Related papers: Energy Landscapes for Digital Alchemy
Simulated landscapes have been used for decades to evaluate search strategies whose goal is to find the landscape location with maximum fitness. Applications include modeling the capacity of enzymes to catalyze reactions and the clinical…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
We explore various design principles for efficient excitation energy transport in complex quantum systems. We investigate energy transfer efficiency in randomly disordered geometries consisting of up to 20 chromophores to explore spatial…
Optimal Learning Machines (OLM) are systems that extract maximally informative representation of the environment they are in contact with, or of the data they are presented. It has recently been suggested that these systems are…
All systems in thermal equilibrium exhibit a spatially variable energy landscape due to thermal fluctuations. Thus at any instant there is naturally a thermodynamically driven localization of energy in parts of the system relative to other…
We analyze differences in dynamics and in properties of the sampled potential energy landscape between different equilibrium trajectories, for a system of rigid water molecules interacting with a two body potential. On entering in the…
The concept of fragility provides a possibility to rank different supercooled liquids on the basis of the temperature dependence of dynamic and/or thermodynamic quantities. We recall here the definitions of kinetic and thermodynamic…
We define the state of minimum energy while the expectation values of the field operators and their time derivatives in a determined moment in such a state are constrained. As an axiom, we consider such a state as the background of the…
We apply two independent data analysis methodologies to locate stable climate states in an intermediate complexity climate model and analyze their interplay. First, drawing from the theory of quasipotentials, and viewing the state space as…
We report a study of the basins of attraction for potential energy minima defined by different minimisation algorithms for an atomic system. We find that whereas some minimisation algorithms produce compact basins, others produce basins…
Generalization is a key challenge in machine learning, specifically in reasoning tasks, where models are expected to solve problems more complex than those encountered during training. Existing approaches typically train reasoning models in…
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…
We discuss the properties of the distributions of energies of minima obtained by gradient descent in complex energy landscapes. We find strikingly similar phenomenology across several prototypical models. We particularly focus on the…
We analyze the properties of a Lennard-Jones system at the level of the potential energy landscape. After an exhaustive investigation of the topological features of the landscape of the systems, obtained studying small size sample, we…
We study glassy dynamics using a simulation of three soft Brownian particles confined to a two-dimensional circular region. If the circular region is large, the disks freely rearrange, but rearrangements are rarer for smaller system sizes.…
Finding Minimum Energy Configurations (MECs) is essential in fields such as physics, chemistry, and materials science, as they represent the most stable states of the systems. In particular, identifying such MECs in multi-component alloys…
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…
A realistic microscopically-based quantum approach to the competition between fusion and quasi-fission in a heavy fusing system is applied to several reactions leading to $^{256}$No. Fusion and quasi-fission are described in terms of a…
Modeling microstructure evolution in electrochemical systems is vital for understanding the mechanism of various electrochemical processes. In this work, we propose a general phase field framework that is fully variational and thus…
The onset of life is often framed around membrane bound compartments and encoded metabolism, leaving unresolved how spatial organization arose before stable boundaries. In this context, environmental gradients are usually treated as…