Related papers: Optimal rectification without forward-current supp…
The synthesis of ATP, life's 'universal energy currency', is the most prevalent chemical reaction in biological systems, and is responsible for fueling nearly all cellular processes, from nerve impulse propagation to DNA synthesis. ATP…
We present a model of an ATP-fueled molecular machine which push a polymer through a pore channel. The machine acts between two levels (working-waiting), and the working one remains active for a fixed time giving a constant force. The…
The motility of cilia and flagella is driven by thousands of dynein motors that hydrolyze adenosine triphosphate (ATP). Despite decades of genetic, biochemical, structural and biophysical studies, some aspects of ciliary motility remain…
In this study, a new approach based on adaptive dynamic programming (ADP) is proposed to control permanent magnet synchronous motors (PMSMs). The objective of this paper is to control the torque and consequently the speed of a PMSM when an…
FoF1-ATP synthases in Escherichia coli (E. coli) bacteria are membrane-bound enzymes which use an internal proton-driven rotary double motor to catalyze the synthesis of adenosine triphosphate (ATP). According to the 'chemiosmotic…
Presented in this paper is a derivation of a 2D catalytic reaction-based model to solve combinatorial optimization problems (COPs). The simulated catalytic reactions, a computational metaphor, occurs in an artificial chemical reactor that…
Cat qubits, for which logical $|0\rangle$ and $|1\rangle$ are coherent states $|\pm\alpha\rangle$ of a harmonic mode, offer a promising route towards quantum error correction. Using dissipation to our advantage so that photon pairs of the…
The effect of mutations on protein structures is usually rather localized and minor. Finding a mutation that can single-handedly change the fold and/or topology of a protein structure is a rare exception. The A31P mutant of the homodimeric…
We investigate the reversible disassembly of VOV1-ATPase in life yeast cells by time resolved confocal FRET imaging. VOV1-ATPase in the vacuolar membrane pumps protons from the cytosol into the vacuole. VOV1-ATPase is a rotary biological…
The bacterial flagellar motor (BFM) converts transmembrane ion flux into directed mechanical rotation, driving bacterial motility. Despite extensive study, the frictional forces and energetics governing its torque generation remain poorly…
Recently, accelerated algorithms using the anchoring mechanism for minimax optimization and fixed-point problems have been proposed, and matching complexity lower bounds establish their optimality. In this work, we present the surprising…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
Artificial Immune Systems (AIS) employing hypermutations with linear static mutation potential have recently been shown to be very effective at escaping local optima of combinatorial optimisation problems at the expense of being slower…
In this paper, a dynamic antiwindup compensator design is proposed which augments the main controller and guarantees robust performance in the event of input saturation. This is a two stage process in which first a robust optimal controller…
Cytoskeletal motor proteins move on filamentous tracks by converting input chemical energy that they derive by catalyzing the hydrolysis of ATP. The ATPase site is the analog of an engine and hydrolysis of ATP is the analog of burning of…
Cytoskeletal filaments are capable of self-assembly in the absence of externally supplied chemical energy, but the rapid turnover rates essential for their biological function require a constant flux of ATP or GTP hydrolysis. The same is…
Trapping nanoscopic objects to observe their dynamic behaviour for extended periods of time is an ongoing quest. Particularly, sub-100nm transparent objects are hard to catch and most techniques rely on immobilisation or transient diffusion…
ATPases cyclically convert chemical energy in the form of ATP gradients into directed motion inside cells. To function, ATPases rely on allosteric communication between at least two binding sites, an internal signaling mechanism that is not…
The origin of biological motion can be traced back to the function of molecular motor proteins. Cytoplasmic dynein and kinesin transport organelles within our cells moving along a polymeric filament, the microtubule. The motion of the…
We analyze the rectified motion of a Brownian particle in a confined environment. We show the emergence of strong cooperativity between the inherent rectification of the ratchet mechanism and the entropic bias of the fluctuations caused by…