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Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output.…
Waste production, carbon dioxide atmospheric accumulation, and dependence on finite natural resources are expressions of the unsustainability of the current industrial networks that supply fuels, energy, and manufacturing products. In…
Strand displacement and tile assembly systems are designed to follow prescribed kinetic rules (i.e., exhibit a specific time-evolution). However, the expected behavior in the limit of infinite time--known as thermodynamic equilibrium--is…
This paper presents a novel framework for the modeling of biological networks. It makes use of recent tools analyzing the robust satisfaction of properties of (hybrid) dynamical systems. The main challenge of this approach as applied to…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
Equations of State model relations between thermodynamic variables and are ubiquitous in scientific modelling, appearing in modern day applications ranging from Astrophysics to Climate Science. The three desired properties of a general…
Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy…
Geometric, topological and graph theory modeling and analysis of biomolecules are of essential importance in the conceptualization of molecular structure, function, dynamics, and transport. On the one hand, geometric modeling provides…
Multi-omics data offer unprecedented insights into complex biological systems, yet their high dimensionality, sparsity, and intricate interactions pose significant analytical challenges. Network-based approaches have advanced multi-omics…
In this paper homogenization of a mathematical model for plant tissue biomechanics is presented. The microscopic model constitutes a strongly coupled system of reaction-diffusion-convection equations for chemical processes in plant cells,…
Chemical and biological networks can describe a wide variety of processes, from gene regulatory networks to biochemical oscillations. Modeled by chemical master equations, these processes are inherently stochastic, as fluctuations dominate…
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of…
Chemical reaction networks (CRNs) are prototypical complex systems because reactions are nonlinear and connected in intricate ways, and they are also essential to understand living systems. Here, I discuss how recent developments in…
The interfaces between metal electrodes and liquid electrolytes are prototypical in electrochemistry. That is why it is crucial to have a molecular and dynamical understating of such interfaces for both electrical properties and chemical…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
Trying to identify the entropy production within a cell has been part of debates and studies in the last century. First the idea was to make a resemblance of a cell with a Carnot engine, which is the most thermodynamically perfect machine.…
As data structures and mathematical objects used for complex systems modeling, hypergraphs sit nicely poised between on the one hand the world of network models, and on the other that of higher-order mathematical abstractions from algebra,…
Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…
This computational experiment demonstrates that chain melting in lipids is a molecular process. BOMD is certainly the best method to reproduce such dynamics properties, since the electronic contributions to the various molecular structures…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…