neonatal preBötzinger complex neurons in Dbx1 reporter mice. Scientific Reports 7(1):8669, 2017. [doi:10.1038/s41598-017-09418-4] [PMID:28819234]

Hammack RH and Smith GD. Cycle bases of reduced powers of graphs. ARS Mathematica Contemporanea 12(1)183–203, 2017. [10.26493/1855-3974.856.4d2]

Wang X, Hardcastle K, Weinberg SH, Smith GD. Population density and moment-based approaches to modeling domain **Ca²⁺-mediated inactivation of L-type Ca²⁺ channels.** Acta Biotheoretica 64(1):11-32, 2016. [doi:10.1007/s10441-015-9271-y]

Wang X, Hao Y, Weinberg SH and Smith GD. **Ca²⁺-activation kinetics modulate successive puff/spark amplitude, duration and inter-event interval correlations in a Langevin model of stochastic Ca²⁺ release.** Mathematical Biosciences 264:101–107, 2015. [doi:10.1016/j.mbs.2015.03.012]

Wang X, Weinberg S, Hao Y, Sobie EA and Smith GD. Calcium homeostasis in a local/global whole cell model of permeabilized ventricular myocytes with a Langevin description of stochastic calcium release. American Journal of Physiology: Heart and Circulatory Physiology. 308(5):H510-H523, 2015. [doi:10.1152/ajpheart.00296.2014] [PMID: 25485896]

Weinberg S and Smith GD. The influence of **Ca²⁺ buffers on free [Ca²⁺] fluctuations and the effective volume of Ca²⁺ microdomains.** Biophysical Journal 106(12):2693-–2709, 2014. [doi:10.1016/j.bpj.2014.04.045] [PMID: 24940787]

Weinberg S and Smith GD. Discrete-state stochastic models of calcium-regulated calcium influx and subspace dynamics are not well-approximated by ODEs that neglect concentration fluctuations. Computational and Mathematical Methods in Medicine: Special issue on Cardiovascular System Modeling. Volume 2012, Article ID 897371. [doi:10.1155/2012/897371]

Siegal-Gaskins D, Mejia-Guerra MK, Smith GD, and Grotewold E. Emergence of switch-like behavior in a large family of simple biochemical networks. PLoS Comput. Bio. 7(5):e1002039, 2011. [doi:10.1371/journal.pcbi.1002039] [PMID: 21589886]

LaMar MD, Kemper P, and Smith GD. Reduction of calcium release site models via moment fitting of phase-type distributions. Phys. Biol. 8:026015, 2011. [doi:10.1088/1478-3975/8/2/026015]

Lamprecht R, Smith GD, and Kemper P. Stochastic Petri net models of signaling complexes and their analysis. Natural Computing. Special Issue: Petri Nets and BioSystems 10:1045-75, 2011. [doi:10.1007/s11047-009-9143-y]

Hartman JM, Sobie EA, and Smith GD. Spontaneous calcium sparks and homeostasis in a minimal model of local and global calcium responses in quiescent ventricular myocytes. American Journal of Physiology: Heart and Circulatory Physiology 299(6):H1996–2008, 2010. [doi:10.1152/ajpheart.00293.2010] [PMID: 20852058]

Huertas MA, Smith GD, and Gyorke S. Calcium alternans in a cardiac myocyte model that uses moment equations to represent heterogeneous junctional SR calcium. Biophys. J. 99(2):377-387, 2010. [doi:10.1016/j.bpj.2010.04.032] [PMID: 20643055]

Williams GSB, Sobie EA, Smith GD, Jafri MS. Models of cardiac excitation-contraction coupling in ventricular myocytes. Mathematical Biosciences. 226:1-15, 2010. [doi:10.1016/j.mbs.2010.03.005]

LaMar MD and Smith GD. The effect of node-degree correlation on synchronization of identical pulse-coupled oscillators. Physical Review E. 84(4):046206, 2010.[doi:10.1103/PhysRevE.81.046206]

Thul R, Smith GD, Coombes S. Sensitisation waves in a bidomain fire-diffuse-fire model of propagating calcium waves. Physica D: Nonlinear Phenomena 238(21):2142-2152, 2009.
[doi:10.1016/j.physd.2009.08.011]

