© 2006 by The International Union of Biochemistry and Molecular Biology BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION

Printed in U.S.A. Vol. 34, No. 6, pp. 417–422, 2006

Articles

Growth of Microbial Populations

MATHEMATICAL MODELING, LABORATORY EXERCISES, AND MODEL-BASED DATA ANALYSIS

Received for publication, January 30, 2006

Alfonsas Juška‡, Genovaitė Gedminienė, and Ru៮ ta Ivanec

From the Vilniaus Gedimino technikos universitetas, Saulėtekio al. 11, 10223 Vilnius 40, Lithuania

This paper has arisen as a result of teaching Models in Biology to undergraduates of Bioengineering at the
Gediminas Technical University of Vilnius. The aim is to teach the students to use a fresh approach to the
problems they are familiar with, to come up with an articulate verbal model after a mental effort, to express
it in rigorous mathematical terms, to solve (with the aid of computers) corresponding equations, and finally,
to analyze and interpret experimental data in terms of their (mathematical) models. Investigation of
microbial growth provides excellent possibilities to combine laboratory exercises, mathematical modeling,
and model-based data analysis. Application of mathematics in this field proved to be very fruitful in getting
deeper insight into the processes of microbial growth. The step-by-step modeling resulted in an extended
model of the growth covering conventional “lag,” “exponential,” and “stationary” phases. In contrast to
known models (differential equations that can be solved only numerically), the present model is expressed
symbolically as a finite combination of elementary functions. The approach can be applied in other areas
of modern biology, such as dynamics of various cellular processes, enzyme and receptor kinetics, and
others.
Keywords: Verhulst equation, logistic equation, growth rate, generation time, lag time.

Performing laboratory exercises, students learn various
techniques and acquire practical skills, whereas while
modeling, they apply all their experience, above all, their
knowledge of mathematics. Students of biochemistry and
molecular biology, among others, are (or at least are sup-
posed to be) computer-literate nowadays. They are sup-
posed to have basic mathematical knowledge as well. Still,
some students seem to have “an aversion to math, ’Math-
ematophobia,’” having “little appreciation for the impor-
tance of models in scientific progress” [1]. Mathematics
does not seem to be properly appreciated by teachers (or
textbook writers), either. In textbooks, mathematical equa-
tions, or “formulae,” if presented at all, often appear to be
just a mandatory tribute to modernity. It is more so in
microbiology textbooks (e.g. see Refs. [2– 4]), where pres-
entation of microbial growth is most primitive, without any
reference to the growth equation (known from the mid-
19th century as the Verhulst or logistic model); neither
“Verhulst” nor “logistic” can be found in the index. (The
“lack of interdisciplinary communication” [5] is sad
enough; it is more so in microbiology, the lack being intra-
disciplinary. The growth equations seem to be ignored in
the textbooks, whereas being considered in scientific jour-
nals (e.g. see Refs. [6 and 7])). On the other hand, research
in the population growth provides excellent possibilities for
both laboratory exercises and qualitative and quantitative
data analysis; such studies (not being highly demanding of
‡ To whom correspondence should be addressed: E-mail:
alfonsas@reda.vtu.lt.
This paper is available on line at http://www.bambed.org
material resources or skills or special knowledge of math-
ematics) can be easily conducted, whereas experience
gained in these exercises and modeling will be very useful
in other areas. The appreciation of role and importance of
models in science and engineering evolves as a result of
this activity.
At the Gediminas Technical University of Vilnius, under-
graduates of bioengineering have a four-credit course of
Models in Biology concurrently with biochemistry, micro-
biology, and other courses with laboratories. As a result of
teaching (and learning), they are expected to use a fresh
approach to the problems they are familiar with, to come
up with an articulate verbal model after a mental effort, to
express it in rigorous mathematical terms, to solve (with
the aid of computers) corresponding equations, and, fi-
nally, to analyze and interpret experimental data in terms
of their (mathematical) models. Students are requested to
submit their work in electronic form rather than hard copy.
The students are encouraged to take part in annual scien-
tific conferences (e.g. see Refs. [8 and 9]). One of the
present writers (R.I.) is a student.
We consider it pedagogically relevant to present step-
by-step modeling of microbial growth and model-based
analysis of experimental data in the main text rather than
putting the modeling in an appendix. Our endeavor in
modeling has been rewarded by what amounts to a little
discovery. The extended model appears to be new (it has
never been published before) and rather simple. It can be
extended further on. The way of getting such a model is of
interest far beyond the area of microbiology education.
417
418 BAMBED, Vol. 34, No. 6, pp. 417–422, 2006
MATHEMATICAL MODELING
It is clear that at any moment, t, (absolute) rate, a, of
growth of a population size (number of cells, total mass,
(optical) density, etc.), A, is proportional to the population
size, i.e.
a ⫽ ␣A (Eq. 1)
the coefficient of proportionality, ␣, being relative rate of
population growth (or specific growth rate). The statement
above (a verbal model of growth, as a matter of fact) can
be expressed mathematically in the form of the differential
equation,
dA
⫽ ␣A (Eq. 2)
dt
The specific growth rate depends on the environmental
conditions, and it may be considered that
␣ ⫽ ␣0 共␣0 ⫽ const兲 (Eq. 3)
as long as the conditions remain unchanged. With the
growth of population size (density), the conditions may
change because of the growth; first of all, the organisms may
have to compete for available resources. Let the initial sup-
ply of the resources equal to 1. This supply may be sup-
posed to be depleted proportionally to the population size;
the availability of resources, therefore, will remain 1 ⫺ A/B,
and, as a consequence, the relative rate of growth will be,

