BEGIN:VCALENDAR
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BEGIN:VEVENT
SUMMARY:David F. Anderson (University of Wisconsin\, Madison (USA))
DTSTART;VALUE=DATE-TIME:20201112T160000Z
DTEND;VALUE=DATE-TIME:20201112T163000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/1
DESCRIPTION:Title: Rea
ction network implementations of neural networks\nby David F. Anderson
(University of Wisconsin\, Madison (USA)) as part of Seminar on the Mathe
matics of Reaction Networks\n\n\nAbstract\nI will give an overview of my r
ecent paper with Badal Joshi and Abhishek Deshpande\, which is entitled "O
n reaction network implementations of neural networks." In particular\, I
will show how reaction networks can be constructed that "implement" a giv
en neural network. I will also detail our theoretical results\, which pro
ve that the ODEs associated with certain reaction network implementations
of neural networks have desirable properties including (i) existence of un
ique positive fixed points that are smooth in the parameters of the model
(necessary for gradient descent)\, and (ii) fast convergence to the fixed
point regardless of initial condition (necessary for efficient implementat
ion). I'll start the talk with a brief primer on neural networks\, but wi
ll assume familiarity with reaction networks.\n
LOCATION:https://researchseminars.org/talk/MoRN/1/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Beatriz Pascual Escudero (Universidad Carlos III (Spain))
DTSTART;VALUE=DATE-TIME:20201203T160000Z
DTEND;VALUE=DATE-TIME:20201203T163000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/2
DESCRIPTION:Title: Nec
essary conditions for ACR in Reaction Networks\nby Beatriz Pascual Esc
udero (Universidad Carlos III (Spain)) as part of Seminar on the Mathemati
cs of Reaction Networks\n\n\nAbstract\nA biological system has absolute co
ncentration robustness (ACR) for some molecular species if the concentrati
on of this species does not vary among the different steady states that th
e network admits. In particular\, this concentration is independent of the
initial conditions. This interesting feature confers the system a highly
desirable property in order to adapt to environmental conditions\, which m
akes it useful\, for instance\, in synthetic biology. While some classes o
f networks with ACR have been described (Shinar and Feinberg 2010\; Karp e
t al. 2012)\, as well as some techniques to check a network for ACR (Pére
z Millán 2011\; Kuwahara et al. 2017)\, finding networks with this proper
ty is a difficult task in general.\n\nMotivated by this problem\, we studi
ed local and global notions of robustness on the set of (real positive) so
lutions of a system of polynomial equations\, and in particular on the set
of steady states of a reaction network. Algebraic geometry allowed us to
provide a practical test on necessary conditions for ACR. Properties of re
al and complex algebraic varieties are necessary for the results\, while t
he test ends up being a linear algebra computation.\n
LOCATION:https://researchseminars.org/talk/MoRN/2/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Casian Pantea (West Virginia University (USA))
DTSTART;VALUE=DATE-TIME:20201203T163000Z
DTEND;VALUE=DATE-TIME:20201203T170000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/3
DESCRIPTION:Title: Inh
eritance of Hopf bifurcations in reaction networks\nby Casian Pantea (
West Virginia University (USA)) as part of Seminar on the Mathematics of R
eaction Networks\n\n\nAbstract\nInspired by recent work on multistationari
ty\, we consider the question: "when can we conclude that a network admits
Hopf bifurcations if one of its subnetworks has them?” In particular\,
we analyze a number of operations on reaction networks (like adding certai
n reactions\, or adding inflows/outflows) that may preserve Hopf bifurcat
ions as we build up the network . This is joint work with C.Conradi\, A. D
ickenstein\, and M. Mincheva.\n
LOCATION:https://researchseminars.org/talk/MoRN/3/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Lea Popovic (Concordia University)
DTSTART;VALUE=DATE-TIME:20201112T163000Z
DTEND;VALUE=DATE-TIME:20201112T170000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/4
DESCRIPTION:Title: A s
patially heterogeneous stochastic model for chemical reaction networks
\nby Lea Popovic (Concordia University) as part of Seminar on the Mathemat
ics of Reaction Networks\n\n\nAbstract\nI will present a measure-valued fr
amework for stochastic modelling of chemical reaction networks with spatia
l heterogeneity. Reactions rates at a spatial location are proportional to
the mass of different species present locally\, and to a location specifi
c chemical rate that is allowed to be a function of the local or global ma
ss of different species. The benefit of the framework is in rigorous appro
ximation limits that exploit multi-scale aspects of the system. When the m
ass of all species scales the same way\, we get classical deterministic li
mit described by PDEs. When the mass of some species in the scaling limit
is discrete while the mass of the others is continuous\, we obtain a new t
ype of spatial random evolution process in which discrete mass evolves sto
chastically and the continuous mass evolves according to PDEs between cons
ecutive jump times of the discrete part. Some useful properties of the lim
iting process are inherited from the pre-limiting sequence\, and could be
used in devising simulation algorithms.\n\nThis is joint work with Amandin
e Veber (Paris V\, Polytechnique-Saclay)\n
LOCATION:https://researchseminars.org/talk/MoRN/4/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Nida Obatake (Texas A&M (USA))
DTSTART;VALUE=DATE-TIME:20201210T160000Z
DTEND;VALUE=DATE-TIME:20201210T163000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/5
DESCRIPTION:Title: Mix
ed volume of reaction networks\nby Nida Obatake (Texas A&M (USA)) as p
art of Seminar on the Mathematics of Reaction Networks\n\n\nAbstract\nAn i
mportant invariant of a chemical reaction network is its maximum number of
positive steady states. This number\, however\, is in general difficult t
o compute. We introduce an upper bound on this number— namely\, a networ
k’s mixed volume — that is easy to compute. We show that\, for certain
biological signaling networks\, the mixed volume does not greatly exceed
the maximum number of positive steady states. We investigate this overcoun
t and also compute the mixed volumes of small networks (those with only a
few species or reactions). Joint work with Anne Shiu\, Dilruba Sofia\, Ang
elica Torres\, and Xiaoxian Tang.\n
LOCATION:https://researchseminars.org/talk/MoRN/5/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Ankit Gupta (ETHZ (Switzerland))
DTSTART;VALUE=DATE-TIME:20201210T163000Z
DTEND;VALUE=DATE-TIME:20201210T170000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/6
DESCRIPTION:Title: Fre
quency Spectra and the Color of Cellular Noise\nby Ankit Gupta (ETHZ (
Switzerland)) as part of Seminar on the Mathematics of Reaction Networks\n
\nAbstract: TBA\n
LOCATION:https://researchseminars.org/talk/MoRN/6/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Polly Yu (University of Wisconsin\, Madison)
DTSTART;VALUE=DATE-TIME:20210114T160000Z
DTEND;VALUE=DATE-TIME:20210114T163000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/7
DESCRIPTION:Title: Dyn
amically Equivalent Mass-Action Systems: A Survey of Recent Results\nb
y Polly Yu (University of Wisconsin\, Madison) as part of Seminar on the M
athematics of Reaction Networks\n\n\nAbstract\nUnder mass-action kinetics\
, each reaction network uniquely gives rise to a system of ODEs. However\,
the converse is not true\; for a given system of ODEs known to come from
a mass-action systems\, there are many reaction networks that serve as a c
andidate. In this talk\, I will introduce the notion of dynamical equivale
nce\, emphasize a convenient way of thinking about it\, and survey some re
cent results on dynamical equivalence to complex-balanced or detailed-bala
nced systems.\n
LOCATION:https://researchseminars.org/talk/MoRN/7/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Chuang Xu (Technical University of Munich)
DTSTART;VALUE=DATE-TIME:20210225T160000Z
DTEND;VALUE=DATE-TIME:20210225T163000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/8
DESCRIPTION:Title: Dyn
amics of one dimensional stochastic reaction networks\nby Chuang Xu (T
echnical University of Munich) as part of Seminar on the Mathematics of Re
action Networks\n\n\nAbstract\nIn this talk\, I will present recent result
s on criteria for dynamics as well as identity and recursive formula of li
mit distributions of one-dimensional mass-action stochastic reaction netw
orks (SRNs). I will also mention applications of these criteria to weakly
reversible SRNs\, and SRNs with transition of dynamics induced by volume s
cales. Finally\, I will list some related topics on bifurcation as well as
tails and approximation of stationary distributions of SRNs . This talk i
s based on joint works with Mads Christian Hansen and Carsten Wiuf.\n
LOCATION:https://researchseminars.org/talk/MoRN/8/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Jinsu Kim (UC Irvine)
DTSTART;VALUE=DATE-TIME:20210128T160000Z
DTEND;VALUE=DATE-TIME:20210128T163000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/9
DESCRIPTION:Title: Ide
ntifiability of Stochastically Modelled Reaction Networks\nby Jinsu Ki
