MOTIVATION For several decades, free energy minimization methods have been the dominant strategy for single sequence RNA secondary structure prediction. More recently, stochastic context-free grammars (SCFGs) have emerged as an alternative probabilistic methodology for modeling RNA structure. Unlike physics-based methods, which rely on thousands of experimentally-measured thermodynamic paramete...

We test the influence of the Coulomb interaction on the thermodynamic and cluster generation properties of a system of classical particles described by different lattice models. Numerical simulations show that the Coulomb interaction produces essentially a shift in temperature of quantities like the specific heat but not qualitative changes. We also consider a cellular model. The thermodynamic ...

This paper proposes three tests to determine whether a given nonlinear device noise model is in agreement with accepted thermodynamic principles. These tests are applied to several models. One conclusion is that the standard Gaussian noise models for nonlinear devices predict thermodynamically impossible circuit behavior: those models should be abandoned. But the nonlinear shot-noise model pred...

Abstract. In this paper we investigate the thermodynamic and the Stokes efficiency for a broad class of models for molecular motors. We use path-space formalism and time-symmetry breaking arguments to show that both efficiencies are smaller than 1. These arguments are model-independant and are thus applicable on a wide range of models. We also consider the motor as a ratchet which gives more bo...

The solubility and solubility trends of organometallic complexes in supercritical carbon dioxide are reviewed. The influence of intermolecular forces, physical properties and the metal chelates on solubility is explored. A number of thermodynamic models used to predict the solubility behavior of organometallic complexes in supercritical carbon dioxide, and the advantages and limitations to thes...

A toolbox for the development and reduction of the dynamical models of nonequilibrium systems is presented. The main components of this toolbox are: Legendre integrators, dynamical postprocessing, and thermodynamic projector. Thermodynamic projector is the tool to transform almost arbitrary anzatz to a thermodynamically consistent model, the postprocessing is the cheapest way to improve the sol...

Constraint-based stoichiometric models are ubiquitous in metabolic research, with Flux Balance Analysis (FBA) being the most widely used method to describe metabolic phenotypes of cells growing in steady-state. Of the many variants of constrainbased modelling methods published throughout the years, only few have focused on thermodynamic issues, in particular the elimination of non-physical and ...

The use of natural gas as an alternative fuel, in recent decades has been proposed. Good combustion properties and cats less than it could be the perfect choice for the next generation. Simulation models can be of great help engine designers. Simulation models to reduce the time and costs for the development of new engines as well as in identifying the technical value that need special attentio...

The linear multivariable modelling of an aircraft gas turbine is presented. A frequency-domain identification method is employed to estimate a family of models from engine data at a range of operating points. It is found that the fuel feed to shaft speed dynamics can be represented by second-order models. This matches the results obtained for the reduced-order linearised thermodynamic models de...