Siegal-Gaskins D, Grotewold E, and Smith GD. The capacity for multistability in gene regulatory motifs. BMC Systems Biology 3:96, 2009. [doi:10.1186/1752-0509-3-96]

Hao Y, Kemper P, and Smith GD. Reduction of calcium release site models via fast/slow analysis and iterative aggregation/disaggregation. Chaos 19:037107, 2009. Focus issue: Intracellular Calcium Dynamics – A Change of Modeling Paradigm? [doi:10.1063/1.3223663]

Goyal R, Angermann JE, Ostrovskaya O, Buchholz JN, Smith GD, Wilson SM. Enhanced capacitative calcium entry and sarcoplasmic-reticulum calcium storage capacity with advanced age in murine mesenteric arterial smooth muscle cells. Exp. Gerontol. 44(3):201-7, 2009. [doi:10.1016/j.exger.2008.10.007]

Goyal R, Creel KD, Chavis E, Smith GD, Longo LD, Wilson SM. Maturation of intracellular calcium homeostasis in sheep pulmonary arterial smooth muscle cells. American Journal of Physiology: Lung Cellular and Molecular Physiology 295(5):L905-14, 2008. [doi:10.1152/ajplung.00053.2008]

DeRemigio H, LaMar MD, Kemper P, and Smith GD. Markov chain models of coupled intracellular calcium channels: Kronecker structured representations and iterative solution methods. Physical Biology 5(3):36003, 2008. [doi:10.1088/1478-3975/5/3/036003] [PMID: 18626127]

Williams GSB, Huertas MA, Sobie EA, Jafri MS, and Smith GD. Moment closure for local control models of **Ca²⁺-induced Ca²⁺ release in cardiac myocytes.** Biophys. J. 95(4):1689-703, 2008. [doi:10.1529/biophysj.107.125948] [PMID: 18487291]

Groff JR and Smith GD. Ryanodine receptor allosteric coupling and the dynamics of **Ca²⁺ sparks.** Biophys. J. 95:135-154, 2008. [doi:10.1529/biophysj.107.119982] [PMID: 18359795]

Groff JR and Smith GD. Calcium-dependent inactivation and the dynamics of calcium puffs and sparks. J. Theor. Biol. 253(3):483-99, 2008. [doi:10.1016/j.jtbi.2008.03.026] [PMID: 18486154]

Williams GSB, Molinelli EJ, and Smith GD. Modeling local and global intracellular calcium responses mediated by diffusely distributed inositol 1,4,5-trisphosphate receptors. J. Theor. Biol. 253:170-188, 2008. [doi:10.1016/j.jtbi.2008.02.040] [PMID: 18405920]

DeRemigio H, Groff JR, and Smith GD. Calcium release site ultrastructure and the dynamics of puffs and sparks. Mathematical Medicine & Biology. 25(1):65-85, 2008.
[doi:10.1093/imammb/dqn004] [PMID: 18359948]

Thul R, Smith GD, Coombes S. A bidomain threshold model of propagating calcium waves. J. Mathematical Biology 56(4):435-63, 2008. [doi:10.1007/s00285-007-0123-5]

Williams GSB, Huertas MA, Sobie EA, Jafri MS, and Smith GD. A probability density approach to modeling local control of **Ca²⁺-induced Ca²⁺ release in cardiac myocytes.** Biophys. J. 92(7):2311-28, 2007. [doi:10.1529/biophysj.106.099861] [PMID: 17237200]

Huertas H and Smith GD. The dynamics of luminal depletion and the stochastic gating of **Ca²⁺-activated Ca²⁺ channels and release sites.** J. Theor. Biol. 246(2):332-54, 2007. [doi:10.1016/j.jtbi.2007.01.003]

Means S, Smith AJ, Shepard J, Shadid J, Fowler J, Wojcikiewicz R, Mazel T, Smith GD, and Wilson BS. Reaction diffusion modeling of calcium dynamics with realistic ER geometry. Biophys. J. 91(2):537-57, 2006. [doi:10.1529/biophysj.105.075036]

Huertas MA and Smith GD. A multivariate population density model of the dLGN/PGN relay. J. Comput. Neurosci. 21(2):171-89, 2006. [doi:10.1529/biophysj.105.075036] [PMID: 16788765]

Zhao X, Outlaw RA, Wang JJ, Zhu MY, Smith GD, and Holloway BC. Thermal desorption of hydrogen from carbon nanosheets. J. Chem. Phys. 124(19):194704, 2006.

