Related papers: An energetic model for macromolecules unraveling
Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and the…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
A theoretical analysis of the unfolding pathway of simple modular proteins in length- controlled pulling experiments is put forward. Within this framework, we predict the first module to unfold in a chain of identical units, emphasizing the…
The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
The classical continuum models used for the woven fabrics do not fully describe the whole set of phenomena that occur during the testing of those materials. This incompleteness is partially due to the absence of energy terms related to some…
Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using…
The strain states of the components of pseudomorphic superlattices can be accurately modeled analytically through the application of linear elasticity. In this particular case of GaN/AlN 'free-standing' superlattices, the predictions…
Far from being a passive information store, the genome is a mechanically dynamic and diverse system in which torsion and tension fluctuate and combine to determine structure and help regulate gene expression. Much of this mechanical…
The building of minimal self-reproducing systems with a physical embodiment (generically called protocells) is a great challenge, with implications for both theory and applied sciences. Although the classical view of a living protocell…
Recent advances in deep learning frameworks have established valuable tools for analyzing the long-timescale behavior of complex systems such as proteins. Especially the inclusion of physical constraints, e.g. time-reversibility, was a…
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
This paper deals with the energy transport properties of charged particles with time-dependent damping force. Based on the proposed nonlinear dimensionless mapping,the stability and dynamical evolution of the particle system is analyzed…
Experimental testing on dry woven fabrics exhibits a complex set of evidences that are difficult to be completely described using classical continuum models. The aim of this paper is to show how the introduction of energy terms related to…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
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…
We consider a singularly-perturbed two-well problem in the context of planar geometrically linear elasticity to model a rectangular martensitic nucleus in an austenitic matrix. We derive the scaling regimes for the minimal energy in terms…
The interplay of electronic and nuclear degrees of freedom presents an outstanding problem in condensed matter physics and chemistry. Computational challenges arise especially for large systems, long time scales, in nonequilibrium, or in…
Mechanical stretching of the I27 domain of titin and of its double and triple repeats are studied through molecular dynamics simulations of a Go-like model with Lennard-Jones contact interactions. We provide a thorough characterization of…