Related papers: Modeling single-molecule stretching experiments us…
Analytical relations for the mechanical response of single polymer chains are valuable for modeling purposes, on both the molecular and the continuum scale. These relations can be obtained using statistical thermodynamics and an idealized…
It is common to study polymer physics through the use of idealized single-chain models, and the most popular of these is the freely jointed chain model. In certain thermodynamic ensembles, statistical mechanical treatment of this model is…
Single-molecule stretching experiments on DNA, RNA, and other biological macromolecules opened up the possibility of an impressive progress in many fields of Life and Medical sciences. The reliability of such experiments may be crucially…
We show how to construct non-equilibrium thermodynamics for systems too small to be considered thermodynamically in a traditional sense. Through the use of a non-equilibrium ensemble of many replicas of the system which can be viewed as a…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
In this paper we compare two polymer stretching experiments. The outcome of both experiments is a force-extension relation. We use a one-dimensional model to show that in general the two quantities are not equal. In certain limits, however,…
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…
In bulk systems the calculation of the main thermodynamic quantities leads to the same expectation values in the thermodynamic limit, regardless of the choice of the statistical ensemble. Single linear molecules can be still regarded as…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
Single-molecule pulling techniques have emerged as versatile tools for probing the noncovalent forces holding together the secondary and tertiary structure of macromolecules. They also constitute a way to study at the single-molecule level…
Stochastic differential equations (SDEs) are established tools to model physical phenomena whose dynamics are affected by random noise. By estimating parameters of an SDE intrinsic randomness of a system around its drift can be identified…
The energy dependent thermoelectric response of a single molecule contains valuable information about its transmission function and its excited states. However, measuring it requires devices that can efficiently heat up one side of the…
I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize…
A method is presented that, when used in conjunction with single molecule experimental techniques, allows for the extraction of rates and mechanical properties of a biomolecule undergoing transitions between mechanically distinct states.…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics like work, heat and entropy production to the level of individual trajectories of well-defined…
All ensembles of statistical mechanics are equivalent in the sense that they give the equivalent thermodynamic functions in the thermodynamic limit. However, when investigating microscopic structures in the first-order phase transition…
We present a statistical mechanics analysis of the finite-size elasticity of biopolymers, consisting of domains which can exhibit transitions between more than one stable state at large applied force. The constant-force (Gibbs) and…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
The methods of statistical mechanics are applied to two-dimensional foams under macroscopic agitation. A new variable -- the total cell curvature -- is introduced, which plays the role of energy in conventional statistical thermodynamics.…