We investigate a quantitative bistable two-dimensional model (MeKS network) of gene expression dynamics describing the competence development in the Bacillus subtilis under the influence of Lévy as well as Brownian motions. To analyze the transitions between the vegetative and the competence regions therein, two dimensionless deterministic quantities, the mean first exit time (MFET) and the first escape probability, are determined from a microscopic perspective, as well as their averaged versions from a macroscopic perspective. The relative contribution factor λ, the ratio of non-Gaussian and Gaussian noise strengths, is adopted to identify an optimum choice in these transitions. Additionally, we use a recent geometric concept, the stochastic basin of attraction (SBA), to exhibit a pictorial comprehension about the influence of the Lévy motion on the basin stability of the competence state. Our main results indicate that (i) the transitions between the vegetative and the competence regions can be induced by the noise intensities, the relative contribution factor λ and the Lévy motion index α; (ii) a higher noise intensity and a larger α with smaller jump magnitude make the MFET shorter, and the MFET as a function of λ exhibits one maximum value, which is a signature of the noise-enhanced stability phenomenon for the vegetative state; (iii) a larger α makes the transition from the vegetative to the adjacent competence region to occur at the highest probability. The Lévy motion index α00.5 (a larger jump magnitude with a lower frequency) is an ideal choice to implement the transition to the non-adjacent competence region; (iv) there is an expansion in SBA when α decreases.

1.
P.
Bressloff
,
Stochastic Processes in Cell Biology
(
Springer
,
2014
).
2.
N. G.
van Kampen
,
Stochastic Processes in Physics and Chemistry
(
North-Holland
,
1992
).
3.
C.
Gardiner
,
Handbook of Stochastic Methods
(
Springer, Berlin
,
2009
).
4.
B.
Øksendal
,
Stochastic Differential Equations: An Introduction with Applications
, 6th ed. (
Springer
,
2005
).
5.
D.
Applebaum
,
Lévy Processes and Stochastic Calculus
, 2nd ed. (
New York Cambridge University Press
,
2009
).
6.
J.
Duan
,
An Introduction to Stochastic Dynamics
(
New York Cambridge University Press
,
2015
).
7.
M.
Kærn
,
T.
Elston
,
W.
Blake
, and
J.
Collins
, “
Stochasticity in gene expression: From theories to phenotypes
,”
Nat. Rev. Genet.
6
,
451
464
(
2005
).
8.
A.
Raj
and
A.
Oudenaarden
, “
Nature, nurture, or chance: Stochastic gene expression and its consequences
,”
Cell
135
,
216
226
(
2009
).
9.
M.
Pal
,
A.
Pal
,
S.
Ghosh
, and
I.
Bose
, “
Early signatures of regime shifts in gene expression dynamics
,”
Phys. Biol.
10
,
036010
(
2013
).
10.
C.
Zeng
,
Q.
Han
,
T.
Yang
,
H.
Wang
, and
Z.
Jia
, “
Noise- and delay-induced regime shifts in an ecological system of vegetation
,”
J. Stat. Mech.
2013
,
P10017
(
2013
).
11.
A.
Eldar
and
M.
Elowitz
, “
Functional roles for noise in genetic circuits
,”
Nature
467
,
167
173
(
2010
).
12.
J.
Levine
,
Y.
Lin
, and
M.
Elowitz
, “
Functional roles of pulsing in genetic circuits
,”
Science
342
,
1193
1200
(
2013
).
13.
B.
Jourdain
,
S.
Méléard
, and
W.
Woyczynski
,“
Lévy flights in evolutionary ecology
,”
J. Math. Biol.
65
,
677
707
(
2012
).
14.
Y.
Zheng
,
L.
Serdukova
,
J.
Duan
, and
J.
Kurths
, “
Transitions in a genetic transcriptional regulatory system under Lévy motion
,”
Sci. Rep.
6
,
29274
(
2016
).
15.
M.
Hao
,
J.
Duan
,
R.
Song
, and
W.
Xu
, “
Asymmetric non-gaussian efficts in a tumor growth model with immunization
,”
Appl. Math. Mod.
38
,
4428
4444
(
2104
).
16.
R.
Dar
et al., “
Transcriptional burst frequency and burst size are equally modulated across the human genome
,”
Proc. Natl. Acad. Sci.
109
,
17454
17459
(
2012
).
17.
Y.
