Related papers: Modeling work-speed-accuracy trade-offs in a stoch…
Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the…
F1-ATPase (or F1), the highly-efficient and reversible biochemical engine, has motivated physicists as well as biologists to imagine the design principles governing machines in the fluctuating world. Recent experiments have clarified yet…
Intracellular transport is mediated by molecular motors that pull cargos along cytoskeletal filaments. Many cargos move bidirectionally and are transported by two teams of motors which move into opposite directions along the filament. We…
Probabilistic Cellular Automata are a generalization of Cellular Automata. Despite their simple definition, they exhibit fascinating and complex behaviours. The stationary behaviour of these models changes when model parameters are varied,…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Molecular motors are found throughout the cells of the human body, and have many different and important roles. These micro-machines move along filament tracks, and have the ability to convert chemical energy into mechanical work that…
Manipulating and coupling molecule gears is the first step towards realizing molecular-scale mechanical machines. Here, we theoretically investigate the behavior of such gears using molecular dynamics simulations. Within a nearly rigid-body…
The output of a motor is work, while the output of a clock is information. Here it is discussed how a molecular motor can produce both, work and information, depending on the load. If the ratio of the backward and forward stepping rates of…
We report new statistical time-series analysis tools providing significant improvements in the rapid, precision extraction of discrete state dynamics from large databases of experimental observations of molecular machines. By building…
Stochastic fluctuations of molecular abundances are a ubiquitous feature of cellular processes and lead to significant cell-to-cell variability. Recent theoretical work established lower bounds for stochastic fluctuations in cells for broad…
Quantitative understanding of the best possible performance of nanomotors allowed by physical laws pertains to study of nanomotors from biology as well as nanotechnology. Biological nanomotor F1-ATPase is the best available model system as…
The performance of industrial robotic work cells depends on optimizing various hyperparameters referring to the cell layout, such as robot base placement, tool placement, and kinematic design. Achieving this requires a bilevel optimization…
Living systems often function with regulatory interactions, but the question of how activity, stochasticity and regulations work together for achieving different goals still remains puzzling. We propose a stochastic model of an active…
The bacterial flagellar motor is a highly efficient rotary machine used by many bacteria to propel themselves. It has recently been shown that at low speeds its rotation proceeds in steps [Sowa et al. (2005) Nature 437, 916--919]. Here we…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
In this paper we study the statistical properties of a reversible cellular automaton in two out-of-equilibrium settings. In the first part we consider two instances of the initial value problem, corresponding to the inhomogeneous quench and…
Inspired by the need for effective stochastic models to describe the complex behavior of biological motor proteins that move on linear tracks exact results are derived for the velocity and dispersion of simple linear sequential models (or…
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…
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator.…
The diffusion of a molecular motor in the presence of a constant external force is considered on the basis of a simple theoretical model. The motor is represented by a Brownian particle moving in a series of parabolic potentials placed…