Related papers: Free-energy landscape of polymer-crystal polymorph…
Free-energy landscapes for short peptides -- specifically for variants of the pH Low Insertion Peptide (pHLIP) -- in the heterogeneous environment of a lipid bilayer or cell membrane are constructed, taking into account a set of dominant…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
Free energies are fundamental quantities governing phase behavior and thermodynamic stability in polymer systems, yet their accurate computation often requires extensive simulations and post-processing techniques such as the Bennett…
Metastable polymorphs often result from the interplay between thermodynamics and kinetics. Despite advances in predictive synthesis for solution-based techniques, there remains a lack of methods to design solid-state reactions targeting…
The complex physics of glass forming systems is controlled by the structure of the low energy portions of their potential energy landscapes. Here, we report that a modified metadynamics algorithm efficiently explores and samples low energy…
Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be…
Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance…
The low-temperature driven or thermally activated motion of several condensed matter systems is often modeled by the dynamics of interfaces (co-dimension-1 elastic manifolds) subject to a random potential. Two characteristic quantitative…
The equilibrium state of a superfluid in a rotating cylindrical vessel is a vortex crystal -- an array of vortex lines which is stationary in the rotating frame. Experimental realisations of this behaviour typically show a sequence of…
Ground state structures found in nature are in many cases of high symmetry. But structure prediction methods typically render only a small fraction of high symmetry structures. Especially for large crystalline unit cells there are many low…
For decades, it was unknown how electron bifurcating systems in Nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron bifurcating molecular machines could not be designed and built.…
We examine the Stillinger-Weber analysis of the potential energy landscape for its stability and conclude that it does not provide a stable description of the system as the free energy slope and curvature vanish simultaneously. An…
The past few years have seen great strides in our ability to build synthetic microscopic machines. However, the function of such machines is often controlled directly by externally applied fields that deterministically specify the…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes…
We study the free energy of the worm-like-chain model, in the constant-extension ensemble, as a function of the stiffness for finite chains of length L. We find that the polymer properties obtained in this ensemble are "qualitatively"…
Particles interacting with short-ranged potentials have attracted increasing interest, partly for their ability to model mesoscale systems such as colloids interacting via DNA or depletion. We consider the free energy landscape of such…
As the number of theoretically predicted materials continues to grow, it becomes increasingly important to assess not only their thermodynamic stability but also their kinetic viability under realistic synthesis conditions. In this study,…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
In order to better understand the occurrence of phase transitions, we adopt an approach based on the study of energy landscapes: The relation between stationary points of the potential energy landscape of a classical many-particle system…