Related papers: Exploring the Protein G Helix Free Energy Surface …
Using a well defined soft model glass in the framework of Molecular Dynamics simulations, the inherent structures are probed by means of a recently developed deformation protocol that aims to capture the Dynamical Heterogeneities (DH), as…
Free surfaces in glassy polymer films are known to induce surface mobile layers with enhanced dynamics. Using molecular dynamics simulations of a bead-spring model, we study a wide variety of layer-resolved structural and dynamical…
The flatness, compactness and high-capacity data storage capability make metasurfaces well-suited for holographic information recording and generation. However, most of the metasurface holograms are static, not allowing a dynamic…
We introduce multistate metadynamics for automatic exploration of conical intersection seams between adiabatic Born-Oppenheimer potential energy surfaces in molecular systems. By choosing the energy gap between the electronic states as a…
We use the torsional angles of the protein chain as generalized coordinates in the canonical formalism, derive canonical equations of motion, and investigate the coordinate dependence of the kinetic energy expressed in terms of the…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
A simple approach is proposed to investigate the protein structure. Using a low complexity model, a simple pairwise interaction and the concept of global optimization, we are able to calculate ground states of proteins, which are in…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Experiments show that isochoric (constant-volume) conditions enhance supercooling stability relative to isobaric (constant-pressure) conditions. Here, combining Helmholtz equilibrium thermodynamics with a first-order perturbation…
We present a clear and rigorous derivation of the Ewald-like method for calculation of the electrostatic energy of the systems infinitely periodic in two-dimensions and of finite size in the third dimension (slabs) which is significantly…
Theoretical design of global optimization algorithms can profitably utilize recent statistical mechanical treatments of potential energy surfaces (PES's). Here we analyze a particular method to explain its success in locating global minima…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
We train an equivariant machine learning model to predict energies and forces for a real-world study of hydrogen combustion under conditions of finite temperature and pressure. This challenging case for reactive chemistry illustrates that…
Reactive, semi-permeable interfaces play important roles in key biological processes such as targeted drug delivery, lipid metabolism, and signal transduction. These systems involve coupled surface reactions, transmembrane transport, and…
The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from {\it in vitro}, {\it in vivo}, and computational experiments (molecular dynamics simulations) are…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
We report a detailed study of the stationary points (zero-force points) of the potential energy surface (PES) of a model structural glassformer. We compare stationary points found with two different algorithms (eigenvector following and…
Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the…