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The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
There are several important bipartite systems of great interest in condensed matter physics and in quantum information science. In condensed matter systems, the subsystems are examined traditionally by using the Green function and…
Predicting the physico-chemical properties of pure substances and mixtures is a central task in thermodynamics. Established prediction methods range from fully physics-based ab-initio calculations, which are only feasible for very simple…
This study estimates the relationships between street network characteristics and transport-sector CO2 emissions across every urban area in the world and investigates whether they are the same across development levels and urban design…
The energy dissipation in a gas of structured objects, e.g. molecules, is considered in density matrix formalism. It is shown that the macroscopic irreversibility of the kinetic processes can be considered as a consequence of the…
State-of-the-art simulations of high-energy nuclear collisions rely on hybrid setups, involving in particular a pre-equilibrium stage to let the system evolve from a far-from-equilibrium initial condition towards a near-equilibrated state…
The chapter presents some new approaches to describing the collective behavior of complex systems of mathematical biology based on the evolution equations of observables such as open systems. This representation of kinetic evolution has…
Multi-valued logical models can be used to describe biological networks on a high level of abstraction based on the network structure and logical parameters capturing regulatory effects. Interestingly, the dynamics of two distinct models…
Carbon dioxide (CO2) emissions have emerged as a critical issue with profound impacts on the environment, human health, and the global economy. The steady increase in atmospheric CO2 levels, largely due to human activities such as burning…
Understanding the set of elementary steps and kinetics in each reaction is extremely valuable to make informed decisions about creating the next generation of catalytic materials. With physical and mechanistic complexity of industrial…
Using a recently developed formalism, we present an in-depth analysis of how the thermodynamics of the climate system varies with CO2 concentration by performing experiments with a simplified yet Earth-like climate model. We find that, in…
Chemical kinetics and reaction engineering consists of the phenomenological framework for the disentanglement of reaction mechanisms, optimization of reaction performance and the rational design of chemical processes. Here, we utilize…
How do sequence models represent their decision-making process? Prior work suggests that Othello-playing neural network learned nonlinear models of the board state (Li et al., 2023). In this work, we provide evidence of a closely related…
Developing accurate dynamical system models from physical insight or data can be impeded when only partial observations of the system state are available. Here, we combine conservation laws used in physics and engineering with artificial…
We present two quantitative behavioral equivalences over species of a chemical reaction network (CRN) with semantics based on ordinary differential equations. Forward CRN bisimulation identifies a partition where each equivalence class…
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems…
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…
We consider the classical dynamics of bosonic and fermionic matrix variables in complex Hilbert space, defined by a trace action, assuming cyclic invariance under the trace and the presence of a global unitary invariance. With plausible and…
Rising atmospheric carbon dioxide due to human activities through fossil fuel emissions and land use changes have increased climate extremes such as heat waves and droughts that have led to and are expected to increase the occurrence of…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…