Related papers: Kinetic Model for a Threshold Filter in an Enzymat…

Living systems efficiently use chemical fuel to do work, process information, and assemble patterns despite thermal noise. Whether high efficiency arises from general principles or specific fine-tuning is unknown. Here, applying a recent…

Engineering, controlling, and simulating quantum dynamics is a strenuous task. However, these techniques are crucial to develop quantum technologies, preserve quantum properties, and engineer decoherence. Earlier results have demonstrated…

Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…

The hyperbolic dependence of catalytic rate on substrate concentration is a classical result in enzyme kinetics, quantified by the celebrated Michaelis-Menten equation. The ubiquity of this relation in diverse chemical and biological…

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,…

Optogenetic modulation of adenosine triphosphatase (ATPase) expression represents a novel approach to maximize bioprocess efficiency by leveraging enforced adenosine triphosphate (ATP) turnover. In this study, we experimentally implement a…

A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…

Models in systems biology are mathematical descriptions of biological processes that are used to answer questions and gain a better understanding of biological phenomena. Dynamic models represent the network through rates of the production…

Motivated by claims about the nature of the observed timescales in protein systems said to fold downhill, we have studied the finite, linear master equation which is a model of the downhill process. By solving for the system eigenvalues, we…

Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference…

Voltage-activated ion channels vary randomly between open and closed states, influenced by the membrane potential and other factors. Signal transduction is enhanced by noise in a simple ion channel model. The enhancement occurs in a finite…

Mathematical modeling is an important theoretical tool which provides researchers with quantification of the permeability of dialyzing systems in renal replacement therapy. In the paper we provide a short review of the most successful…

In living systems, collective molecular behavior is driven by thermodynamic forces in the form of chemical gradients. Leveraging recent advances in the field of nonequilibrium physics, I show that increasing the thermodynamic force alone…

We study biochemical reaction networks capable of product discrimination inspired by biological proofreading mechanisms. At equilibrium, product discrimination, the selective formation of a "correct" product with respect to an "incorrect…

We develop a stochastic model for the programmed frameshift of ribosomes synthesizing a protein while moving along a mRNA template. Normally the reading frame of a ribosome decodes successive triplets of nucleotides on the mRNA in a…

The renormalization group has proven to be a very powerful tool in physics for treating systems with many length scales. Here we show how it can be adapted to provide a new class of algorithms for discrete optimization. The heart of our…

Reliable in-silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the…

This paper focuses on designing a particle filter for randomly delayed measurements with an unknown latency probability. A generalized measurement model is adopted which includes measurements that are delayed randomly by an arbitrary but…

We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product…

Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…