m (UC Irvine) as part of Seminar on the Mathematics of Reaction Networks\n
\n\nAbstract\nWhen an underlying reaction network is given for a biochemic
al system\, the system dynamics can be modeled with various mathematical f
rameworks such as continuous-time Markov processes. In this manuscript\, t
he identifiability of the underlying network structure with a given stocha
stic system dynamics is studied. It is shown that some data types related
to the associated stochastic dynamics can uniquely identify the underlying
network structure as well as the system parameters. The accuracy of the p
resented network inference is investigated when given dynamical data is ob
tained via stochastic simulations.\n
LOCATION:https://researchseminars.org/talk/MoRN/9/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Elisa Tonello (Freie Universität\, Berlin)
DTSTART;VALUE=DATE-TIME:20210211T160000Z
DTEND;VALUE=DATE-TIME:20210211T163000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/11
DESCRIPTION:Title: Bo
olean interaction networks: some classical results and recent trends\n
by Elisa Tonello (Freie Universität\, Berlin) as part of Seminar on the M
athematics of Reaction Networks\n\n\nAbstract\nBoolean interaction network
s are one of the tools in the arsenal of\nmodellers investigating biologic
al systems. They aim to capture\nqualitative behaviours\, and can be usefu
l especially in absence of\ndetailed kinetic information. I will start by
giving an overview of the\nmain graph structures associated to Boolean net
works. I will then\nsummarise some of the results that connect structure t
o dynamics\, and\ntouch on some current trends and directions of research.
\n
LOCATION:https://researchseminars.org/talk/MoRN/11/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Angelyn Lao (De La Salle University Manila)
DTSTART;VALUE=DATE-TIME:20210211T163000Z
DTEND;VALUE=DATE-TIME:20210211T170000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/12
DESCRIPTION:Title: Ch
emical reaction network decompositions and realizations of S-systems\n
by Angelyn Lao (De La Salle University Manila) as part of Seminar on the M
athematics of Reaction Networks\n\n\nAbstract\nWe present novel decomposit
ion classes of chemical reaction networks (CRNs) derived from S-system kin
etics. Based on the network decomposition theory initiated by Feinberg in
1987\, we introduce the concept of incidence independent decompositions an
d develop the theory of $\\mathscr{C}$- and $\\mathscr{C}^*$- decompositio
ns which partition the set of complexes and the set of nonzero complexes r
espectively\, including their structure theorems in terms of linkage class
es. Analogous to Feinberg's independent decomposition\, we demonstrate the
important relationship between sets of complex balance equilibria for an
incidence independent decomposition of weakly reversible subnetworks for a
ny kinetics. We show that the $\\mathscr{C}^*$-decompositions are also in
cidence independent. We also introduce in this paper a new realization for
an S-system that is analyzed using a newly defined class of species cover
able CRNs. This led to the extension of the deficiency formula and charact
erization of fundamental decompositions of species decomposable reaction n
etworks.\n
LOCATION:https://researchseminars.org/talk/MoRN/12/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Justin Eilertsen (University of Michigan)
DTSTART;VALUE=DATE-TIME:20210114T163000Z
DTEND;VALUE=DATE-TIME:20210114T170000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/13
DESCRIPTION:Title: Th
e current state of quasi-steady-state approximations: manifolds\, time sca
les\, singularities\, and stochastic fluctuations\nby Justin Eilertsen
(University of Michigan) as part of Seminar on the Mathematics of Reactio
n Networks\n\n\nAbstract\nOver the past decade\, mathematicians have made
considerable progress concerning the theory and\napplicability of quasi-st
eady-state (QSS) approximations in chemical kinetics. The application of F
enichel theory has revealed that QSS reduction in chemical kinetics is far
richer than previously thought\, even in low-dimensional systems that do
not exhibit oscillatory behavior. In this talk\, I will discuss recent dis
coveries that have emerged in the \nfield of mathematical enzyme kinetics\
, including methodologies for obtaining perturbation parameters\, singular
points\, dynamic bifurcations and scaling laws. If time permits\, I will
also discuss the applicability of QSS reductions in stochastic environment
s\, and comment on some open problems in both deterministic and stochastic
enzyme kinetics.\n
LOCATION:https://researchseminars.org/talk/MoRN/13/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Mark Curiel (University of Hawaii at Manoa)
DTSTART;VALUE=DATE-TIME:20210128T163000Z
DTEND;VALUE=DATE-TIME:20210128T170000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/14
DESCRIPTION:Title: Wh
en do two networks have the same steady-state ideal?\nby Mark Curiel (
University of Hawaii at Manoa) as part of Seminar on the Mathematics of Re
action Networks\n\n\nAbstract\nUnder the assumption of mass action kinetic
s\, the associated dynamical system of a reaction network is polynomial. W
e consider the ideals generated by these polynomials\, which are called st
eady-state ideals. Steady-state ideals appear in multiple contexts within
the chemical reaction network literature\, however they have yet to be sys
tematically studied. To begin such a study\, we ask and partially answer t
he following question: when do two reaction networks give rise to the same
steady-state ideal? In particular\, our main results describe three opera
tions on the reaction graph that preserve the steady-state ideal. Furtherm
ore\, since the motivation for this work is the classification of steady-s
tate ideals\, monomials play a primary role. To this end\, combinatorial
conditions are given to identify monomials in a steady-state ideal\, and w
e give a sufficient condition for a steady-state ideal to be monomial.\n
LOCATION:https://researchseminars.org/talk/MoRN/14/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Linard Hoessly (University of Copenhagen)
DTSTART;VALUE=DATE-TIME:20210325T160000Z
DTEND;VALUE=DATE-TIME:20210325T163000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/15
DESCRIPTION:Title: On
an algebraic approach to product-form stationary distributions of some re
action networks\nby Linard Hoessly (University of Copenhagen) as part
of Seminar on the Mathematics of Reaction Networks\n\n\nAbstract\nExact re
sults for product-form stationary distributions of Markov chains are of in
terest in different fields. In stochastic reaction networks (CRNs)\, stati
onary distributions are mostly known in special cases where they are of pr
oduct-form. However\, there is no full characterization of the classes of
networks whose stationary distributions have product-form. We develop an a
lgebraic approach to product-form stationary distributions in the framewor
k of CRNs. Under certain hypotheses on linearity and decomposition of the
state space for conservative ergodic CRNs\, this gives sufficient and nece
ssary algebraic conditions for product-form stationary distributions. Corr
espondingly we obtain a semialgebraic subset of the parameter space that c
aptures rates where\, under the corresponding hypotheses\, CRNs have produ
ct-form. We employ the developed theory to CRNs and some models of statist
ical mechanics\, besides sketching the pertinence in other models from app
lied probability.\n
LOCATION:https://researchseminars.org/talk/MoRN/15/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Stefan Müller (University of Vienna)
DTSTART;VALUE=DATE-TIME:20210311T163000Z
DTEND;VALUE=DATE-TIME:20210311T170000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/16
DESCRIPTION:Title: De
tailed balance = complex balance + cycle balance\nby Stefan Müller (U
niversity of Vienna) as part of Seminar on the Mathematics of Reaction Net
works\n\n\nAbstract\nWe further clarify the relation between detailed-bala
nced and complex-balanced equilibria\nof reversible chemical reaction netw
orks.\nOur results hold for arbitrary kinetics and also for boundary equil
ibria.\n\nDetailed balance\, complex balance\, ''formal balance''\, and th
e new notion of ''cycle balance''\nare all defined in terms of the underly
ing graph.\nThis fact allows elementary graph-theoretic (non-algebraic) pr
oofs of \na previous result (detailed balance = complex balance + formal b
alance)\, \nour main result (detailed balance = complex balance + cycle ba
lance)\,\nand a corresponding result in the setting of continuous-time Mar
kov chains.\n\nJoint work with Badal Joshi.\n
LOCATION:https://researchseminars.org/talk/MoRN/16/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Balazs Boros (University of Vienna)
DTSTART;VALUE=DATE-TIME:20210225T163000Z
DTEND;VALUE=DATE-TIME:20210225T170000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/17
DESCRIPTION:Title: Dy
namics of planar deficiency-one mass-action systems\nby Balazs Boros (
University of Vienna) as part of Seminar on the Mathematics of Reaction Ne
tworks\n\n\nAbstract\nFor a deficiency-zero mass-action system with a sing
le linkage class\, whenever there exists a positive equilibrium\, it is gl
obally asymptotically stable. In this talk we discuss what other qualitati
ve behaviors could arise when the deficiency is one. We restrict our atten