冉 冊
␣ ⫽ ␣0 1 ⫺
A
B
(Eq. 4)

the meaning of the coefficient of proportionality, 1/B, or

rather, of its reciprocal, B, will become clear in the next
section (it can be noted now that ␣ ⫽ 0 when A ⫽ B).
Equation 4 can be interpreted as a manifestation of neg-
ative feedback occurring in various systems in many fields
including molecular biology (e.g. see Ref. [9]). For A ⬍⬍ B,
Equation 4 is reduced to Equation 3.
The solution of Equation 2, taking into account Equa-
tions 3 or 4, results in either exponential or logistic (Ver-
hulst) models. In defining parameter ␣ in Equation 2, other
reasonable considerations (beyond Equations 3 and 4) can FIG. 1. Time course of microbial growth in linear (A) and
be taken into account, giving rise to new models. semilogarithmic (B) scale and growth rate (C). Circles symbol-
ize experimental data points (the open circles (in red) correspond
LABORATORY EXERCISES AND MODEL-BASED DATA ANALYSIS to routine experiment, the closed circles (in blue) correspond to
an experiment performed after bacteria were kept in an ice bath
Obtaining viable count data being time-consuming and for 2 h). a and a⬘, MUG; b and b⬘, MLG; c and c⬘, extended model
expensive, we were using a more rapid method of accu- (EM). A0 ⫽ 0.18, B ⫽ 2.8, ␣0 ⫽ 0.0153 min⫺1 (shared by both
mulating the data. We were measuring optical density models), ␤ ⫽ 0.040 min⫺1 (used in EM).
(OD)1 of microbial culture, OD being related to the turbidity
presented in Fig. 1 (open circles). Conventionally, for anal-
or density of the culture. The culture (Escherichia coli) was
ysis of such data, the growth curve is divided into separate
grown in 100 ml of Luria-Bertani medium in 1-liter flasks
phases [3, 4, 6]; more promising seems to be using the
under conventional conditions (37 °C, agitated at 150
above models directly. The exponential model (curves a)
rpm). At high density (OD ⬎ 0.5), for the measurement of
optical density, the culture was diluted to obtain OD ⱕ 0.5. A ⫽ A0e␣0t (Eq. 5)
The dilutions (and OD measurements) were made in du-
plicate to obtain more data for statistical analysis. (which is the solution of Equation 2, taking into account
Typical student-generated microbial growth data are Equation 3 under the initial condition A (0) ⫽ A0 (A0 being
the inoculum size)) is quite close to experimental data
1
The abbreviations used are: OD, optical density; MLG, model points at the beginning of growth and suggests the tend-
of limited growth; MUG, model of unrestricted growth; EM, ex- ency which, however, can hardly be considered as a sep-
tended model. arate “exponential phase” since the model deviates con-

