Related papers: Rebinding kinetics from single-molecule force spec…
We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape…
We develop a linear response theory to provide a unified description of two recent spectroscopy protocols for probing one-dimensional supersolid states realized in cold-atom systems. Both protocols involve applying a periodic optical…
We study the reaction kinetics of end-functionalized polymer chains dispersed in an unreactive polymer melt. Starting from an infinite hierarchy of coupled equations for many-chain correlation functions, a closed equation is derived for the…
By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a…
Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment…
Quantum simulation with ultracold atoms provides a versatile platform to emulate condensed-matter models. In particular, momentum-space lattices enable the realization of programmable tight-binding Hamiltonians. Here, we generalize this…
RNA binding proteins play a crucial role in post-transcriptional gene regulation by controlling the transport, processing, and translation of their target RNAs. Post-transcriptional gene regulation leads to the differential expression of…
The forcing of particles in turbulent environments influences dynamical properties pertinent to many fundamental applications involving particle-flow interactions. Current study explores the determination of forcing for one-way coupled…
Reconstructing spectral densities from Euclidean lattice correlators requires an inverse Laplace transform, which is inherently ill-conditioned when applied to numerical data with statistical uncertainties. The maximum amount of information…
This paper applies the multibond graph approach for rigid multibody systems to model the dynamics of general spatial mechanisms. The commonly used quick return mechanism which comprises of revolute as well as prismatic joints has been…
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.…
Sacrificial bonds and hidden length in structural molecules account for the greatly increased fracture toughness of biological materials compared to synthetic materials without such structural features, by providing a molecular-scale…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
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…
The local balance equations for the density, momentum, and energy of a dilute gas of elastic or inelastic hard spheres, strongly confined between two parallel hard plates are obtained. The starting point is a Boltzmann-like kinetic…
We describe in this paper a crossbridge model in which an attached crossbridge behaves like a linear spring with a variable rest length. We assume in particular that the rest length has a linear force-velocity relation, and that the force…
In the past one hundred years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years,…
The measurement of cellular traction forces on soft elastic substrates has become a standard tool for many labs working on mechanobiology. Here we review the basic principles and different variants of this approach. In general, the…
Stochastic contraction analysis is a recently developed tool for studying the global stability properties of nonlinear stochastic systems, based on a differential analysis of convergence in an appropriate metric. To date, stochastic…
We study the influence of filament elasticity on the motion of collective molecular motors. It is found that for a backbone flexibility exceeding a characteristic value (motor stiffness divided through the mean displacement between attached…