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Dynamic networks reflect temporal changes occurring to the graph's structure and are used to model a wide variety of problems in many application fields. We investigate the design space of dynamic graph visualization along two major…
Molecular dynamics simulations produce data with complex nonlinear dynamics. If the timestep behavior of such a dynamic system can be represented by a linear operator, future states can be inferred directly without expensive simulations.…
Online social networks have emerged as useful tools to communicate or share information and news on a daily basis. One of the most popular networks is Twitter, where users connect to each other via directed follower relationships.…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
Our ability to uncover complex network structure and dynamics from data is fundamental to understanding and controlling collective dynamics in complex systems. Despite recent progress in this area, reconstructing networks with stochastic…
We apply a temporal edge prediction model for weighted dynamic graphs to predict time-dependent changes in molecular structure. Each molecule is represented as a complete graph in which each atom is a vertex and all vertex pairs are…
We study the finite-temperature dynamics of thin elastic sheets in a single-clamped cantilever configuration. This system is known to exhibit a tilt transition at which the preferred mean plane of the sheet shifts from horizontal to a plane…
Understanding the dynamic processes of the glassy system continues to be challenging. Recent advances have shown the power of graph neural networks (GNNs) for determining the correlation between structure and dynamics in the glassy system.…
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 develop a novel parallel decomposition strategy for unweighted, undirected graphs, based on growing disjoint connected clusters from batches of centers progressively selected from yet uncovered nodes. With respect to similar previous…
This paper addresses the problem of identifying the topology of an unknown, weighted, directed network running a consensus dynamics. We propose a methodology to reconstruct the network topology from the dynamic response when the system is…
We propose generalizations of a number of standard network models, including the classic random graph, the configuration model, and the stochastic block model, to the case of time-varying networks. We assume that the presence and absence of…
We propose an analytic approach for the steady-state dynamics of Markov processes on locally tree-like graphs. It is based on time-translation invariant probability distributions for edge trajectories, which we encode in terms of infinite…
Motivated by applications of distributed linear estimation, distributed control and distributed optimization, we consider the question of designing linear iterative algorithms for computing the average of numbers in a network. Specifically,…
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless developments of computer architectures and algorithms. This explosion in the number and extent (in size and time) of MD…
In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…
Understanding the behavior of complex molecular systems is a fundamental problem in physical chemistry. To describe the long-time dynamics of such systems, which is responsible for their most informative characteristics, we can identify a…
Effective information analysis generally boils down to properly identifying the structure or geometry of the data, which is often represented by a graph. In some applications, this structure may be partly determined by design constraints or…