20 papers · ranked by Valyu relevance
David F. Anderson, Daniele Cappelletti, Masanori Koyama, Thomas G. Kurtz
Stochastic reaction networks are mathematical models that describe the time evolution of the counts of interacting objects. Despite their general formulation, these models are primarily associated with biochemistry and cell biology, where they are utilized to describe the dynamics of systems of interacting proteins…
Anika Küken, Philipp Wendering, Damoun Langary, Zoran Nikoloski
Large-scale biochemical models are of increasing sizes due to the consideration of interacting organisms and tissues. Model reduction approaches that preserve the flux phenotypes can simplify the analysis and predictions of steady-state metabolic phenotypes. However, existing approaches either restrict functionality of…
Anika Küken, Damoun Langary, Angela Angeleska, Zoran Nikoloski
Metabolism operates under physico-chemical constraints that result in multireaction dependencies. Understanding how multireaction dependencies affect metabolic phenotypes remains challenging, hindering their biotechnological applications. Here, we propose the concept of a forcedly balanced complex that allows to…
Linard Hoessly, Carsten Wiuf, Panqiu Xia
Reaction networks have become a major modelling framework in the biological sciences from epidemiology and population biology to genetics and cellular biology. In recent years, much progress has been made on stochastic reaction networks (SRNs) that in particular are applicable when copy numbers are low (as in cellular…
Arjan van der Schaft, Shodhan Rao, Bayu Jayawardhana
The characterization of the notions of complex and detailed balancing for mass action kinetics chemical reaction networks is revisited from the perspective of algebraic graph theory, in particular Kirchhoff's Matrix Tree theorem for directed weighted graphs. This yields an elucidation of previously obtained results, in…
Seirana Hashemi, Zahra Razaghi-Moghadam, Zoran Nikoloski, Costas D. Maranas
Intracellular fluxes represent a joint outcome of cellular transcription and translation and reflect the availability and usage of nutrients from the environment. While approaches from the constraint-based metabolic framework can accurately predict cellular phenotypes, such as growth and exchange rates with the…
Stefan Müller, Badal Joshi
We further clarify the relation between detailed-balanced and complex-balanced equilibria of reversible chemical reaction networks. Our results hold for arbitrary kinetics and also for boundary equilibria. Detailed balance, complex balance, “formal balance,” and the new notion of “cycle balance” are all defined in…
Damoun Langary, Anika Küken, Zoran Nikoloski
Balanced complexes in biochemical networks are at core of several theoretical and computational approaches that make statements about the properties of the steady states supported by the network. Recent computational approaches have employed balanced complexes to reduce metabolic networks, while ensuring preservation…
Damoun Langary, Anika Küken, Zoran Nikoloski
Balanced complexes in biochemical networks are at core of several theoretical and computational approaches that make statements about the properties of the steady states supported by the network. Recent computational approaches have employed balanced complexes to reduce metabolic networks, while ensuring preservation…
Stefan C. Müller, Badal Joshi
Detailed balance, complex balance, "formal balance", and the new notion of "cycle balance" are all defined in terms of the underlying graph. This fact allows elementary graph-theoretic (non-algebraic) proofs of a previous result (detailed balance = complex balance + formal balance), our main result (detailed balance =…
György Lipták, Katalin M. Hangos, Mihály Pituk, Gábor Szederkényi
In this letter we introduce a class of delayed kinetic systems derived from mass action type reaction network models. We define the time delayed positive stoichiometric compatibility classes and the notion of complex balanced time delayed kinetic systems. We prove the uniqueness of equilibrium solutions within the time…
Catherine Jose, Eduardo Mendoza, Dylan Antonio SJ. Talabis
A complex balanced kinetic system is absolutely complex balanced (ACB) if every positive equilibrium is complex balanced. Two results on absolute complex balancing were foundational for modern chemical reaction network theory (CRNT): in 1972, M. Feinberg proved that any deficiency zero complex balanced system is…
David O Holland, Margaret E Johnson
Stoichiometric balance, or dosage balance, implies that proteins that are subunits of obligate complexes (e.g. the ribosome) should have copy numbers expressed to match their stoichiometry in that complex. Establishing balance (or imbalance) is an important tool for inferring subunit function and assembly bottlenecks.…
Authors not listed
We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and protons/hydroxide are treated explicitly, so both mass and charge are balanced. We…
Ali Doroodchi
Postural complexity may shape how the nervous system processes plantar cutaneous input. We tested whether somatosensory evoked potentials (SEPs) elicited by foot-sole stimulation scale with balance demands, hypothesizing larger responses for more complex tasks. Thirty-one healthy adults performed standing…
Authors not listed
Two kinetic schemes of the general modifier mechanism have been analysed in a quasi-steady state approximation, assuming that the reaction product concentration is negligible (a natural assumption for the initial rate method) and without additional simplifying assumptions. The characteristic equations have been…
Authors not listed
This paper introduces Post-Inspection Analysis (PIA), a concept for understanding and reverse engineering balanced equations of similar reactions. Here we explore the idea that balanced equations contain useable information observed by grouping and analysing similar equations, allowing us to uncover observations that…
Shabnam Behrangrad, Maryam Zoghi, Farshad Mansouri, Shapour Jaberzadeh
Our ability to interact flexibly with the surrounding environment and achieve an adaptive goal-directed response is one of the necessities of balance control. This study aimed to examine the interaction between cognitive demand and the necessity for keeping balance in unstable conditions. We examined the effects of…
Rucha Kulkarni, Francis M. Grover, Anna Shafer, Xenia Schmitz + 1 more
The interplay between stability and manoeuvrability is fundamental for human walking. Previous research finds conflicting perspectives on how these attributes interact – mechanisms for stable walking can either facilitate or impede manoeuvrability. We postulate that these views can be explained by considering manoeuvre…
ALESSANDRO ALIPRANDI, Dario Alessi, Luca Morgan, Elisa Pelorosso + 1 more
Self-organization is a key pathway to achieving high levels of matter complexity. However, an energy-consuming active process, such as a dissipative regime, is essential for adaptation and evolution to occur. In this study, we transform the passive self-organization of a luminescent square planar Pt(II) complex into an…