tion to the planar case. Joint work with Josef Hofbauer.\n
LOCATION:https://researchseminars.org/talk/MoRN/17/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Tung Nguyen (University of Wisconsin-Madison)
DTSTART;VALUE=DATE-TIME:20210311T160000Z
DTEND;VALUE=DATE-TIME:20210311T163000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/18
DESCRIPTION:Title: Pr
evalence of deficiency zero for random reaction networks\nby Tung Nguy
en (University of Wisconsin-Madison) as part of Seminar on the Mathematics
of Reaction Networks\n\n\nAbstract\nIn the study of reaction networks\, t
here is usually a strong connection between the network structure and the
qualitative behavior of the dynamical system. Certain network structures s
uch as deficiency zero ensure many desirable behaviors of the dynamical sy
stems including existence and stability of equilibrium.\n\nIn this talk\,
I will attempt to address a natural question: how prevalent these structur
es (in particular deficiency zero) are among random reaction networks. To
answer this question\, it is important to have a framework to generate ran
dom reaction networks. I will present two such frameworks: an Erdos-Renyi
framework\, and a stochastic block model framework-which is essentially a
more generalized version of Erdos-Renyi. Next\, I will examine the scaling
limit (as the number of species goes to infinity) of the probability that
a random reaction network has deficiency zero.\n
LOCATION:https://researchseminars.org/talk/MoRN/18/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Alan Rendall (Johannes Gutenberg University Mainz)
DTSTART;VALUE=DATE-TIME:20210408T153000Z
DTEND;VALUE=DATE-TIME:20210408T160000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/19
DESCRIPTION:Title: Us
ing Bogdanov-Takens bifurcations to study existence and stability of perio
dic solutions\nby Alan Rendall (Johannes Gutenberg University Mainz) a
s part of Seminar on the Mathematics of Reaction Networks\n\n\nAbstract\nH
opf bifurcations are a favourite way to prove the existence of periodic\ns
olutions of a dynamical system. The aim of this talk is to describe a vari
ant\nof this procedure using the less familiar concept of a Bogdanov-Taken
s\nbifurcation. Surprisingly\, the latter procedure has the advantage that
\nalthough the bifurcation itself is more complicated the conditions which
need\nto be checked to determine the stability of the periodic solutions
produced are\nmore straightforward. I will give a general discussion of th
ese matters\,\nillustrating them by the example of a model for the kinase
Lck. This is\nbased on work with Lisa Kreusser\, where we studied the occu
rrence of\ninteresting dynamical features\, such as multistability\, perio
dic solutions and\nhomoclinic loops\, in models for enzymes subject to aut
ophosphorylation. I will\nalso discuss how features of this type can be li
fted from smaller to larger\nreaction networks.\n
LOCATION:https://researchseminars.org/talk/MoRN/19/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Xiaoxian Tang (Beihang University)
DTSTART;VALUE=DATE-TIME:20210422T150000Z
DTEND;VALUE=DATE-TIME:20210422T150000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/20
DESCRIPTION:Title: Mu
ltistability of One-Dimensional Reaction Networks\nby Xiaoxian Tang (B
eihang University) as part of Seminar on the Mathematics of Reaction Netwo
rks\n\n\nAbstract\nWe report our recent progress on multistability of reac
tion networks. For the networks with one-dimensional stoichiometric subspa
ce\, we have the following results.\n (1) If the maximum number of positiv
e steady states is an even number N\, then the maximum number of stable po
sitive steady states\n is N/2.\n (2) If the maximum number of positive ste
ady states is an odd number N\, then we provide a condition on the network
such that the maximum number of stable positive steady states is (N-1)/2
if this condition is satisfied\, and this maximum number is (N+1)/2 otherw
ise.\n
LOCATION:https://researchseminars.org/talk/MoRN/20/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Hyukpyo Hong (KAIST)
DTSTART;VALUE=DATE-TIME:20210513T150000Z
DTEND;VALUE=DATE-TIME:20210513T153000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/21
DESCRIPTION:Title: De
rivation of stationary distributions of stochastic chemical reaction netwo
rks via network translation\nby Hyukpyo Hong (KAIST) as part of Semina
r on the Mathematics of Reaction Networks\n\n\nAbstract\nLong-term behavio
rs of biochemical reaction networks are described by steady states in dete
rministic models and stationary distributions in stochastic models. Unlike
deterministic steady states\, stationary distributions capturing inherent
