Download Glossary Appendix A List of acronyms

Appendix A
Glossary
List of acronyms
BHI
BioTeC
CFU
ESAB
FC
FS
IbM
IbMs
INDISIM
MOSIMBIO
MSE
MSZ
NMTA
PBC
RBC
SCT-UB
SS
Brain Heart Infusion
Bioprocess Technology and Control group
Colony Forming Unit
Escola Superior d'Agricultura de Barcelona
Flow Cytometer
Forward Scattered light (ow cytometry)
Individual-based Modelling
Individual-based Models
INDividual DIScrete SIMulation
Modelling and Computer Simulation of Biological Systems group
Mean sum of Squared Errors
Multisizer
Nelder-Mead Threshold Accepting
Periodic Boundary Conditions
Red Blood Cells
Scientic-Technical Services of the Universitat de Barcelona
Side Scattered light (ow cytometry)
174
Glossary
SSE
TIP
TA
UB
UPC
Sum of Squared Errors
Thermodynamics of Irreversible Processes
Threshold Accepting
Universitat de Barcelona
Universitat Politècnica de Catalunya
List of abbreviations
beg
bib
EN V EN V +
exp
inf
max
min
ref
s.u.
sup
X0
Xf
beginning
bibliography
pre-inoculation environment
present environment
exponential phase
inferior
maximum
minimum
reference
simulation units
superior
initial value of 'X'
nal value of 'X'
Glossary
175
List of symbols
λ
µ
D(t)
Dm (t)
Dpk (t)
m
m(t)
md
mR
N (t)
pkm (t)
tF D
tG
tR
U
lag parameter
growth rate
product distance
mean mass distance
mass distribution distance
bacterial individual mass
bacterial mean mass of a culture
individual bacterial mass at division
invidual mass to initiate reproduction cycle
cell density
instantaneous cell's biomass relative frequency
time to the rst division
generation time or doubling time
reproduction cycle duration
uptaken nutrient particles
Chapter 1
α(t)
τi
b, c, Tmin , Tmax
G(t)
g1 , g2
kn
M
N G(t)
Q(t)
s
s∗
smin
tai
tLAGi
tmi
adjustment function
individual adjustment period
parameters of Equation 1.4
growing fraction population
mathematical attractors for dening lag parameter
constant for Equation 1.9
cell biomass
non-growing fraction population
physiological
excess biomass per cell
total biomass per cell
minimum biomass per cell
individual adjustment period
individual lag time
individual generation time
176
Glossary
Chapter 2
ρ
σ
(x, y)
B
b
Bi
cs
d
dmax
Ds
Exy
Enz
I
Igen
Js
m1 , m2
nenz
Nmon
pmov
tenz
Venz
Y
Yenz
Z1 , α, c, k , n
parameter to x an interval of the growth curve
standard deviation
coordinates of a spatial cell
increase in bacterial biomass
parameter of Equation 2.2
vector that describes a bacterium
concentration of substance s
mean distance between neighbouring cells
maximum movement radius
diusion coecient of a substance
vector that describes a spatial cell
enzyme particles in a bacterial cell
maintenance constant
index to control the extracellular enzyme particles synthesis
ux of a substance between neighbouring cells
individual bacterial masses after division
enzyme particles synthesized by a bacterial cell
number of monomers contained in a polymer
probability for a bacteria to move
time duration of extracellular enzyme particles
enzyme synthesis rate per unit of mass and time step
metabolic eciency
energy cost of enzyme synthesis
parameters of the uptake model
Chapter 3
Ek
r
T
mean kinetic energy of the nutrient particles
radius of the accessible volume of nutrient particles around a
bacterium
temperature
Glossary
177
Chapter 4
∆m
λpseudo
λreal
µB
µN
ρ
τ B , tB
a
B(t)
mi
p(mi )
PEXP
PI(B)
PI(N )
PT (B)
PT (N )
R
t 1 , t2
te , N e
Z, γ, β
biomass interval to dene the classes of biomass
apparent lag or pseudolag of a culture
real lag of a culture
total biomass growth rate
cell density growth rate
parameter to x an interval of the growth curve
parameters to distinguish the balanced growth
parameter of Equation 4.10
total biomass of a culture
class of biomass
biomass probability distribution of a bacterial culture
exponential phase
initial phase in total biomass
initial phase in cell density
transition phase in total biomass
transition phase in cell density
mean of duplications per hour of an individual cell
temporal limits of transition phase in cell density
coordinates of an exponential point of the growth curve
parameters of Equation 4.4
Chapter 5
d
Dd (t)
Dpkd (t)
Dd (t)
fs
N
pkm (t)
R
ss
equivalent diameter
mean diameter distance
diameter distribution distance
product distance
forward scatter channels
number of channels
instantaneous cell's diameter relative frequency
mean of duplications per hour of an individual cell
side scatter channels
178
Glossary
Chapter 6
Γ, α , β
γ , ρ, χ, σ
ξ
ρ
ρ̂
τr
A, B , C
Cexp (t)
Csim (t)
f (m; A, B)
→
F (−
x)
g
m
n
npi
nR
nS,r
pi
p̂i
→
Q(−
x)
R1 , R2 , R 3
ts
umax
Vd
→
−
x
Y
parameters to x the thresholds (NMTA)
coecients of NMTA geometric operations
random simplex shift probability (NMTA)
radius of the trust region (NEWUOA)
re-scaled radius of the trust region (NEWUOA)
threshold value for round r (NMTA)
parameters of a Weibull distribution
experimentally measured cell concentration
simulation output of cell concentration
Weibull distribution
objective function (NEWUOA)
number of generations per hour
number of interpolation points (NEWUOA)
total number of data points
number of points to be tested for each parameter (grid search)
number of stepping rounds (NMTA)
number of simplex steps in round r (NMTA)
parameters to be estimated
re-scaled parameters to be estimated (NEWUOA)
quadratic model (NEWUOA)
number of evaluations of the objective function at each
simplex vertex (NMTA)
time step
mean maximum uptake rate
bacterial volume at division
vector with a combination of parameters to be estimated
(NEWUOA)
yield