FIG. 2. Printout of Maple work-
sheet with working examples. Left-
aligned expressions (in red) are Maple
inputs; centered expressions (in blue)
are Maple outputs. A, the input pre-
sented in Maple notations; B and C,
the input in standard math (the display
can be changed by toggling). The ex-
amples can be used as templates re-
placing the bracketed expressions in
Maple inputs by any reasonable ones.
siderably from further experimental data (a larger part of
the data, as a matter of fact; Fig. 1A). However, before
discarding the model, let us note that according to this
model, at the moment of T0 (which has yet to be found), the
population doubles, i.e.
A0e␣0T0 ⫽ 2A0 (Eq. 6)
from where (taking the natural logarithm of both sides of
the equation)
ln 2
T0 ⫽ (Eq. 7)
␣0
Parameter T0 is called the generation time. It follows from
Equation 6 (by dividing both parts of that equation by A0
and raising them to power n) that
en␣0T0 ⫽ 2n (Eq. 8)
That means that whereas the model (Equation 5) is con-
tinuous, the doubling in the number of microorganisms as
a result of binary fission at discrete time intervals, T0, is
essentially a discrete process making a geometric pro-
gression. Analysis of microbial growth provides, therefore,
an excellent opportunity to demonstrate once more that
(discrete) geometric progression can be extended by a
more general (continuous) exponential function.
Students may need to be reminded of how to solve the
above equation or just shown how to use popular com-
puter programs such as Mathcad or Maple [10]. Without
entering into a detailed discussion on how to use Maple in
general or its computing possibilities, students are pre-
sented with a working example (Fig. 2) of solving the first
order differential equation, the right-hand part of which
can be substituted by any reasonable expression. Entering
419
the right-hand part of Equation 4, we obtain immediately a
model that is equivalent to the Verhulst or logistic equation
(the equivalence can be verified by Maple as well; Fig. 2B).
We present the equation in a slightly different form
A0e␣0t
A⫽ (Eq. 9)
A0
1 ⫹ 共e␣0t ⫺ 1兲
B
which is more convenient for analysis and comparing with
other models. (Other models are presented in a similar
way, differing from the immediate Maple output. Although
appearing rather complicated, they can be visualized di-
rectly in a Maple worksheet as graphs of population size
versus time or copied and pasted into Excel worksheet.)
Note that the numerator of the above model is the right-
hand part of Equation 5. It can be seen that for t 3 ⬁ A 3
B, thus the meaning of parameter B; it is the asymptotic
value of population size. It would be reasonable, therefore,
to refer to Equation 9 as a model of limited growth (MLG)
in contrast to Equation 5, which might be designated a
model of unrestricted growth (MUG). For B ⬎⬎ A0, MLG is
close to MUG, and for B 3 ⬁, it is reduced to MUG (Figs.
1 and 2C).
Once a model has been accepted as “good enough” to
approximate experimental data, all the information con-
tained in the data should be considered to be contained (in
a generalized mathematical form) in the model, there being
no need ever to come back to the data; everything of
interest can be derived from the model. The latter can be
used to model the growth under conditions (technically)
inconvenient for direct experimental investigation. In Fig.
3, the right-hand curves correspond to the inoculum size
about a thousand times lower than that used in the above
420
FIG. 3. Model curves of microbial growth (A and B) and of
growth rate (C) identical (except for the difference in time
scale and the difference in vertical scale for panels B) to
those presented in Fig. 1 (left curves) and respective curves
(d, e, and eⴕ) with the same B and ␣0 but the inoculum being
⬃1000 times lower (right curves).
experiments, other conditions being the same. To obtain
such curves experimentally using turbidometric methods
is not possible because it is impossible to observe (and
measure) very low optical densities. (Of course, one can
obtain such curves using viable counts, but that method,
as mentioned above, is rather inconvenient.) It should be
noted that one can observe the exponential growth of
microbial population in Fig. 2 based on MLG.
(Absolute) rate of population growth, i.e. the rate of
change in population size, is the first derivative of the latter
BAMBED, Vol. 34, No. 6, pp. 417–422, 2006
(the right-hand part of Equation 9); this rate divided by the
population size (the right-hand part of the same equation)
yields the time course of the relative (or specific) growth rate,
共B ⫺ A0兲e⫺␣0t
␣ ⫽ ␣0 (Eq. 10)
共B ⫺ A0兲e⫺␣0t ⫹ A0
as shown in Fig. 1, curve b⬘. It can be seen that the relative
rate declines over time, the initial rate (at t ⫽ 0) being
冉
␣initial ⫽ ␣0 1 ⫺
B冊
A0
(Eq. 11)
i.e ␣ ⬍ ␣0 for any finite B; ␣0, therefore, means asymptotic
relative rate of growth for B 3 ⬁ (cf. Equation 4 and Fig. 1).
Although several factors causing the slowing of popula-
tion growth are pointed out in textbooks [3], as mentioned
above, only one has been taken into account in Equation 4,
namely, competition for available resources. This is suffi-
cient to cause the decline in growth rate.
As stated above, experimental data obtained by the
students as a result of their laboratory exercises can be
reasonably approximated by Equation 9. The data do not
seem to suggest a “lag” in the growth. The lag (if any) is
supposed to reflect the time necessary for the microorga-
nisms to adapt to the new environment after their transfer
from the storage medium. It seems reasonable to assume
that the period of time necessary for the adaptation depends
on the contrast between the old and the new environments.
The next experiment was based on this assumption.
MODEL EXTENSION
To get experimentally observable lag, the microorga-
nisms were kept before inoculation under 0 °C (in ice bath)
for 2 h other conditions being identical to those of the pre-
vious experiment. The data are presented in Fig. 1 (closed
circles). To approximate these data, the model had to be
extended; the MLG (curve b) is not acceptable in this case.
The modeling above is carried out routinely by the stu-
dents of bioengineering at the university in the Models in
Biology classes. The material above has been presented at
a student scientific conference [8]. What follows is beyond
the curriculum. To extend the model, let us assume that
the microbial population from the moment of inoculation
(i.e. the moment of change in the environment) proceeds
from state D (“dormant”) to state G (“growing”).
␤
DO
¡G
TRANSITION 1
Let d and g denote the relative size of the population in the
respective state, ␤, rate constant (or relative rate) of the
transit. States D and G can be attributed as well to an
individual cell (or organism, or any entity in molecular
biology). Parameters d and g can be considered as prob-
abilities that the entity is in state D or G.
This transition is independent of the growth (the orga-
nisms, undergoing the transition, and those, taking part in
the growth, are not the same), so temporal increase in g
can be modeled independently. There are two unknowns,
d and g, and it is clear that d ⫹ g ⫽ 1. That makes one of
two equations of the system, necessary to find these un-
 421
knowns; another equation is based on the rate of Transi- sumes, as a matter of fact, that the separate phases do
tion 1. So the system is exist as something intrinsic to the microorganisms or their