fluctuations of reactions are extremely difficult to derive analytically
due to the curse of dimensionality. In this talk\, we introduce a new meth
od to derive stationary distributions from deterministic steady states by
transforming reaction networks to have a special dynamic property based on
chemical reaction network theory. Specifically\, we merge nodes and edges
to make a steady state complex balanced\, i.e.\, the in- and out-flows of
each node are equal\, and then we derive a stationary distribution from t
he complex balanced steady state. Furthermore\, we provide a user-friendly
computational package\, called CASTANET\, that transforms BRNs and then a
nalytically derives their stationary distributions.\n
LOCATION:https://researchseminars.org/talk/MoRN/21/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Amirhosein Sadeghimanesh (Coventry University)
DTSTART;VALUE=DATE-TIME:20210422T153000Z
DTEND;VALUE=DATE-TIME:20210422T160000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/22
DESCRIPTION:Title: St
udying dynamical behavior of the three connected populations with Allee ef
fect using algebraic tools\nby Amirhosein Sadeghimanesh (Coventry Univ
ersity) as part of Seminar on the Mathematics of Reaction Networks\n\n\nAb
stract\nWe consider three connected populations with the strong Allee effe
ct\, and give a complete classification of the steady state structure of t
he system with respect to the Allee threshold and the dispersal rate. One
may expect that by increasing the dispersal rate between the patches\, the
system would become more well-mixed hence simpler. However\, we show that
it is not always the case\, and the number of steady states may (temporar
ily) increase by increasing the dispersal rate. Besides sequences of pitch
fork and saddle-node bifurcations\, we find triple-transcritical bifurcati
ons and also a sun-ray shaped bifurcation where twelve steady states meet
at a single point then disappear. The major tool of our investigations is
a novel algorithm that decomposes the parameter space with respect to the
number of steady states using cylindrical algebraic decomposition with res
pect to the discriminant variety of the polynomial system. This is a joint
work with Gergely Röst.\n
LOCATION:https://researchseminars.org/talk/MoRN/22/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Nicolette Meshkat (Santa Clara University)
DTSTART;VALUE=DATE-TIME:20210408T150000Z
DTEND;VALUE=DATE-TIME:20210408T150000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/23
DESCRIPTION:Title: Ab
solute concentration robustness in networks with many conservation laws\nby Nicolette Meshkat (Santa Clara University) as part of Seminar on the
Mathematics of Reaction Networks\n\nAbstract: TBA\n
LOCATION:https://researchseminars.org/talk/MoRN/23/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Carsten Wiuf (University of Copenhagen)
DTSTART;VALUE=DATE-TIME:20210520T150000Z
DTEND;VALUE=DATE-TIME:20210520T153000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/24
DESCRIPTION:Title: On
the sum of two reactions\nby Carsten Wiuf (University of Copenhagen)
as part of Seminar on the Mathematics of Reaction Networks\n\n\nAbstract\n
It is standard in (bio)chemistry to represent a series of reactions by a s
ingle reaction\, often called a complex reaction in contrast to an element
ary reaction. For example\, photosynthesis $6\\ \\text{CO}_2+6\\ \\text{H}
_2\\text{O}\\ \\to \\ \\text{C}_6\\text{H}_{12}\\text{O}_6+6\\ \\text{O}_2
$ is such complex reaction. We introduce a mathematical operation that cor
responds to summing two chemical reactions. Specifically\, we define an as
sociative and non-communicative operation on the product space $\n_0^n\\ti
mes \n_0^n$ (representing the reactant and the product of a chemical react
ion\, respectively). The operation models the overall effect of two reacti
ons happening in succesion\, one after the other. We study the algebraic p
roperties of the operation and apply the results to stochastic reaction ne
tworks\, in particular to reachability of states\, and to reduction of rea
ction networks.\n
LOCATION:https://researchseminars.org/talk/MoRN/24/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Mercedes Perez Millan (Universidad de Buenos Aires)
DTSTART;VALUE=DATE-TIME:20210520T153000Z
DTEND;VALUE=DATE-TIME:20210520T160000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/25
DESCRIPTION:Title: Ci
rcuits of multistationarity in structured enzymatic networks\nby Merce
des Perez Millan (Universidad de Buenos Aires) as part of Seminar on the M
athematics of Reaction Networks\n\n\nAbstract\nIn this work we focus on mi
nimal sets of intermediate species\nand their location in the network to a
llow for multistationarity in the\ncorresponding mass-action chemical reac
