Related papers: Error-speed correlations in biopolymer synthesis
We consider the dependence of the electron transfer in photosynthetic complexes on correlation properties of random fluctuations of the protein environment. The electron subsystem is modeled by a finite network of connected electron…
New advances in nano sciences open the door for scientists to study biological processes on a microscopic molecule-by-molecule basis. Recent single-molecule biophysical experiments on enzyme systems, in particular, reveal that enzyme…
We have investigated instability of a superconducting quantum computer by continuously monitoring the qubit output. We found that qubits exhibit a step-like change in the error rates. This change is repeatedly observed, and each step…
We simultaneously study the dynamics of the growth of errors and the question of the faithfulness of simulations of $N$-body systems. The errors are quantified through the numerical reversibility of small-$N$ spherical systems, and by…
We present a practical scheme for performing error estimates for Density Functional Theory calculations. The approach which is based on ideas from Bayesian statistics involves creating an ensemble of exchange-correlation functionals by…
The problem of errors, arising due to finite BPM resolution, in the difference orbit parameters, which are found as a least squares fit to the BPM data, is one of the standard and important problems of accelerator physics. Even so for the…
Many fundamental cellular processes involve small numbers of molecules. When numbers are small, fluctuations dominate, and stochastic models, which account for these fluctuations, are required. In this chapter, we describe minimal…
We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of protein as a model system. We follow the dimerization…
In biochemistry, heteropolymers encoding biological information are assembled out of equilibrium by sequentially incorporating available monomers found in the environment. Current models of polymerization treat monomer incorporation as a…
Bacterial growth depends crucially on metabolic fluxes, which are limited by the cell's capacity to maintain metabolic enzymes. The necessary enzyme amount per unit flux is a major determinant of metabolic strategies both in evolution and…
We study the statistics of infima, stopping times and passage probabilities of entropy production in nonequilibrium steady states, and show that they are universal. We consider two examples of stopping times: first-passage times of entropy…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Stochastic restart may drastically reduce the expected run time of a computer algorithm, expedite the completion of a complex search process, or increase the turnover rate of an enzymatic reaction. These diverse first-passage-time (FPT)…
Polymer electrolytes are promising candidates for the next generation lithium-ion battery technology. Large scale screening of polymer electrolytes is hindered by the significant cost of molecular dynamics (MD) simulation in amorphous…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
Achieving error rates that meet or exceed the fault-tolerance threshold is a central goal for quantum computing experiments, and measuring these error rates using randomized benchmarking is now routine. However, direct comparison between…
Stochastic kinetic models of genetic expression are able to describe protein fluctuations. A comparative study of the canonical and a feedback model is given here by using stochastic simulation methods. The feedback model is skeleton model…
Velocity errors in particle tracking velocimetry (PTV) are studied. When using high-speed video cameras, the velocity error may increase at a high camera frame rate. This increase in velocity error is due to particle-position uncertainty,…
Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…
Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as…