再
growth, and those phases by implication possess their
d⫹g⫽1 specific characteristics or parameters. Indeed, the stu-
dg (Eq. 12) dents often ask about the duration of the phases, espe-
⫽ ␤d
dt cially about that of the lag phase. The lag is of great
Solution of this system with respect to g taking into ac- importance in food microbiology; in the papers of the field,
count the initial condition (let g(0) ⫽ G (0 ⱕ G ⱕ 1), i.e. at it is often denoted as L or ␭. However, as Buchanan et al.
the moment of inoculation portion G of the population is [7] point out, “there is currently no generally accepted
growing) results in definition for lag phase that is based on physiological
events occurring in the bacterial population.” Estimation of
g ⫽ 1 ⫺ 共1 ⫺ G兲e⫺␤t (Eq. 13) this parameter, as well as its incorporation into growth
equations, is bound, therefore, to serious difficulties. The
Now Equation 2 can be modified taking into account both reason of these difficulties, as Baty and Delignette-Muller
Equation 4 and Equation 13. [11] put it, “is the lack of physiological understanding of the
dA
dt
A
⫽ ␣0共1 ⫺ 共1 ⫺ G兲e⫺␤t兲 1 ⫺ A
B 冉 冊 (Eq. 14)
lag phenomenon. In actual fact, little knowledge is avail-
able concerning this physiological stage and only few au-
thors were able to put some biological information about ␭
The solution of the above equation is into model equations. The second reason is related to the
⫺␤t共1⫺G兲␣0/␤
first one and comes from the fact that the actual definition
A0e␣0t⫹e of ␭ is either purely geometric or purely mathematic.” The