Zhang
et al., “
Data assimilation and parameter estimation for a multiscale stochastic system with α-stable Lévy noise
,”
J. Stat. Mech.
2017
,
113401
(
2017
).
18.
D.
Dubnau
, “
DNA uptake in bacteria
,”
Annu. Rev. Microbiol.
53
,
217
244
(
1999
).
19.
A.
Grossman
, “
Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis
,”
Annu. Rev. Genet.
29
,
477
508
(
1995
).
20.
T.
Cagătay
,
M.
Turcotte
,
M.
Elowitz
, and
G.
Süel
, “
Architecture-dependent noise discriminates functionally analogous differentiation circuits
,”
Cell
139
,
512
522
(
2009
).
21.
A.
Mugler
et al., “
Noise expands the response range of the bacillus subtilis competence circuit
,”
PLoS Comput. Biol.
12
,
1
12
(
2015
).
22.
G.
Süel
,
J.
Garcia-Ojalvo
,
L.
Liberman
, and
M.
Elowitz
, “
An excitable gene regulatory circuit induces transient cellular differentiation
,”
Nat. Lett.
440
,
545
550
(
2006
).
23.
T.
Gao
,
J.
Duan
,
X.
Li
, and
R.
Song
, “
Mean exit time and escape probability for dynamical systems driven by lévy noises
,”
SIAM J. Sci. Comput.
36
,
A887
A906
(
2014
).
24.
H.
Chen
,
J.
Duan
,
X.
Li
, and
C.
Zhang
, “
A computational analysis for mean exit time under non-gaussian lévy noises
,”
Appl. Math. Comput.
218
,
1845
1856
(
2011
).
25.
X.
Wang
,
J.
Duan
,
X.
Li
, and
Y.
Luan
, “
Numerical methods for the mean exit time and escape probability of two-dimensional stochastic dynamical systems with non-Gaussian noises
,”
Appl. Math. Comput.
258
,
282
295
(
2015
).
26.
D.
Li
,
C.
Zhang
, and
J.
Wen
, “
A note on compact finite difference method for reaction-diffusion equations with delay
,”
Appl. Math. Model.
39
,
1749
1754
(
2015
).
27.
D.
Li
and
C.
Zhang
, “
Split Newton iterative algorithm and its application
,”
Appl. Math. Comp.
217
(5),
2260
2265
(
2010
).
28.
J.
Lee
,
A.
Cinar
, and
J.
Duan
, “
Dynamical behavior of the activator-repressor circuit model under random fluctuations
,”
Commun. Nonlin. Sci. Numer. Simul.
16
,
1978
1985
(
2011
).
29.
F.
Wu
,
X.
Cheng
,
D.
Li
, and
J.
Duan
, “
A two-level linearized compact ADI scheme for two-dimensional nonlinear reaction-diffusion equations
,”
Comput. Math. Appl.
75
,
2835
2850
(
2018
).
30.
R.
Cai
,
X.
Chen
,
J.
Duan
,
J.
Kurths
, and
X.
Li
, “
Lévy noise-induced escape in an excitable system
,”
J. Stat. Mech.
2017
,
063503
(
2017
).
31.
T.
Yang
et al., “
Delay and noise induced regime shift and enhanced stability in gene expression dynamics
,”
J. Stat. Mech.
2014
,
P12015
(
2014
).
32.
D.
Kim
,
O.
Rath
,
W.
Kolch
, and
K.
Cho
, “
A hidden oncogenic positive feedback loop caused by crosstalk between Wnt and ERK pathways
,”
Oncogene
26
,
4571
4579
(
2007
).
33.
N.
Kellershohn
and
M.
Laurent
, “
Prion diseases: Dynamics of the infection and properties of the bistable transition
,”
Biophys. J.
81
,
2517
2529
(
2001
).
34.
S.
Huang
, “
Genetic and non-genetic instability in tumor progression: Link between the fitness landscape and the epigenetic landscape of cancer cells
,”
Cancer Metastasis Rev.
32
,
423
448
(
2013
).
35.
C.
Jia
,
M.
Qian
,
Y.
Kang
, and
D.
Jiang
, “
Modeling stochastic phenotype switching and bet-hedging in bacteria: Stochastic nonlinear dynamics and critical state identification
,”
Quant. Biol.
2
,
110
125
(
2014
).
36.
K.
Turgay
,
J.
Hahn
,
J.
Burghoorn
, and
D.
Dubnau
, “
Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor
,”
Embo J.
