The visualization of multidimensional energy landscapes is important, providing insight into the kinetics and thermodynamics of a system, as well the range of structures a system can adopt. It is, however, highly nontrivial, with the number of dimensions required for a faithful reproduction of the landscape far higher than can be represented in two or three dimensions. Metric disconnectivity gr...

The role of symmetry in the folding of proteins is discussed using energy landscape theory. An analytical argument shows it is much easier to find sequences with funneled energy landscape capable of fast folding if the structure is symmetric. The analogy with phase transitions of small clusters with magic numbers is discussed.

A popular approach to the computational modeling of ligand/receptor interactions is to use an empirical free energy like model with adjustable parameters. Parameters are learned from one set of complexes, then used to predict another set. To improve these empirical methods requires an independent way to study their inherent errors. We introduce a toy model of ligand/receptor binding as a workbe...

The idea in molecular docking is to design pharmaceuticals computationally by identifying potential drug candidates targeted against proteins. The candidates can be found using a docking algorithm that tries to identify the bound conformation of a small molecule ligand to a macromolecular target at its active site, which is the region of an enzyme where natural substrate binds. Mathematically, ...

By means of two supramolecular systems--peptide amphiphiles engaged in hydrogen-bonded β-sheets, and chromophore amphiphiles driven to assemble by π-orbital overlaps--we show that the minima in the energy landscapes of supramolecular systems are defined by electrostatic repulsion and the ability of the dominant attractive forces to trap molecules in thermodynamically unfavourable configurations...

Sai Teja Pusuluri, Alex H. Lang, 3 Pankaj Mehta, 3 and Horacio E. Castillo 4 Department of Physics and Astronomy and Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH, 45701, USA Physics Department, Boston University, Boston, Massachusetts 02215, USA Center for Regenerative Medicine, Boston University, Boston, MA, 02215 Corresponding author: [email protected] (Dated: Novemb...

Introduction T he amount of data in our world has been increasing at a rapid rate in a wide variety of applied disciplines such as in fi nance (the advent of high-frequency algorithmic trading) and genetics (recent experimental advances have led to vast amounts of new data-sets). As a result, analyzing large data sets is becoming a key basis of competition, supporting new waves of productivity ...

Translating the complex, multi-dimensional data from simulations of biomolecules to intuitive knowledge is a major challenge in computational chemistry and biology. The so-called “free energy landscape” is amongst the most fundamental concepts used by scientists to understand both static and dynamic properties of biomolecular systems. In this paper we use Markov models to design a strategy for ...

We describe how several metrics are possible in thermodynamic state space but that only one, Weinhold’s, has achieved widespread use. Lengths calculated based on this metric have been used to bound dissipation in finite-time (irreversible) processes be they continuous or discrete, and described in the energy picture or the entropy picture. Examples are provided from thermodynamics of heat conve...