Related papers: Modeling single-molecule stretching experiments us…
Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of…
We review the physical properties of macromolecular networks, consisting of semiflexible polymers such as actin. We start by giving a theoretical analysis of the conformational statistics and mechanical response of single filaments.…
We propose a detailed investigation of the schematic mode-coupling approach to experimental data, a method based on the use of simple mode-coupling equations to analyze the dynamics of supercooled liquids. Our aim here is to clarify…
The aim of this review is to provide a concise overview of some of the generic approaches that have been developed to deal with the statistical description of large systems of interacting dissipative 'units'. The latter notion includes,…
A modeling framework for the internal conformational dynamics and external mechanical movement of single biological macromolecules in aqueous solution at constant temperature is developed. Both the internal dynamics and external movement…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
Translating metabolic networks into dynamic models is difficult if kinetic constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction elasticities by independent random numbers. Here I propose a variant that accounts for…
Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and the…
Isomorphs are curves in the thermodynamic phase diagram of invariant excess entropy, structure, and dynamics, while pseudoisomorphs are curves of invariant structure and dynamics, but not of the excess entropy. The latter curves have been…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Recent developments of microscopic mechanical experiments allow the manipulation of individual polymer molecules in two main ways: \textit{uniform} stretching by external forces and \textit{non-uniform} stretching by external fields. Many…
Electronic transport properties for single-molecule junctions have been widely measured by several techniques, including mechanically controllable break junctions, electromigration break junctions or by means of scanning tunneling…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…
We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that…
Thermodynamics of nanoscale devices is an active area of research. Despite their noisy surrounding they often produce mechanical work (e.g. micro-heat engines), display rectified Brownian motion (e.g. molecular motors). This invokes…
Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the non-linear case of systems under non-equilibrium external…
Small systems in a thermodynamic medium --- like colloids in a suspension or the molecular machinery in living cells --- are strongly affected by the thermal fluctuations of their environment. Physicists model such systems by means of…
A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific…
We study a class of models for brittle fracture: elastic theory models which allow for cracks but not for plastic flow. We show that these models exhibit, at all finite temperatures, a transition to fracture under applied load similar to…
It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow…