Related papers: Molecular Motor or Molecular Clock: A Question of …
Cell is the structural and functional unit of life. This Resource Letter serves as a guide to the literature on nano-machines which drive not only intracellular movements, but also motility of the cell. These machines are usually proteins…
Machine learning encompasses a set of tools and algorithms which are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as well, where machine learning offers promises of extracting…
Multi-component molecular machines are ubiquitous in biology. We review recent progress on describing their thermodynamic properties using autonomous bipartite Markovian dynamics. The first and second laws can be split into local versions…
A firm can complete the tasks needed to produce output using either machines or workers. Unlike machines, workers have private information about their preferences over tasks. I study how this information asymmetry shapes the mechanism used…
A Brownian information machine extracts work from a heat bath through a feedback process that exploits the information acquired in a measurement. For the paradigmatic case of a particle trapped in a harmonic potential, we determine how…
Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
We consider mechanically generated molecular braids composed of two molecules where long range interactions between them can be considered to be very weak. We describe a model that takes account of the thermal fluctuations of the braid,…
Formal grammars are extensively used in Computer Science and related fields to study the rules which govern production of a language. The use of these grammars can be extended beyond mere language production. One possibility is to view…
Computers are nonlinear dynamical systems that exhibit complex and sometimes even chaotic behavior. The models used in the computer systems community, however, are linear. This paper is an exploration of that disconnect: when linear models…
The performance of quantum heat engines is generally based on the analysis of a single cycle. We challenge this approach by showing that the total work performed by a quantum engine need not be proportional to the number of cycles.…
Atomic clocks are typically operated by locking a local oscillator (LO) to a single atomic ensemble. In this article we propose a scheme where the LO is locked to several atomic ensembles instead of one. This results in an exponential…
On a chassis of gear model, we have offered a quantitative description for our method to synthesize a chemical clock signal with various duty cycles in Part I. As Part II of the study, this paper devotes itself in proposing a design…
The nanoscopic isothermal machines are not only energy but also information transducers. We show that the generalized fluctuation theorem with information creation and entropy reduction can be fulfilled for the enzymatic molecular machines…
Spintronics is the ability of injecting, manipulating and detecting electron spins into solid state systems. Molecular-electronics investigates the possibility of making electronic devices using organic molecules. Traditionally these two…
Molecular motors walk along filaments until they detach stochastically with a force-dependent unbinding rate. Here, we show that this unbinding rate can be obtained from the analysis of experimental data of molecular motors moving in…
This chapter gives an overview of the core concepts of machine learning (ML) -- the use of algorithms that learn from data, identify patterns, and make predictions or decisions without being explicitly programmed -- that are relevant to…
Electrical machines are devices that change either mechanical or electrical energy to the other and also can alternate the voltage levels of an alternating current. The need for electrical machines cannot be overemphasized since they are…
The recently proposed set-up of source coding with a side information "vending machine" allows the decoder to select actions in order to control the quality of the side information. The actions can depend on the message received from the…
The mechanics of crawling cells on a substrate is investigated by using a minimal model that satisfies the force-free condition. A cell is described by two subcellular elements connected by a linear actuator that changes the length of the…