冉 冊
A⫽
共1⫺G兲␣0/␤
A0 ␣0t ⫹ e⫺␤t共1 ⫺ G兲␣0/␤
e ⫹ e ⫺ e共1 ⫺ G兲␣0/␤
B
where A0, as above, is inoculation size comprised of the
cells both in dormant and in growing states. As can be
seen, for G ⫽ 1 (at the moment of inoculation, all the
population is in the growing state) or ␤ ⬎⬎ ␣, Equation 15
is reduced to Equation 9. Similarly, for B 3 ⬁, it is reduced
to Equation 5. For G ⫽ 0 (at the moment of inoculation, all
the population is completely in the dormant state), it
becomes
⫺␤t
A0e␣0t⫹e ␣0/␤
(Eq. 15)
very approach (the attempts to incorporate ␭ into model
equations) implies tacitly the lag to be of “primary” or
“fundamental” order. Such a “hidden assumption” [5]
seems to be more a hindrance than a help in getting at the
essence of the processes that lead to the lag. The lag can
be redefined painlessly on the basis of Transition 1 (con-
sidered above) both in mathematical (probabilistic) and in
geometrical terms.
Indeed, the lag is caused, presumably, by the inability of
microorganisms residing in state D (dormant) to take part
in the growth of the population, the duration of the lag, ␭,
being determined by the duration of residence of the or-

冉 冊
A⫽ (Eq. 16) ganisms in state D. The transition D 3 G, presumably, is a
A0 ␣0t⫹e⫺␤t␣0/␤ random process, the duration of residence of an individual
e ␣ 0 /␤ ⫹ e ⫺ e ␣ 0 /␤
B organism in state D being a random value whose proba-
bility distribution can be found the following way.
As can be seen for ␤ ⬎⬎ ␣0 (very high rate of transition from
The relative number of the organisms, d, residing in state
the dormant to the growing state), both Equation 15 and
D in the course of time is the solution of Equation 12 with
Equation 16 are reduced to Equation 9. Equation 16 was
respect to d taking into account the initial conditions. Let
fitted to the experimental data without any significant de-
d(0) ⫽ 1 (i.e. at the moment of inoculation, all the orga-
viation (Fig. 1, curve c and closed circles). Equations 15
nisms are in state D). Thus,
and 16, therefore, can be considered to approximate ex-
perimental data adequately. The extended model (EM), d ⫽ e ⫺ ␤t (Eq. 18)
therefore, being more general than MLG, in addition to the
latter, also covers the “lag phase.” By analogy with Equa- This solution multiplied by ␤ can be considered, therefore,
tion 9, the dynamics of the relative growth rate can be as density of probability distribution of the duration of
determined for EM as well, residence of the organisms in state D.
⫺␤t␣01/␤
The mean duration of residence of the organisms in this
共B ⫺ A0兲共1 ⫺ e⫺␤t兲e⫺␣0t⫺e state, therefore, is
␣ ⫽ ␣0 ⫺␣0t⫺e⫺␤t␣0/␤ (Eq. 17)
(B ⫺ A0)e ⫹ A0e⫺␣0/␤

冕
⬁

For ␤ ⬎⬎ ␣, this equation is reduced to Equation 10. It is 1

t 䡠 ␤e⫺␤tdt ⫽ (Eq. 19)
worth noting that the EM (Equations 15 and 16) is rather ␤
simple. First of all, it is expressed as a finite combination of 0

elementary functions. Other features of the model will be

discussed in the next section. This mean can be expected to be equal to the lag, i.e.

