Related papers: Direction dependent mechanical unfolding and Green…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
The relation between cooperativity of protein folding and the Random-Field Ising Model (RFIM) is established. Generalization of the Imry-Ma argument predicts cooperative folding transition for small heterogeneity of the interactions…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are…
We investigate the dynamics of an intruder pulled by a constant force in a dense two-dimensional granular fluid by means of event-driven molecular dynamics simulations. In a first step, we show how a propagating momentum front develops and…
A fluorescent image analysis procedure to determine the distribution of species concentration and density in a gas flow is proposed. The fluorescent emission is due to the excitation of atoms/molecules of a gas that is intercepted by an…
On the basis of the tight-binding formalism and Green function technique we obtain all the Green functions matrix elements for a biased chain with a linear variation of the electron on-site energy. Their dependence on the system parameters…
Photoactive proteins absorb light and undergo structural changes that enable them to perform essential biological functions. These proteins are critical for understanding light-induced biological processes, making them important in…
We model analytically the dynamics of a cytoskeletal filament in a motility assay. The filament is described as rigid rod free to slide in two dimensions. The motor proteins consist of polymeric tails tethered to the plane and modeled as…
The mechanical response of static, unconfined, overcompressed face centred cubic, granular arrays is studied using large-scale, discrete element method simulations. Specifically, the stress response due to the application of a localised…
Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable…
The problem of reconstructing the time dependence of the dynamic pressure of a plasma jet impinging on one end of a solid rod based on the measured displacement of the opposite end has been solved. This solution allows for a reduction in…
In this study the possibility of combining commercial Scanning Force Microscopes (SFM) with stretching devices for the investigation of microscopic surface changes during stepwise elongation is investigated. Different types of stretching…
We present force-clamp data on the collapse of ubiquitin polyproteins in response to a quench in the force. These nonequilibrium trajectories are analyzed using a general method based on a diffusive assumption of the end-to-end length to…
Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the…
The d-dimensional n-spin facilitated kinetic Ising model is studied analytically starting from usual master equations and their transformation into a Fock-space representation. The evolution of relevant operators is rewritten in terms of a…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…
The Ising model, in presence of an external magnetic field, is isomorphic to a model of localized interacting particles satisfying the Fermi statistics. By using this isomorphism, we construct a general solution of the Ising model which…