17
,
6730
6738
(
1998
).
37.
M.
Ogura
,
L.
Liu
,
M.
Lacelle
,
M.
Nakano
, and
P.
Zuber
, “
Mutational analysis of ComS: Evidence for the interaction of ComS and MecA in the regulation of competence development in Bacillus subtilis
,”
Mol. Microbiol.
32
,
799
812
(
1999
).
38.
H.
Maamar
and
D.
Dubnau
, “
Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop
,”
Mol. Microbiol.
56
,
615
624
(
2005
).
39.
W.
Smits
et al., “
Stripping Bacillus: ComK auto-stimulation is responsible for the bistable response in competence development
,”
Mol. Microbiol.
56
,
604
614
(
2005
).
40.
D.
Sinderen
et al., “
comK encodes the competence transcription factor, the key regulatory protein for competence development in Bacillus subtilis
,”
Mol. Microbiol.
15
,
455
462
(
1995
).
41.
M.
Samoilov
,
G.
Price
, and
A.
Arkin
, “
From fluctuations to phenotypes: The physiology of noise
,”
Sci. Stke
2006
,
re17
(
2006
).
42.
J.
Veening
,
W.
Smits
, and
O.
Kuipers
, “
Bistability, epigenetics, and bet-hedging in bacteria
,”
Ann. Rev. Microbiol.
62
,
193
210
(
2008
).
43.
J.
Pomerening
, “
Uncovering mechanisms of bistability in biological systems
,”
Curr. Opin. Biotechnol.
19
,
381
388
(
2008
).
44.
J.
Ferrell
and
W.
Xiong
, “
Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible
,”
Chaos
11
,
227
236
(
2001
).
45.
A.
Raj
,
C.
Peskin
,
D.
Tranchina
,
D.
Vargas
, and
S.
Tyagi
, “
Stochastic mRNA synthesis in mammalian cells
,”
Plos Biol.
4
,
1707
(
2006
).
46.
X.
Sun
,
X.
Li
, and
Y.
Zheng
, “
Governing equations for probability densities of Marcus stochastic differential equations with Lévy noise
,”
Stoch. Dyn.
17
,
1750033
(
2017
).
47.
A.
Dubkov
,
B.
Spagnolo
, and
V.
Uchaikin
, “
Lévy flight superdiffusion: An introduction
,”
Int. J. Bifurcat. Chaos
18
(
9
),
2649
2672
(
2008
).
48.
P.
Menck
,
J.
Heitzig
,
N.
Marwan
, and
J.
Kurths
, “
How basin stability complements the linear-stability paradigm
,”
Nat. Phys.
9
,
89
92
(
2014
).
49.
L.
Serdukova
,
Y.
Zheng
,
J.
Duan
, and
J.
Kurths
, “
Stochastic basin of attraction for metastable states
,”
Chaos
26
,
1
11
(
2016
).
50.
I.
Dayan
,
M.
Gitterman
, and
G.
Weiss
, “
Stochastic resonance in transient dynamics
,”
Phys. Rev. A
46
,
757
761
(
1992
).
51.
R.
Mantegna
and
B.
Spagnolo
, “
Noise enhanced stability in an unstable system
,”
Phys. Rev. Lett.
76
,
563
(
1996
).
52.
A.
Fiasconaro
,
B.
Spagnolo
, and
S.
Boccaletti
, “
Signatures of noise-enhanced stability in metastable states
,”
Phys. Rev. E
72
,
061110
(
2005
).
53.
A.
Fiasconaro
and
B.
Spagnolo
, “
Stability measures in metastable states with Gaussian colored noise
,”
Phys. Rev. E
80
,
041110
(
2009
).
54.
P.
Imkeller
and
I.
Pavlyukevich
, “
Lévy flights: Transitions and meta-stability
,”
J. Phys. A: Math. Gen.
39
,
L237
L246
(
2006
).
55.
P.
Imkeller
,
I.
Pavlyukevich
, and
T.
Wetzel
, “
First exit times for lévy-driven diffusions with exponentially light jumps
,”
Ann. Probab.
37
,
530
564
(
2009
).
56.
K.
Sato
,
Lévy Processes and Infinitely Divisible Distributions
(
New York Cambridge University Press
,
1999
).
57.
G.
Samorodnitsky
and
M.
Taqqu
,
Stable Non-Gaussian Random Processes: Stochastic Models with Infinite Variance
(
London Chapman Hall
,
1994
).
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