Related papers: Direction dependent mechanical unfolding and Green…
Unfolding, in the context of high-energy particle physics, refers to the process of removing detector distortions in experimental data. The resulting unfolded measurements are straightforward to use for direct comparisons between…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
A Green's function formalism is used to calculate the spectrum of localized modes of an impurity layer implanted within a ferromagnetic thin film. The equations of motion for the Green's functions are determined in the framework of the…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either…
In the current AFM experiments the distribution of unfolding times, P(t), is measured by applying a constant stretching force f_s from which the apparent unfolding rate is obtained. To describe the complexity of the underlying energy…
A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40~nm in absorption maxima and only 18~nm in emission. The five proteins -- Dronpa, rsFastLime, rsKame, Padron(anionic form) and bsDronpa -- carry…
Feedforward control is essential to achieving good tracking performance in positioning systems. The aim of this paper is to develop an identification strategy for inverse models of systems with nonlinear dynamics of unknown structure using…
It is crucial to measure position and conformational changes of a membrane-interacting protein relative to the membrane surface. This is however challenging because the thickness of a membrane is usually only about 4 nm. We developed a…
The recently proposed fluctuation relation in unfolding forces [Phys. Rev. E ${\bf 84}$, $060101$(R) $(2011)$] is re-examined taking into account the explicit time dependence of the force distribution. The stretching of a tethered Rouse…
Introduced more than fifty years ago, dynamic light scattering is routinely used to determine the size distribution of colloidal suspensions, as well as of macromolecules in solution, such as proteins, nucleic acids, and their complexes.…
Inertial lift forces are exploited within inertial microfluidic devices to position, segregate, and sort particles or droplets. However the forces and their focusing positions can currently only be predicted by numerical simulations, making…
This article demonstrates that flexible and statistically tractable multi-modal diffusion models can be attained by transformation of simple well-known diffusion models such as the Ornstein-Uhlenbeck model, or more generally a Pearson…
In many experimental contexts, it is necessary to statistically remove the impact of instrumental effects in order to physically interpret measurements. This task has been extensively studied in particle physics, where the deconvolution…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
In certain systems which are subject to significant constant external forcing such as an airplane in wind or an underwater glider in ocean currents, the ability to detect the forcing depends on both the measurements available and whether…
As a problem in data science the inverse Ising (or Potts) problem is to infer the parameters of a Gibbs-Boltzmann distributions of an Ising (or Potts) model from samples drawn from that distribution. The algorithmic and computational…
The function of proteins arises from cooperative interactions and rearrangements of their amino acids, which exhibit large-scale dynamical modes. Long-range correlations have also been revealed in protein sequences, and this has motivated…
We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it…
A statistical mechanical description of flexible and semi-flexible polymer chains in a poor solvent is developed in the constant force and constant distance ensembles. We predict the existence of many intermediate states at low temperatures…