Related papers: New force replica exchange method and protein fold…
Many proteins in cells are capable of sensing and responding to piconewton scale forces, a regime in which conformational changes are small but significant for biological processes. In order to efficiently and effectively sample the…
The thermodynamic driving force in the self-assembly of the secondary structure of a class of donor-acceptor oligorotaxanes is elucidated by means of molecular dynamics simulations of equilibrium isometric single-molecule force spectroscopy…
The interior of cells is crowded thus making it important to assess the effects of macromolecules on the folding of proteins. Using the Self-Organized Polymer (SOP) model, which is a coarse-grained representation of polypeptide chains, we…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
We study the elastic properties of a single A/B copolymer chain with a specific sequence. We predict a rich structure in the force extension relations which can be addressed to the sequence. The variational method is introduced to probe…
We present an extremely simplified model of multiple-domains polymer stretching in an atomic force microscopy experiment. We portray each module as a binary set of contacts and decompose the system energy into a harmonic term (the…
A novel mathematical model for fiber-reinforced materials is proposed. It is based on a 1-dimensional beam model for the thin fiber structures, a flexible and general 3-dimensional elasticity model for the matrix and an overlapping domain…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
The escape process from the native valley for proteins subjected to a constant stretching force is examined using a model for a Beta-barrel. For a wide range of forces, the unfolding dynamics can be treated as one-dimensional diffusion,…
We consider a stiff polymer chain in poor solvent and apply a force at one end of the chain. We find that by varying the stiffness parameter, polymer undergoes a transition from the globule state to the folded like state. The conformation…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…
Although, several factors have been attributed to thermostability, the stabilization strategies used by proteins are still enigmatic. Studies on recombinant xylanase which has the ubiquitous (\b{eta}/{\alpha})8 TIM (Triosephosphate…
The primary limitation for the application of alchemical free energy methods to a wider variety of complex molecular systems is achieving reasonable sampling. Flexible binding complexes often have high free energy barriers, which require…
We consider reversible breaking of adhesion bonds or folding of proteins under the influence of a constant external force. We discuss the stochastic properties of the unbinding/rebinding events and analyze their mean number and their…
A living cell actively generates traction forces on its environment with its actin cytoskeleton. These forces deform the cell elastic substrate which, in turn, affects the traction forces exerted by the cell and can consequently modify the…
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…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…