The main purpose of this paper is to introduce a class of simple random mechanical model systems that may help in shedding light on the mechanisms whereby steady state, out of equilibrium thermodynamical behavior can emerge in random dynamics. In the spirit of classical statistical mechanics, our random systems arise as a certain form of course-graining of Hamiltonian mechanical models; among t...

This paper represents a preliminary effort in considering how protein motors could harness thermal fluctuations to generate force and movement. The initial premise for this model is the thermal motor described by Feynman which consists of a ratchet and an interdigitating, spring-loaded pawl. By analogy, one can imagine that biological motors interact weakly with their filament subunit substrate...

The high computational cost of carrying out molecular dynamics simulations of even small–size proteins is a major obstacle in the study, at atomic detail and in explicit solvent, of the physical mechanism which is at the basis of the folding of proteins. Making use of a biasing algorithm, based on the principle of the ratchet–and–pawl, we have been able to calculate eight folding trajectories (...

The maximum power of Feynman’s ratchet as a heat engine and the corresponding efficiency (η∗) are investigated by optimizing both the internal parameter and the external load. When a perfect ratchet device (no heat exchange between the ratchet and the paw via kinetic energy) works between two thermal baths at temperatures T1 > T2, its efficiency at maximum power is found to be η∗ = η 2 C /[ηC −...

Hormones and neuropeptides are generally synthesized as large precursor molecules: i.e. prohormones and proneuropeptides which undergo endoproteolysis to produce biologically active peptides. Corticotrophin releasing hormone (CRH) is a 41 aminoacid peptide which plays a major role in the regulation of the endocrine response to stress. CRH( 1-41) is generated after endoproteolytic cleavage at pa...

M yosin molecular motors bind to and exert force upon actin filaments. Between 24 (1) and 37 (2) myosin subfamilies are currently recognized (3), the myriad members of which are specialized for tasks ranging from muscle contraction through to mechano-sensation and signaling, cell polarization, the sliding and tensioning of cytoskeletal elements, organelle transport, exocytosis and endocytosis, ...

Motor proteins are enzymes that convert chemical energy derived from the hydrolysis of ATP into mechanical work used to power directed movement along cytoskeletal filaments inside cells. Motor proteins have essential biological functions such as driving the contraction of muscle, the beating of sperm and cilia, and the transport of intracellular cargoes. Motor proteins are also interesting from...

Protein misfolding is implicated in many diseases, including the serpinopathies. For the canonical inhibitory serpin α1-antitrypsin (A1AT), mutations can result in protein deficiencies leading to lung disease and polymerization prone mutants can accumulate in hepatocytes leading to liver disease. Using all-atom simulations based on the recently developed Bias Functional algorithm we elucidate h...

Computing Machine Models. To gauge the computational power of a family of mechanical computers, we will use a widely known abstract computational model known as the Turing Machine, defined in this section. The Turing Machine. The Turing machine model formulated by Alan Turing [1] was the first complete mathematical model of an abstract computing machine that possessed universal computing power....

Computing Machine Models. To gauge the computational power of a family of mechanical computers, we will use a widely known abstract computational model known as the Turing Machine, defined in this section. The Turing Machine. The Turing machine model formulated by Alan Turing [1] was the first complete mathematical model of an abstract computing machine that possessed universal computing power....