Related papers: A geometrical approach to computing free energy la…
Understanding the geometry and topology of configuration or conformational spaces of molecules has relevant applications in chemistry and biology such as the proteins folding problem, drug design and the structure activity relationship…
Given discrete degrees of freedom (spins) on a graph interacting via an energy function, what can be said about the energy local minima and associated inherent structures? Using the lid algorithm in the context of a spin glass energy…
Several protocols are proposed to build continuous energy surfaces of many-body quantum systems, regarding both energy and states. The standard variational principle is augmented with constraints on state overlap, ensuring arbitrary…
We find the minimum and the maximum value for the local energy of an arbitrary finite bipartite system for any given amount of entanglement, also identifying families of states reaching these bounds and sharing formal analogies with thermal…
Graphical models for finite-dimensional spin glasses and real-world combinatorial optimization and satisfaction problems usually have an abundant number of short loops. The cluster variation method and its extension, the region graph…
The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…
We derive a formula that expresses the density of states of a system with continuous degrees of freedom as a function of microcanonical averages of squared gradient and Laplacian of the Hamiltonian. This result is then used to propose a…
The manifold of pure quantum states is a complex projective space endowed with the unitary-invariant geometry of Fubini and Study. According to the principles of geometric quantum mechanics, the detailed physical characteristics of a given…
A quantum particle moving under the influence of singular interactions on embedded surfaces furnish an interesting example from the spectral point of view. In these problems, the possible occurrence of a bound state is perhaps the most…
The quasipotential is a natural generalization of the concept of energy functions to non-equilibrium systems. In the analysis of rare events in stochastic dynamics, it plays a central role in characterizing the statistics of transition…
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model,…
We study the {\it quasi-classical limit} of a quantum system composed of finitely many non-relativistic particles coupled to a quantized field in Nelson-type models. We prove that, as the field becomes classical and the corresponding…
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…
In this short paper I discuss how conformal geometric algebra models for euclidean and minkowski targetspaces determine the allowed quantum mechanical statespaces for free particles. I explicitly treat 2-dimensional euclidean space and…
The concept of a protein diffusing in its free energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We…
Despite their fundamentally non-equilibrium nature, the individual and collective behavior of active systems with polar propulsion and isotropic interactions (polar-isotropic active systems) are remarkably well captured by equilibrium…
Recently, the stochastic dynamical model based on the free energy landscape was proposed to quantify the kinetics of the black hole phase transition. An essential concept is the generalized free energy of the fluctuating black hole, which…
Phoretic colloids self-propel thanks to surface flows generated in response to surface gradients (thermal, electrical, or chemical), that are self-induced and/or generated by other particles. Here we present a scalable and versatile…
A realistic analysis shows that constraining a quantomechanical system produces the effective dynamics to be coupled with {\sl abelian/non-abelian gauge fields} and {\sl quantum potentials} induced by the {\sl intrinsic} and {\sl extrinsic…
We construct a N-dimensional Gaussian landscape with multiscale, translation invariant, logarithmic correlations and investigate the statistical mechanics of a single particle in this environment. In the limit of high dimension N>>1 the…