DISCUSSION 1/␤ ⫽ ␭ (Eq. 20)

The success in the modeling presented here is due Model parameters, including ␤, were estimated as a
mainly to disregard of the conventional division of micro- result of fitting the models (both MLG and EM) to the
bial growth into separate “phases.” Such a division pre- experimental data. There is good agreement of the models
422
with the data. The temporal shift of EM with respect to
MLG, as expected (Fig. 1B), appears to be equal to pa-
rameter ␭. Thus, the geometrical definition is that the lag is
the shift of EM with respect to MLG. Equation 20 (read
from the right to the left) can be considered as the prob-
abilistic definition of the lag.
Transition 1 was postulated on the basis of “common
sense.” It should be considered as a “guess” or as a first
approximation of the processes taking place in reality.
However, even such simplification results in a quite ac-
ceptable model. It is clear that, if necessary, a multistep
transition can be taken into account in Equation 2 follow-
ing the above reasoning.
It should be noted that the lag discussed above and the
delay (as depicted in Fig. 2) are essentially different things,
the latter depending on the inoculum size. This distinction
is not always properly recognized (e.g. see Ref. [4]). On the
other hand, whereas experimental data corresponding to
the inoculum pre-treatment by keeping it in cold can be
explained by Transition 1 and modeled by Equations 15 or
16, this explanation cannot be considered as the only one
possible. Indeed, a portion of the cells as a result of
keeping them under unfavorable conditions may be dead
(the optical density remaining unchanged) with only those
alive taking part in population growth; that would result in
a delay or “quasilag” of the growth curve with the initial
value unchanged.
The known models developed to simulate the lag phase
[12–14] are rather complicated mainly because of the
problems related to the nature of the lag phenomenon
mentioned above. The corresponding equations can be
solved only numerically.
The models presented (Equations 9, 15, or 16) do not
cover the “death phase.” This phase is supposed to arise
because of changes in the environment caused by the
activity of the microorganisms: first of all, by the depletion
of resources and accumulation of (toxic) waste products
(e.g. see Ref. [3]). (Note that in Equation 4, only competi-
tion for available resources (i.e. for “building materials”)
was taken into account.) Presumably, the decline in the
ability of the environment to sustain the population is
proportional to (cumulative) depletion of resources and
waste accumulation, the decline depending both on the
size of the population and on the duration of its activity.
Thus, to compute the decline, the population size (multi-
plied by a factor corresponding to the depletion and the
accumulation) has to be integrated over a period of time.
Then this integral has to be substituted for the population
size in Equation 4. That will result in a second order dif-
ferential equation. Such an extension of the model, how-
ever, is beyond the scope of the present report.
CONCLUSIONS
Investigation of microbial growth provides excellent
possibilities to combine laboratory exercises, mathemat-
BAMBED, Vol. 34, No. 6, pp. 417–422, 2006
ical modeling, and model-based data analysis. Applica-
tion of mathematics proved to be very fruitful in getting
deeper insight into the processes of microbial growth.
The step-by-step modeling resulted in an extended
model of the growth covering conventional lag and ex-
ponential and stationary phases. In contrast to known
models (differential equations that can be solved only
numerically), the present model is expressed symboli-
cally as a finite combination of elementary functions. The
approach can be applied in other areas of modern biol-
ogy, such as dynamics of various cellular processes (e.g.
see Ref. [15]) and enzyme and receptor kinetics (e.g. see
Ref. [16]) and others).
Acknowledgments—A.J. thanks his postgraduates I.
Sutkevičiu៮ tėand S. Ališauskaitė for comments on the manuscript
and checking the equations and Ph.D. student M. Morku៮ nas for
stimulating discussions.
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