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Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
In order to obtain a good understanding of astrochemistry, it is crucial to better understand the key parameters that govern grain-surface chemistry. For many chemical networks, these crucial parameters are the binding energies of the…
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…
A novel method combining maximum entropy principle, the Bayesian-inference of ensembles approach, and the optimization of empirical forward models is presented. Here we focus on the Karplus parameters for RNA systems, which relate the…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
Numerical modeling of proton exchange membrane fuel cells is at the verge of becoming predictive. A crucial requisite for this, though, is that material properties of the membrane-electrode assembly and their functional dependence on the…
Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. In this work, we use the…
The observation that, through a titration mechanism, microRNAs (miRNAs) can act as mediators of effective interactions among their common targets (competing endogenous RNAs or ceRNAs) has brought forward the idea ('ceRNA hypothesis') that…
In biopharmaceutical manufacturing, fermentation processes play a critical role in productivity and profit. A fermentation process uses living cells with complex biological mechanisms, leading to high variability in the process outputs,…
Recent work has shown that expression level is the main predictor of a gene’s evolutionary rate, and that more highly expressed genes evolve slower. A possible explanation for this observation is selection for proteins which fold…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
Stochastic modelling provides an indispensable tool for understanding how random events at the molecular level influence cellular functions. In practice, the common challenge is to calibrate a large number of model parameters against the…
Affinity-based biosensors have become indispensable in modern diagnostics and health monitoring. While considerable research has focused on optimizing analyte transport and binding kinetics, a fundamental parameter - sample volume - remains…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene…
Predicting enzyme kinetic parameters quantifies how efficiently an enzyme catalyzes a specific substrate under defined biochemical conditions. Canonical parameters such as the turnover number ($k_\text{cat}$), Michaelis constant…
We present a novel formulation for biochemical reaction networks in the context of signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select…
The molecular motor protein kinesin plays a key role in fundamental cellular processes such as intracellular transport, mitotic spindle formation, and cytokinesis, with important implications for neurodegenerative and cancer disease…
We explore a Markov model used in the analysis of gene expression, involving the bursty production of pre-mRNA, its conversion to mature mRNA, and its consequent degradation. We demonstrate that the integration used to compute the solution…
A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…