Huertas MA, Groff JR, and Smith GD. Feedback inhibition and throughput properties of an integrate-and-fire-or-burst network model of retinogeniculate transmission. J. Comput. Neurosci. 19(2):147-180, 2005. [doi:10.1007/s10827-005-1084-6] [PMID: 16133817]

Mazzag B, Tignanelli C and Smith GD. The effect of residual Ca²⁺ on the stochastic gating of Ca²⁺-regulated Ca²⁺ channel models. J. Theor. Biol. 235(1):121-150, 2005. [doi:10.1016/j.jtbi.2004.12.024]

Nguyen VD, Mathias R, and Smith GD. A stochastic automata network descriptor for Markov chain models of instantaneously-coupled intracellular **Ca²⁺ channels.** Bull. Math. Biol. 67(3):393-432, 2005. [doi:10.1016/j.bulm.2004.08.010] [PMID: 15820736]

Wilson SM, Mason HS, Smith GD, Nicholson N, Johnston L, Janiak R, and Hume JR. Comparative capacitative **Ca²⁺ entry mechanisms in canine pulmonary and renal arterial smooth muscle cells.** J. Physiol. (London) 543(Pt 3)917-31, 2002. [doi:10.1113/jphysiol.2002.021998]

Smith GD and Sherman SM. Detectability of excitatory vs. inhibitory drive in a thalamocortical relay neuron model. J. Neurosci. 22(23):10242-10250, 2002. [PMID: 12451125]

Coombes S, Owen MR, and Smith GD. Mode-locking in a periodically forced integrate-and-fire-or-burst neuron model. Phys. Rev. E 64(041914):1-12, 2001.[doi:10.1103/PhysRevE.64.041914] [PMID: 11690059]

Smith GD, Dai L, Miura R, Sherman A. Asymptotic analysis of equations for the buffered diffusion of intracellular **Ca²⁺.** SIAM. J. Appl. Math. 61(5):1816-1838, 2001. http://www.jstor.org/stable/3061854

Smith GD, Cox CL, Sherman SM, and Rinzel J. A firing-rate model of spike-frequency adaptation in sinusoidally-driven thalamocortical relay neurons. Thalamus and Related Systems 1(2):135-156, 2001. [doi:10.1016/S1472-9288(01)00012-7]

Smith GD, Cox CL, Sherman SM, and Rinzel J. Fourier analysis of sinusoidally driven thalamocortical relay neurons and a minimal integrate-and-fire-or-burst model. J. Neurophys. 83(1)588-610, 2000. [http://jn.physiology.org/cgi/content/full/83/1/588] [PMID: 10634897]

Bertram R, Smith GD, and Sherman A. A modeling study of the effects of overlapping **Ca²⁺ microdomains on neurotransmitter release.** Biophys. J. 76(2):735-50, 1999. [doi:10.1016/S0006-3495(99)77240-1] [PMID: 9929478]

Keizer J, Smith GD, Ponce-Dawson S, and Pearson J. Saltatory propagation of **Ca²⁺ waves by Ca²⁺ sparks.** Biophys. J. 75(8):595-600, 1998. [doi:10.1016/S0006-3495(98)77550-2] [PMID: 9675162]

Smith GD, Keizer J, Stern M, Lederer WJ, and Cheng H. A simple numerical model of **Ca²⁺ spark formation and detection in cardiac myocytes.** Biophys. J. 75(7)15-32, 1998. [doi:10.1016/S0006-3495(98)77491-0] [PMID: 9649364]

Keizer J and Smith GD. Spark-to-wave transition: saltatory transmission of **Ca²⁺ waves in cardiac myocytes*. *Biophys. Chem. 72:87-100, 1998. [doi:10.1016/S0301-4622(98)00125-2] [PMID: 9652087]

