相关论文: A graph theoretical analysis of the energy landsca…

The thermodynamic behavior of collapse transition in a fully flexible coarse-grained model of energy polydisperse polymer (EPP), a statistical model of random heteropolymer, is investigated in an implicit solvent by means of molecular…

We introduce an algorithm for the reduction of computer generated atomistic polymer samples to networks of primitive paths. By examining network ensembles of Polyethylene and cis-1,4 Polybutadiene melts, we quantify the underlying…

The interplay between different types of disorder and electron-electron interactions in graphene planes is studied by means of Renormalization Group techniques. The low temperature properties of the system are determined by fixed points…

In the theory of renormalization for classical dynamical systems, e.g. unimodal maps and critical circle maps, topological conjugacy classes are stable manifolds of renormalization. Physically more realistic systems on the other hand may…

To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been…

Many physical properties of small organic molecules are dependent on the current crystal packing, or polymorph, of the material, including bioavailability of pharmaceuticals, optical properties of dyes, and charge transport properties of…

In the study of dynamical systems on networks/graphs, a key theme is how the network topology influences stability for steady states or synchronized states. Ideally, one would like to derive conditions for stability or instability that…

We develop methods to efficiently reconstruct the topology and line parameters of a power grid from the measurement of nodal variables. We propose two compressed sensing algorithms that minimize the amount of necessary measurement resources…

Networks are ubiquitous throughout science and engineering. A number of methods, including some from our own group, have explored how one goes about computing or predicting the dynamics of networks given information about internal models of…

In order to efficiently explore the chemical space of all possible small molecules, a common approach is to compress the dimension of the system to facilitate downstream machine learning tasks. Towards this end, we present a data driven…

One of the hallmarks of real networks is their ability to perform increasingly complex tasks as their topology evolves. To explain this, it has been observed that as a network grows certain subsets of the network begin to specialize the…

We examine the Stillinger-Weber analysis of the potential energy landscape for its stability and conclude that it does not provide a stable description of the system as the free energy slope and curvature vanish simultaneously. An…

The potential energy landscape (PEL) of supercooled binary Lennard-Jones (BLJ) mixtures exhibits local minima, or inherent structures (IS), which are organized into meta-basins (MB). We study the particle rearrangements related to…

Dynamical networks are powerful tools for modeling a broad range of complex systems, including financial markets, brains, and ecosystems. They encode how the basic elements (nodes) of these systems interact altogether (via links) and evolve…

Semiflexible polymers in poor solvents exhibit a rich variety of collapsed morphologies, including globules, toroids, and rodlike bundles, arising from the competition between attractive interactions and chain stiffness. Computer…

A central issue in the study of polymer physics is to understand the relation between the geometrical properties of macromolecules and various dynamics, most of which are encoded in the Laplacian spectra of a related graph describing the…

We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…

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…

Dynamical connectivity graphs, which describe dynamical transition rates between local energy minima of a system, can be displayed against the background of a disconnectivity graph which represents the energy landscape of the system. The…

Hard-sphere models exhibit many of the same kinds of supercooled-liquid behavior as more realistic models of liquids, but the highly non-analytic character of their potentials makes it a challenge to think of that behavior in…