Related papers: Biomolecular System Energetics
To illustrate the power of the biophysical approach in solving important problems in life science, I present here one of our current research projects as an example. We have developed special biophotonic techniques to study the dynamic…
The species-area relationship is one of the central generalizations in ecology however its origin has remained a puzzle. Since ecosystems are understood as energy transduction systems, the regularities in species richness are considered to…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Information exchange is a critical process in all communication systems, including biological ones. The concept of retroactivity represents the loads that downstream modules apply to their upstream systems in biological circuits. This paper…
In systems biology and pharmacology, large-scale kinetic models are used to study the dynamic response of a system to a specific input or stimulus. While in many applications, a deeper understanding of the input-response behaviour is highly…
The dynamics of systems biological processes are usually modeled by a system of ordinary differential equations (ODEs) with many unknown parameters that need to be inferred from noisy and sparse measurements. Here, we introduce…
Predicting structural and energetic properties of a molecular system is one of the fundamental tasks in molecular simulations, and it has use cases in chemistry, biology, and medicine. In the past decade, the advent of machine learning…
Conventional energy production based on fossil fuels causes emissions which contribute to global warming. Accurate energy system models are required for a cost-optimal transition to a zero-emission energy system, an endeavor that requires…
We present two main contributions which help us in leveraging the theory of graphons for modeling evolutionary processes. We show a generative model for digraphons using a finite basis of subgraphs, which is representative of biological…
System dynamics is a popular approach in many fields of science and technology, but it has not been investigated for cell signaling pathways yet. It is a well formulated methodology used to analyze the components of a system considering the…
Bioelectrochemical systems are electrochemical cells that rely on conductive biofilms covering an electrode. We consider the example of a microbial fuel cell, and we derive a dynamic model of ion transport, biochemical reactions and…
Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of Escherichia coli metabolism can be sustained against single-gene or even multiple-gene mutations by…
An important part of the analysis of bio-molecular networks is to detect different functional units. Different functions are reflected in a different evolutionary dynamics, and hence in different statistical characteristics of network…
Increasingly sophisticated experiments, coupled with large-scale computational models, have the potential to systematically test biological hypotheses to drive our understanding of multicellular systems. In this short review, we explore key…
We extend the traditional framework of steady state energy transduction -- typically characterized by a single input and output -- to multi-resource transduction in open chemical reaction networks (CRNs). Transduction occurs when…
Bio-loggers, electronic devices used to track animal behaviour through various sensors, have become essential in wildlife research. Despite continuous improvements in their capabilities, bio-loggers still face significant limitations in…
Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence,…
Critical experimental design issues connecting energy transduction and inheritable information within a protocell are explored and elucidated. The protocell design utilizes a photo-driven energy transducer (a ruthenium complex) to turn…
Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not…
First we shortly review the different kinds of network modelling methods for systems biology with an emphasis on the different subtypes of logical models, which we review in more detail. Then we show the advantages of Boolean networks…