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My
primary interests are mathematical models in biology and delay differential
equations. Below is a list of some problems on which I am working. (Last
updated Oct. 1, 2004.)
Modeling Cellular
Control Systems
One of the important
questions, which scientists are currently investigating, concerns how the
cell cycle begins in bacterial cells. I have been using information that
is known about the biochemical processes in Escherichia coli to try
to determine the key controlling steps in the initiation of DNA replication.
My studies have examined several aspects of growing cultures of bacterial
cells using biochemical kinetics to study cellular control problems from
a theoretical perspective. It is hoped that my studies will assist the experimental
studies in discovering the most significant steps initiating the cell cycle.
Age-Structured
Models for Erythropoiesis
My studies of cellular
control systems included some studies on how the process of diffusion can
result in effects that are similar to delays in simpler systems of differential
equations. My study of age-structured models for erythropoiesis began as
an inquiry into the relation between complicated age-structured models to
the significantly simpler systems of delay differential equations. In collaboration
with Jacques Bélair and Mike Mackey, I have studied some models for
hematopoiesis, which have interesting results for both studying hematopoietic
diseases and the mathematical study of state-dependent delay differential
equations. Recent work has shown how the variable velocity of aging in erythropoiesis
can stabilize the mathematical model.
Modeling
Marine Phage
Marine bacteriophage
play a vital role in the ecology of the oceans, cycling about 25% of the
carbon daily. However, little is known about this very important community.
I am collaborating with a number of biologists and mathematicians at SDSU
to learn more about the diversity and population dynamics of this community.
Molecular mechanisms are being modeled to better understand the lytic and
lysogenic lifestyles of phage. Also, new models are being developed to help
understand the role of diversity and heterogeneity for phage in the marine
environment. Modeling efforts have helped narrow the number of "species"
of phage in a temperate marine environment and have shown that rank-abundance
curves these "species" follow a power law distribution. Experiments
are being designed to determine key kinetic parameters to better understand
the dynamics of phage and their hosts.
Recent Publications
- J.
M. Mahaffy and J. W. Zyskind (1989) A model for the initiation of replication
in Escherichia coli, J. Theor. Biol.140, 453-477.
- J. M. Mahaffy
and J. W. Zyskind (1991) A comparison of two models for initiation of
replication in Escherichia coli, Proceedings of the Second International
Conference on Mathematical Population Dynamics (eds. O. Arino, D.
E. Axelrod, and M. Kimmel), Marcel Dekker, 747-766.
- J. M. Mahaffy,
D. A. Jorgensen and R. L. Vanderheyden (1992) Oscillations in a model
of repression with external control, J. Math. Biol. 30,
669-691.
- J. M. Mahaffy,
D. A. Jorgensen and R. L. Vanderheyden (1992) Stability results for
a model of repression with external control, Quart. Appl. Math.,
50, 415-435.
- J.
M. Mahaffy (1993) Variation in concentrations of RNAs and proteins involved
in gene expression of Escherichia coli}, J. Theor. Biol., 162,
153-186.
- J. M. Mahaffy,
P. J. Zak and K. M. Joiner (1995) A geometric analysis of stability
regions for a linear differential equation with two delays, Int.
J. Bifur. Chaos, 5, 779-796.
- J.
M. Mahaffy, P. J. Zak and K. M. Joiner (1993) A three parameter stability
analysis for a linear differential equation with two delays, Technical
Report, Department of Mathematical Sciences, San Diego State University,
San Diego, CA.
- J.
Bélair, M. C. Mackey and J. M. Mahaffy (1995) Age-structured
and two delay models for erythropoiesis, Math. Biosci., 128,
317-346.
- J. M. Mahaffy
(1996) Modeling erythropoiesis: Relating age-structure and delays, in
Differential Equations and Applications to Biology and to Industry,
eds. M. Martelli, K. Cooke, E. Cumberbatch, B. Tang, and H. Thieme,
World Scientific, Singapore, 327-336.
- J.
M. Mahaffy, J. Bélair and M. C. Mackey (1998) Hematopoietic model
with moving boundary condition and state dependent delay: Applications
in erythropoiesis, J. Theor. Biol. 190, 135-146.
- J.
M. Mahaffy and E. S. Savev (1999) Stability analysis for mathematical
models of the lac operon, Quart. Appl. Math. 57,
37-53.
- J.
M. Mahaffy, Samuel W. Polk, and Roland K. W. Roeder (1999) An age-structured
model for erythropoiesis following a phlebotomy, Technical Report, Centre
recherches mathématiques, Université de Montréal,
CRM-2598
- J.
M. Mahaffy (1999) Age-structured modeling of hematopoiesis, Technical
Report, Centre recherches mathématiques, Université de
Montréal, CRM-2609
- M.
Santillán, J. M. Mahaffy, J.
Bélair and M. C. Mackey (2000) Regulation of platelet
production: The normal response to perturbation and cyclical platelet
disease. J. Theor. Biol. 206, 585-603.
- J.
Bélair and J. M. Mahaffy (2001) Variable maturation velocity
and parameter sensitivity in a model of haematopoiesis. IMA Journal
of Mathematics Applied in Medicine and Biology 18, 193-211.
- M.
Breitbart, P. Salamon, B. Andresen, J. M. Mahaffy, A. M. Segall, D.
Mead, F. Azam, and F. Rohwer (2002) Genomic analysis of uncultured marine
viral communities. PNAS 99, 14250-14255.
- A.
V. Grigorian, R. B. Lustig, E. C. Guzman, J. M. Mahaffy, and J. W. Zyskind
(2002) Escherichia coli cells with increased levels of DnaA require
recombinant repair for viability. J. Bacteriol. 185, 630-644.
- M.
Breitbart, I. Hewson, B. Felts, J. M. Mahaffy, J. Nulton, , P. Salamon,
and F. Rohwer (2003) Metagenomic analysis of an uncultured viral community
from human feces. J. Bacteriol.
185, 6220-6223.
- M.
Breitbart, B. Felts, S. Kelley, J. M. Mahaffy, J. Nulton, P. Salamon,
and F. Rohwer (2004) Diversity and population structure of a nearshore
marine sediment viral community. Proceedings of the Royal Society
B.
Recent Invited Talks:
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