Related papers: Exploring the Free Energy Landscape: From Dynamics…
The equilibrium state of a superfluid in a rotating cylindrical vessel is a vortex crystal -- an array of vortex lines which is stationary in the rotating frame. Experimental realisations of this behaviour typically show a sequence of…
One of the most common problem-solving heuristics is by analogy. For a given problem, a solver can be viewed as a strategic walk on its fitness landscape. Thus if a solver works for one problem instance, we expect it will also be effective…
How do we search for the entire family tree without unwanted random guesses, starting from a high-index and high-energy stationary state on the energy landscape? Here we introduce a general numerical method that constructs the pathway map…
Soft porous crystals are flexible metal-organic frameworks that respond to physical stimuli such as temperature, pressure, and gas adsorption by large changes in their structure and unit cell volume. While they have attracted a lot of…
The lifetime of protein domains and ligand-receptor complexes under force is crucial for mechanosensitive functions, while many aspects of how force affects the lifetime still remain poorly understood. Here, we report a new analytical…
Understanding the impact of extractant functionalization in solvent extraction is essential to guide the development of better separations processes. Traditionally, computational extractant design uses electronic structure calculations to…
Switch-like responses arising from bistability have been linked to cell signaling processes and memory. Revealing the shape and properties of the set of parameters that lead to bistability is necessary to understand the underlying…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
The evolution of chemical reaction networks is often analyzed through kinetic models and energy landscapes, but these approaches fail to capture the deeper structural constraints governing complexity growth. In chemical reaction networks,…
Energy landscape approaches have become increasingly popular for analysing a wide variety of chemical physics phenomena. Basic to many of these applications has been the inherent structure mapping, which divides up the potential energy…
It has recently been demonstrated that many biological networks exhibit a scale-free topology where the probability of observing a node with a certain number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has been…
An oft-used concept in modeling macromolecules is the free energy landscape, obtained by coarse-graining a vast number of microstates into a low-dimensional mesh of mesostates. If the landscape contains two or more local minima…
The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and…
Qualitative attributes of the region between order and disorder are examined to explore models of genetic and protein networks. Results show how the connectivity of vertices and the strength of their connections are related and how their…
An efficient algorithm is developed to construct disconnectivity graphs by a random walk over basins of attraction. This algorithm can detect a large number of local minima, find energy barriers between them, and estimate local thermal…
The training of neural networks is a complex, high-dimensional, non-convex and noisy optimization problem whose theoretical understanding is interesting both from an applicative perspective and for fundamental reasons. A core challenge is…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
Modeling environmental ecosystems is critical for the sustainability of our planet, but is extremely challenging due to the complex underlying processes driven by interactions amongst a large number of physical variables. As many variables…
The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes enhanced sampling methods are used. While many such methods…
Network theory provides various tools for investigating the structural or functional topology of many complex systems found in nature, technology and society. Nevertheless, it has recently been realised that a considerable number of systems…