Related papers: Modeling single-molecule stretching experiments us…
Results of recent large-scale molecular dynamics simulations of dislocation-mediated solid plasticity are campared with predictions of the statistical thermodynamic theory of these phenomena. These computational and theoretical analyses are…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
We describe some recent results concerning the statistical properties of a self-interacting polymer stretched by an external force. We concentrate mainly on the cases of purely attractive or purely repulsive self-interactions, but our…
Ultra-precision machining of metals, the breaking of nanowires under tensile stress and fracture of nanoscale materials are examples of technologically important processes which are both extremely difficult and costly to investigate…
In simulations of a water-like model (ST2) that exhibits a liquid-liquid phase transition, we test for the occurrence of a thermodynamic region in which the liquid can be modelled as a two-component mixture. We assign each molecule to one…
In this work we study the spreading dynamics of tiny liquid droplets on solid surfaces in the case where the ends of the molecules feel different interactions with respect to the surface. We consider a simple model of dimers and short…
We introduce three stochastic cooperative models for particle deposition and evaporation relevant to ionic self-assembly of nanoparticles with applications in surface fabrication and nanomedicine. We present a method for mapping a…
Sintering, as a thermal process at elevated temperature below the melting point, is widely used to bond contacting particles into engineering products such as ceramics, metals, polymers, and cemented carbides. Modelling and simulation as…
Exploration of structure-property relationships as a function of dopant concentration is commonly based on mean field theories for solid solutions. However, such theories that work well for semiconductors tend to fail in materials with…
Thermodynamic length is a path function that generalizes the notion of length to the surface of thermodynamic states. Here, we show how to measure thermodynamic length in far-from-equilibrium single molecule experiments using the work…
Physical theories that depend on many parameters or are tested against data from many different experiments pose unique challenges to statistical inference. Many models in particle physics, astrophysics and cosmology fall into one or both…
We examine a biomolecular machine involving a driven, observable process coupled to a hidden process in a kinetically cooperative manner. A stochastic thermodynamics framework is employed to analyze a fluctuation theorem for the…
Entangled polymers are an important class of materials for their toughness, processability, and functionalizability. However, physically detailed modeling of highly entangled polymers can prove challenging, especially as one considers…
Single-chain elasticity of polyethylene at $\theta$ point up to 90% of stretching with respect to its contour length is computed by Monte-Carlo simulation of an atomistic model in continuous space. The elasticity law together with the…
A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearest-neighbor interaction of a Morse-like potential…
The dynamics of quantum entanglement plays a central role in explaining the emergence of thermal equilibrium in isolated many-body systems. However, entanglement is notoriously hard to measure. Recent works have introduced a notion of…
Physical kinetic roughening processes are well known to exhibit universal scaling of observables that fluctuate in space and time. Are there analogous dynamic scaling laws that are unique to the chemical reaction mechanisms available…
Quantum dots (QDs) are good model systems for fundamental studies of mesoscopic transport phenomena using thermoelectric effects because of their small size, electrostatically tunable properties and thermoelectric response characteristics…
In this paper we survey recent work on the use of statistical model checking techniques for biological applications. We begin with an overview of the basic modelling techniques for biochemical reactions and their corresponding stochastic…
Single-molecule experimental techniques track the real-time dynamics of molecules by recording a small number of experimental observables. Following these observables provides a coarse-grained, low-dimensional representation of the…