Smith GD. Analytical steady-state solution to the rapid buffering approximation near an open **Ca²⁺ channel.** Biophys. J. 71(6):3064-3072, 1996. [doi:10.1016/S0006-3495(96)79500-0] [PMID: 8968577]

Smith GD, Wagner J, and Keizer J. Validity of the rapid buffering approximation near a point source of **Ca²⁺ ions.** Biophys. J. 70(6):2527-2539, 1996. [doi:10.1016/S0006-3495(96)79824-7] [PMID: 8744292]

Smith GD, Lee RJ, Oliver JM, and Keizer J. The effect of **Ca²⁺ influx on intracellular free Ca²⁺ responses in antigen-stimulated RBL-2H3 cells.** Am. J. Physiol. 270(3 Pt 1):C939-952, 1996. [http://ajpcell.physiology.org/cgi/reprint/270/3/C939]

Keizer J, Maki L, Greathouse J, Smith GD, and Bruinsma P. Bistability and fluctuations for an incandescent light bulb. J. Phys.Chem. 99(2):844-852, 1995. [doi:10.1021/j100002a056]

Moscicki AB, Broering J, Powell K, Klein J, Clayton L, Smith GD, Broero S, Darragh TM, Brescia RJ, and Palefsky J. Comparison between colposcopic, cytologic, and histologic findings in women positive and negative for human papillomavirus DNA. J. Adolesc. Health 14(2):74-79, 1993. [doi:10.1016/1054-139X(93)90088-7]

Moscicki AB, Palefsky J, Smith GD, Siboshski S, and Schoolnik G. Variability of human papillomavirus DNA testing in a longitudinal cohort of young women. Obstet. Gynecol. 82(4 Pt 1):578-85, 1993. [doi:10.1097/00006250-199310000-00021]

Moscicki AB, Palefsky JM, Gonzales J, Smith GD, and Schoolnik GK. Colposcopic and histologic findings and human papillomavirus (HPV) DNA test variability in young women positive for HPV DNA. J. Infect. Dis. 166(5):951-7, 1992. [doi:10.1093/infdis/166.5.951]

Book Chapters

Groff JR, DeRemigio H, and Smith GD. Markov chain models of ion channels and **Ca²⁺ release sites.** In: Stochastic Methods in Neuroscience. Laing C and Gabriel L, eds. Pages 29-64. Oxford University Press. 2009. [doi:10.1093/acprof:oso/9780199235070.003.0002]

Huertas MA and Smith GD. Population density model of the driven LGN/PGN. In: Stochastic Methods in Neuroscience. Laing C and Gabriel L, eds. Pages 217-241. Oxford University Press. 2009. [doi:10.1093/acprof:oso/9780199235070.003.0008]

Smith GD. Modeling intracellular calcium: diffusion, dynamics, and domains. In: Modeling in the Neurosciences: From Biological Systems to Cognitive Robotics (Foundations of Analytical Neuroscience), 2nd edition. Reeke GN, Poznanski RR, Lindsay KA, Rosenberg JR, and Sporns O, eds. Pages 339-374. Taylor & Francis, 2005. [doi:10.1201/9780203390979.ch13]

Smith GD. Modeling the stochastic gating of ion channels. In: Computational Cell Biology, Fall C, Marland E, Wagner J, Tyson J, editors. Pages 285-319. Springer-Verlag. 2002. [doi:10.1007/978-0-387-22459-6_11]

Smith GD, Pearson J, and Keizer J. Modeling intracellular Ca²⁺ waves and sparks. In: Computational Cell Biology, Fall C, Marland E, Wagner J, Tyson J, editors. Pages 198-229. Springer-Verlag. 2002. [doi:10.1007/978-0-387-22459-6_8]

Smith GD. Modeling local and global **Ca²⁺ signals using reaction-diffusion equations.** In: Computational Neuroscience: Realistic Modeling for Experimentalists, De Schutter E, editor. Pages 49-85. CRC Press. 2000. [doi:10.1201/9781420039290.ch3]