tion system. This question has also\nbeen studied in Feliu and Wiuf (2013)
and also in Sadeghimanesh and Feliu\n(2019) using degree theory technique
s. Our results simplify the analysis\nfor chemical reaction systems with c
ertain structure\, called "linearly\nbinomial networks" [Dickenstein\, P.M
.\, Shiu\, Tang (2019)]. We apply our\nresults on several signaling networ
ks. We also refer to the problem of\nlifting of multistationarity\, and we
give easy combinatorial conditions\nfor MESSI networks [P.M.\, Dickenste
in (2018)] to be linearly binomial.\nThis is joint work with Alicia Dicken
stein\, Magalí Giaroli and Rick\nRischter.\n
LOCATION:https://researchseminars.org/talk/MoRN/25/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Nicola Vassena (FU Berlin)
DTSTART;VALUE=DATE-TIME:20210513T153000Z
DTEND;VALUE=DATE-TIME:20210513T160000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/26
DESCRIPTION:Title: Si
gn-sensitivity of metabolic networks: which structures determine the sign
of the responses\nby Nicola Vassena (FU Berlin) as part of Seminar on
the Mathematics of Reaction Networks\n\n\nAbstract\nPerturbations are ubiq
uitous in metabolism. A central tool to understand\ntheir effect is sensit
ivity analysis\, which investigates how the network\nresponds to external
perturbations. In this talk we follow a structural\napproach\, only based
on the network stoichiometry and not requiring any\nquantitative knowledge
of the reaction rates. We consider perturbations of\nreaction rates\, at
equilibrium\, and we investigate the responses of the\nreaction fluxes. We
focus in particular on the sign of such responses\,\ni.e. whether a respo
nse is positive\, negative or whether its sign depends\non the reaction ra
tes parameters. We identify and describe certain kernel\nvectors of the st
oichiometric matrix\, which are the main players in the\nsign description.
\n
LOCATION:https://researchseminars.org/talk/MoRN/26/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Nidhi Kaihnsa (Brown University)
DTSTART;VALUE=DATE-TIME:20211028T153000Z
DTEND;VALUE=DATE-TIME:20211028T160000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/27
DESCRIPTION:by Nidhi Kaihnsa (Brown University) as part of Seminar on the
Mathematics of Reaction Networks\n\nAbstract: TBA\n
LOCATION:https://researchseminars.org/talk/MoRN/27/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Tang Quoc Bao (Karl-Franzens-University of Graz)
DTSTART;VALUE=DATE-TIME:20210923T153000Z
DTEND;VALUE=DATE-TIME:20210923T160000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/28
DESCRIPTION:Title: Co
nvergence to equilibrium for chemical reaction-diffusion systems\nby T
ang Quoc Bao (Karl-Franzens-University of Graz) as part of Seminar on the
Mathematics of Reaction Networks\n\n\nAbstract\nThis talk presents the qua
ntitative large time behaviour of reaction-diffusion systems modelling com
plex balanced chemical reaction networks. The convergence to equilibrium i
s investigated by using the so-called entropy method\, which is robust eno
ugh to apply to renormalised solutions. When the system possesses no bound
ary equilibria\, the solution is shown to converge exponentially to equili
brium with a semi-explicit rate. For certain systems with boundary equilib
ria\, we investigate the competition between attraction of the positive eq
uilibrium and hypothetical convergence towards the boundary to show the do
minance of the former.\n\nThis talk is based on joint works with Laurent D
esvillettes and Klemens Fellner.\n
LOCATION:https://researchseminars.org/talk/MoRN/28/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Badal Joshi (California State University San Marcos)
DTSTART;VALUE=DATE-TIME:20210916T153000Z
DTEND;VALUE=DATE-TIME:20210916T160000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/29
DESCRIPTION:Title: Dy
namic Absolute Concentration Robustness\nby Badal Joshi (California St
ate University San Marcos) as part of Seminar on the Mathematics of Reacti
on Networks\n\n\nAbstract\nOutput or functional robustness in biochemical
systems has been experimentally observed in the IDHKP-IDH glyoxylate bypas
s regulation system and the EnvZ/OmpR system in E. coli. To model output r
obustness\, we define the notion of dynamic absolute concentration robustn
ess (dynamic ACR) in systems of ODEs. A species in a biochemical reaction
network has dynamic ACR if its concentration converges to the same positiv
e value irrespective of overall initial conditions. Dynamic ACR builds on
the notion of static ACR wherein the concentration of a species has the sa
me value in any positive steady state. We will define stronger and weaker
forms of both static and dynamic ACR along with various naturally occurri
