Related papers: Exploring the Free Energy Landscape: From Dynamics…
Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus. Revealing thermodynamic origin of a given…
We use topological data analysis (TDA) to study how data transforms as it passes through successive layers of a deep neural network (DNN). We compute the persistent homology of the activation data for each layer of the network and summarize…
A major challenge in nonadiabatic molecular dynamics is to automatically and objectively identify the key reaction coordinates that drive molecules toward distinct excited-state decay channels. Traditional manual analyses are inefficient…
Random walks on multidimensional nonlinear landscapes are of interest in many areas of science and engineering. In particular, properties of adaptive trajectories on fitness landscapes determine population fates and thus play a central role…
A family of fast sampling methods is introduced here for molecular simulations of systems having rugged free energy landscapes. The methods represent a generalization of a strategy consisting of adjusting a model for the free energy as a…
Energy landscape models characterize neural dynamics by assigning energy values to each brain state that reflect their stability or probability of occurrence. The conventional energy landscape models rely on binary brain state…
We show that the interplay between excluded volume effects, hydrophobicity, and hydrogen bonding of a tube-like representation of a polypeptide chain gives rise to free energy landscapes that exhibit a small number of metastable minima…
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…
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with a simple effective, coarse-grained off-lattice model to study the structure and the topology of the energy surface. The multicanonical method…
The ability to explain decisions made by machine learning models remains one of the most significant hurdles towards widespread adoption of AI in highly sensitive areas such as medicine, cybersecurity or autonomous driving. Great interest…
We propose a network characterization of combinatorial fitness landscapes by adapting the notion of inherent networks proposed for energy surfaces. We use the well-known family of NK landscapes as an example. In our case the inherent…
The complexity and unpredictability of postbuckling responses in even simple thin shells have raised great challenges to emerging technologies exploiting buckling transitions. Here we comprehensively survey the buckling landscapes to show…
A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores…
On the basis of the density functional theory, we give a clear definition of the free energy landscape. To show the usefulness of the definition, we construct the free energy landscape for rearrangement of atoms in an FCC crystal of hard…
Mesoscopic quantum systems exhibit complex many-body quantum phenomena, where interactions between spins and charges give rise to collective modes and topological states. Even simple, non-interacting theories display a rich landscape of…
Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
We extend the non-parametric framework of reaction coordinate optimization to non-equilibrium ensembles of (short) trajectories. For example, we show how, starting from such an ensemble, one can obtain an equilibrium free energy profile…
How useful it is to think about the potential energy landscape of a complex many-body system depends in large measure on how direct the connection is to the system's dynamics. In this paper we show that, within what we call the potential…
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…