Related papers: Optimal rectification without forward-current supp…
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…
Cytoskeletal motor proteins are involved in major intracellular transport processes which are vital for maintaining appropriate cellular function. The motor exhibits distinct states of motility: active motion along filaments, and…
Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity. We model the backtracking mechanism of RNA polymerase, which…
Biomolecular machines transduce free energy from one form to another to fulfill many important roles inside cells, with dissipation required to achieve directed progress. We investigate how to break time-reversal symmetry at a given…
A molecular motor is made of either a single macromolecule or a macromolecular complex. Just like their macroscopic counterparts, molecular motors "transduce" input energy into mechanical work. All the nano-motors considered here operate…
We show how to switch on and off the ratchet potential of a collective Brownian motor, depending only on the position of the particles, in order to attain a current higher than or at least equal to that induced by any periodic flashing.…
The inherent probabilistic nature of the biochemical reactions, and low copy number of species can lead to stochasticity in gene expression across identical cells. As a result, after induction of gene expression, the time at which a…
We study a magnetization reversal by an electric current pulse in a superconductor/insulating ferromagnet/superconductor Josephson junction placed on top of a 3D topological insulator. It is demonstrated that such a system is perspective…
We present flow matching for reaction coordinates (FMRC), a novel deep learning algorithm designed to identify optimal reaction coordinates (RC) in biomolecular reversible dynamics. FMRC is based on the mathematical principles of…
This research rigorously investigates the convergence of adaptive finite element methods for regularized variational models of quasi-static brittle fracture in elastic solids. We specifically examine a novel Ambrosio-Tortorelli (AT1)…
To monitor conformational changes of individual membrane transporters in liposomes in real time, we attach two fluorophores to selected domains of a protein. Sequential distance changes between the dyes are recorded and analyzed by Forster…
The one dimensional motion of a massless Brownian particle on a symmetric periodic substrate can be rectified by re-injecting its driving noise through a realistic recycling procedure. If the recycled noise is multiplicatively coupled to…
This paper presents a reformulation for the automatic generation control (AGC) in a decomposed convex relaxation algorithm. It finds an optimal solution to the AC optimal power flow (ACOPF) problem that is secure against a large set of…
Anomalously slow passive diffusion, $\langle \delta x^2(t)\rangle\simeq t^{\alpha}$, with $0<\alpha<1$, of larger tracers such as messenger RNA and endogenous submicron granules in the cytoplasm of living biological cells has been…
Kinesins move processively toward the plus end of microtubules by hydrolyzing ATP for each step. From an enzymatic perspective, the mechanism of mechanical motion coupled to the nucleotide chemistry is often well explained using a…
Many real-world systems are governed by the time-dependent, nonlinear differential equations. Dynamics of an electrical system are also best described using the very equations. Being one of the preferred machines when using advanced control…
Gradient-based first-order adaptive optimization methods such as the Adam optimizer are prevalent in training artificial networks, achieving the state-of-the-art results. This work attempts to answer the question whether it is viable for…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
Thermophilic enzymes can operate at higher temperatures but show reduced activities at room temperature. They are in general more stable during preparation and, accordingly, are considered to be more rigid in structure. Crystallization is…
Previous kinetic models had assumed that the reaction medium was reacting at random and without a turnover associated to thermodynamics exchanges, with a rigid active site on the enzyme. The experimental studies show that coupling factor 1…