ng domains/basins for each. We will give a complete classification of smal
l networks\, using both algebraic and topological characterization\, by th
eir static ACR\, strong static ACR\, dynamic ACR\, and weak dynamic ACR pr
operties.\n
LOCATION:https://researchseminars.org/talk/MoRN/29/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Anne Shiu (Texas A&M University)
DTSTART;VALUE=DATE-TIME:20210916T150000Z
DTEND;VALUE=DATE-TIME:20210916T153000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/30
DESCRIPTION:Title: Ab
solute concentration robustness and multistationarity\nby Anne Shiu (T
exas A&M University) as part of Seminar on the Mathematics of Reaction Net
works\n\n\nAbstract\nA reaction system exhibits “absolute concentration
robustness” (ACR) in some species if the positive steady-state value of
that species does not depend on initial conditions. We present results cha
racterizing ACR for small networks\, specifically\, those with only a few
species or reactions - or with low-dimensional stoichiometric subspace. W
e also investigate the relationship between ACR and multistationarity (tha
t is\, the capacity of a network to admit multiple positive steady states)
. Finally\, we highlight several open problems on these topics.\n
LOCATION:https://researchseminars.org/talk/MoRN/30/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Hye-Won Kang (University of Maryland)
DTSTART;VALUE=DATE-TIME:20210923T150000Z
DTEND;VALUE=DATE-TIME:20210923T153000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/31
DESCRIPTION:Title: St
ochastic Modeling of Reaction-Diffusion Processes in Biology\nby Hye-W
on Kang (University of Maryland) as part of Seminar on the Mathematics of
Reaction Networks\n\n\nAbstract\nInherent fluctuations may play an importa
nt role in biochemical and biophysical systems when the system involves so
me species with low copy numbers. This talk will present the recent work o
n the stochastic modeling of reaction-diffusion processes in glucose metab
olism. In this talk\, I will introduce a compartment-based model for a sim
ple glycolytic pathway using a continuous-time Markov jump process\, which
describes system features at different scales of interest. Then\, we will
see how the multiscale approximate method reduces the model complexity. W
e will briefly discuss how the compartment size in the spatial domain can
affect the spatial patterns of the system.\n
LOCATION:https://researchseminars.org/talk/MoRN/31/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Giulia Giordano (University of Trento)
DTSTART;VALUE=DATE-TIME:20211111T163000Z
DTEND;VALUE=DATE-TIME:20211111T170000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/32
DESCRIPTION:by Giulia Giordano (University of Trento) as part of Seminar o
n the Mathematics of Reaction Networks\n\nAbstract: TBA\n
LOCATION:https://researchseminars.org/talk/MoRN/32/
END:VEVENT
BEGIN:VEVENT
SUMMARY:***
DTSTART;VALUE=DATE-TIME:20211014T150000Z
DTEND;VALUE=DATE-TIME:20211014T160000Z
DTSTAMP;VALUE=DATE-TIME:20210926T132639Z
UID:MoRN/33
DESCRIPTION:Title: **
* Networking event (closed to registered participants) ***\nby *** as
part of Seminar on the Mathematics of Reaction Networks\n\n\nAbstract\nDea
r colleagues\,\n\nThank you very much for participating in the ‘Mathemat
ics of Reaction Networks’ seminar series! We will resume the series in S
eptember\, and information on the exact dates will appear on https://resea
rchseminars.org/seminar/MoRN as usual.\n\nWe are very happy that so many o
f you attended the talks and engaged in inspiring discussions afterwards!
To our surprise\, we also noticed many new names/faces among the attendees
. We are excited about this\, and we would like to provide an opportunity
to get to know each other better.\n\nWe would like to host a ‘networking
event’ in October (tentatively on October 14)\, at the same time as the
regular seminars. The idea is that all interested people may briefly intr
oduce themselves or give a short presentation (indicating their base insti
tution\, research interests and background\, and optionally showing some r
esults or advertising open research positions). The presentations will tak
e place either in one or several rooms\, and interaction will be encourage
d.\n\nAs soon as we know how many people are interested\, we will send out
further details. So\, please let us know if you would like to participate
by sending an email by August 30.\n\nHave a nice Summer!\n\nDaniele\, Eli
senda\, and Stefan (organizers of MoRN)\n\nThis is a closed event announce
d through the mailing list. Only people that registered earlier can join.\
n
LOCATION:https://researchseminars.org/talk/MoRN/33/
END:VEVENT
END:VCALENDAR