Related papers: Exploring the Free Energy Landscape: From Dynamics…
In single molecule laser optical tweezer (LOT) pulling experiments a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates folding trajectories under force in terms of time-dependent…
The topography of the free energy landscape in phase space of a dense hard sphere system characterized by a discretized free energy functional of the Ramakrishnan-Yussouff form is investigated numerically using a ``microcanonical'' Monte…
Persistent homology captures the evolution of topological features of a model as a parameter changes. The most commonly used summary statistics of persistent homology are the barcode and the persistence diagram. Another summary statistic,…
Proteins evolve through complex sequence spaces, with fitness landscapes serving as a conceptual framework that links sequence to function. Fitness landscapes can be smooth, where multiple similarly accessible evolutionary paths are…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
We explore whether the topology of energy landscapes in chemical systems obeys any rules and what these rules are. To answer this and related questions we use several tools: (i)Reduced energy surface and its density of states, (ii)…
One of the key limitations of Molecular Dynamics simulations is the computational intractability of sampling protein conformational landscapes associated with either large system size or long timescales. To overcome this bottleneck, we…
The energy landscape picture is a central tool to study many-body systems. In particular, the energy landscapes of glass-forming liquids, jammed packings, constraint satisfaction problems, or neural networks contain a plethora of minima…
A complete understanding of the precipitous onset of slow dynamics in systems such as supercooled liquids requires making direct connections between dynamics and the underlying potential energy landscape. With the aid of a switch 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…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
We investigate the phenomenon of protein induced tubulation of lipid bilayer membranes within a continuum framework using Monte Carlo simulations coupled with the Widom insertion technique to compute excess chemical potentials. Tubular…
We review recent results on the topological properties of two spatial scale-free networks, the inherent structure and Apollonian networks. The similarities between these two types of network suggest an explanation for the scale-free…
In this paper we explore challenges in developing a topological framework in which machine learning can be used to robustly characterize global dynamics. Specifically, we focus on learning a useful discretization of the phase space of a…
We apply energy landscape methods to digital alchemy, defining a system in which the parameters of the potential are treated as degrees of freedom. Using geometrical optimisation, we locate minima and transition states on the landscape for…
Temporal gene expression data (Wen, et. al.) was analyzed using the recently introduced inverse modeling technique of Embedded Complex Logistic Maps (ECLM). Preliminary results indicate scale-free structure in the gene regulatory network…
Quantifying the adaptive landscape in a given dynamical processes has been one of most important goals in theoretical biology. It can have immediate implications for many dynamical properties, such as robustness and plasticity. Based on…
With the help of a simple 20 letters, lattice model of heteropolymers, we investigate the energy landscape in the space of designed good-folder sequences. Low-energy sequences form clusters, interconnected via neutral networks, in the space…
We present phase diagrams, free-energy landscapes, and order-parameter distributions for a model spin-crossover material with a two-step transition between the high-spin and low-spin states (a square-lattice Ising model with…
We study the free energy and dynamics of a closed elastic filament (a one-dimensional curve in two dimensions) whose local internal state is specified by curvature, stretch, and a scalar density field representing, for example, the…