Related papers: Modeling single-molecule stretching experiments us…
Constitutive modeling of dielectric elastomers has been of long standing interest in mechanics. Over the last two decades rigorous constitutive models have been developed that couple the electrical response of these polymers with large…
Whole-cell modelling is constrained by the laws of nature in general and the laws of thermodynamics in particular. This paper shows how one prolific source of information, stoichiometric models of biomolecular systems, can be integrated…
Statistical mechanics and thermodynamics for ideal fractional exclusion statistics with mutual statistical interactions is studied systematically. We discuss properties of the single-state partition functions and derive the general form of…
We extend the theory of stochastic thermodynamics in three directions: (i) instead of a continuously monitored system we consider measurements only at an arbitrary set of discrete times, (ii) we allow for imperfect measurements and…
A variety of experimental techniques have improved the 2D and 3D spatial resolution that can be extracted from \emph{in vivo} single-molecule measurements. This enables researchers to quantitatively infer the magnitude and directionality of…
Single-molecule mechanical manipulation has enabled the quantitative understanding of the kinetics of bond ruptures as well as protein unfolding mechanism. Single-molecule experiments with theoretical models have allowed one to gain insight…
The field of chemical computation attempts to model computational behavior that arises when molecules, typically nucleic acids, are mixed together. Thermodynamic binding networks (TBNs) is a highly abstracted model that focuses on which…
Ensemble averaging of molecular states is fundamental for the experimental determination of thermodynamic quantities. A special case occurs for single-molecule investigations under equilibrium conditions, for which free energy, entropy and…
Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output.…
We deduce a fully analytical model to predict the artifacts of the measuring device handles in Single Molecule Force Spectroscopy experiments. As we show, neglecting the effects of the handle stiffness can lead to crucial overestimation or…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
We propose a protocol to model accurately the electromechanical behavior of dielectric elastomer membranes using experimental data of stress-stretch and voltage-stretch tests. We show how the relationship between electric displacement and…
A fundamental theory is presented for the mechanical response of polymer networks undergoing large deformation which seamlessly integrates statistical mechanical principles with macroscopic thermodynamic constitutive theory. Our formulation…
There are two paradigms to study nanoscale engines in stochastic and quantum thermodynamics. Autonomous models, which do not rely on any external time-dependence, and models that make use of time-dependent control fields, often combined…
Stochastic chains represent a wide and key variety of phenomena in many branches of science within the context of Information Theory and Thermodynamics. They are typically approached by a sequence of independent events or by a memoryless…
Single-molecule tracking is a powerful way to look at the dynamic organization of plasma membranes. However, there are some limitations to its use. For example, it was recently observed, using numerical simulation, that time-averaging…
In many chemical and biological applications, systems of differential equations containing unknown parameters are used to explain empirical observations and experimental data. The DEs are typically nonlinear and difficult to analyze,…
The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
Tethered particle motion (TPM) --- the motion of a micro- or nanoparticle tethered to a substrate by a macromolecule --- is a system that has proven extremely useful for its ability to reveal physical features of the tether, because the…