Related papers: Visualizing Free Energy Landscapes for Four Hard D…
Granular systems confined in vertically vibrated shallow horizontal boxes (quasi two-dimensional geometry) present a liquid to solid phase transition when the frequency of the periodic forcing is increased. An effective model, where grains…
Enhanced sampling techniques have become an essential tool in computational chemistry and physics, where they are applied to sample activated processes that occur on a time scale that is inaccessible to conventional simulations. Despite…
A geometric analysis of the global properties of the energy landscape of a minimalistic model of a polypeptide is presented, which is based on the relation between dynamical trajectories and geodesics of a suitable manifold, whose metric is…
We investigate relations between spatial properties of the free energy and the radius of Gaussian curvature of the underlying curved lattice geometries. For this purpose we derive recurrence relations for the analysis of the free energy…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
The long-standing, dominant approach to robotic obstacle negotiation relies on mapping environmental geometry to avoid obstacles. However, this approach does not allow for traversal of cluttered obstacles, hindering applications such as…
The separation between physics at low and high energies is essential for physics to have any utility; the details of quantum gravity are not necessary to calculate the trajectory of a cannon ball. However, physics at low and high energies…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
A holistic view of the cosmological appearance and development of space is obtained by studying space as a spherically closed surface of a 4-sphere in a zero energy balance between motion and gravitation. Such an approach re-establishes…
The dynamics of individual colloidal particles in random potential energy landscapes were investigated experimentally and by Monte Carlo simulations. The value of the potential at each point in the two-dimensional energy landscape follows a…
Quantifying stochastic processes is essential to understand many natural phenomena, particularly in biology, including cell-fate decision in developmental processes as well as genesis and progression of cancers. While various attempts have…
Physics and economics are two disciplines that share the common challenge of linking microscopic and macroscopic behaviors. However, while physics is based on collective dynamics, economics is based on individual choices. This conceptual…
We calculate the statistical properties of the energy landscape of a minimal model for strong network-forming liquids. Dynamics and thermodynamic properties of this model can be computed with arbitrary precision even at low temperatures. A…
An exact description of the complete jamming landscape is developed for a system of hard discs of diameter $\sigma$, confined between two lines separated by a distance $1+\sqrt{3/4} < H/\sigma < 2$. By considering all possible local packing…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
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…
Supercooled liquids are metastable states realized by suppressing crystallization below the melting temperature. While it is well established that their dynamics slow down dramatically and become spatially heterogeneous upon cooling, the…
To clarify the relation of energy shifts to scattering phase shifts in one-body and many-body problems, we examine their relation in a number of different situations. We derive, for a particle in a container of arbitrary shape with a…
We present a method for the direct evaluation of the difference between the free energies of two crystalline structures, of different symmetry. The method rests on a Monte Carlo procedure which allows one to sample along a path, through…
We review a class of energy landscape analysis method that uses the Ising model and takes multivariate time series data as input. The method allows one to capture dynamics of the data as trajectories of a ball from one basin to a different…