相关论文: Experimentally implemented dynamic optogenetic opt…
Biotechnology offers many opportunities for the sustainable manufacturing of valuable products. The toolbox to optimize bioprocesses includes \textit{extracellular} process elements such as the bioreactor design and mode of operation,…
Biotechnology can benefit from dynamic control to improve production efficiency. In this context, optogenetics enables modulation of gene expression using light as an external input, allowing fine-tuning of protein levels to unlock dynamic…
Adenosine triphosphate (ATP) is a high-energy phosphate compound and the most direct energy source in organisms. ATP is an essential biomarker for evaluating cell viability in biology. Researchers often use ATP bioluminescence to measure…
Translation of proteins is a fundamental part of gene expression that is mediated by ribosomes. As ribosomes significantly contribute to both cellular mass and energy consumption, achieving efficient management of the ribosome population is…
Dynamic metabolic control allows key metabolic fluxes to be modulated in real time, enhancing bioprocess flexibility and expanding available optimization degrees of freedom. This is achieved, e.g., via targeted modulation of metabolic…
Adenosine 5'-triphosphate (ATP) is the nearly ubiquitous "energy currency" of living organisms, and thus is a crucial participant in the majority of enzymatic reactions. The standard models in enzyme kinetics generally ignore the temporal…
Predicting the response of an observed system to a known input is a fruitful first step to accurately control the system's dynamics. Despite the recent advances in fully data-driven algorithms, the most interpretable way to reach this goal…
Apoptosis is an important area of research because of its role in keeping a mature multicellular organism's number of cells constant hence, ensuring that the organism does not have cell accumulation that may transform into cancer with…
The actin cytoskeleton of cells is in continuous motion due to both polymerization of new filaments and their contraction by myosin II molecular motors. Through adhesion to the substrate, such intracellular flow can be converted into cell…
We experimentally showed that biological molecular motor F$_1$-ATPase (F$_1$) implements an optimal rectification mechanism. F$_1$ hardly suppresses adenosine triphosphate (ATP) synthesis, which is the F$_1$'s physiological role while…
We demonstrate asymmetric enzyme kinetics of a biomolecular motor F1-ATPase between synthesis and hydrolysis of adenosine triphosphate (ATP). Our experiments show that ATP hydrolysis follows Michaelis-Menten kinetics, but ATP synthesis,…
Confocal time resolved single-molecule spectroscopy using pulsed laser excitation and synchronized multi channel time correlated single photon counting (TCSPC) provides detailed information about the conformational changes of a biological…
F$_{1}$-ATPase is a rotary molecular motor that \emph{in vivo} is subject to strong nonequilibrium driving forces. There is great interest in understanding the operational principles governing its high efficiency of free-energy…
The hematopoietic system has a highly regulated and complex structure in which cells are organized to successfully create and maintain new blood cells. Feedback regulation is crucial to tightly control this system, but the specific…
Living organisms continuously harness energy to perform complex functions for their adaptation and survival while part of that energy is dissipated in the form of heat or chemical waste. Determining the energetic cost and the efficiency of…
Optimizing solution-processed organic solar cells is a complex task due to the vast parameter space in organic photovoltaics (OPV). Classical Edisonian or one-variable-at-a-time (OVAT) optimization approaches are laborious, time-consuming,…
Motivation: Modeling biological signaling networks using ordinary differential equations (ODEs) has proven to be a powerful technique for generating insight into cellular dynamics, but it typically requires estimating rate parameters based…
Aqueous two-phase systems (ATPSs), that is, phase-separating solutions of water soluble but mutually immiscible molecular species, offer fascinating prospects for selective partitioning, purification, and extraction. Here, we formulate a…
This article proposes an improved trajectory optimization approach for stochastic optimal control of dynamical systems affected by measurement noise by combining optimal control with maximum likelihood techniques to improve the reduction of…
This paper presents a two-phase protein folding optimization on a three-dimensional AB off-lattice model. The first phase is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid…