Related papers: Computationally Efficient Characterization of Pote…

Smartphones, laptops, and data centers are CMOS-based technologies that ushered our world into the information age of the 21st century. Despite their advantages for scalable computing, their implementations come with surprisingly large…

There is a rich recent literature on how to assist secure communication between a single transmitter and receiver at the physical layer of wireless networks through techniques such as cooperative jamming. In this paper, we consider how…

The number of observable degrees of freedom is typically limited in experiments. Here, we consider discrete Markov networks in which an observer has access to a few visible transitions and the waiting times between these transitions.…

Using random walk sampling methods for feature learning on networks, we develop a method for generating low-dimensional node embeddings for directed graphs and identifying transition states of stochastic chemical reacting systems. We…

Optimizing paths on networks is crucial for many applications, from subway traffic to Internet communication. As global path optimization that takes account of all path-choices simultaneously is computationally hard, most existing routing…

We propose network coding as an energy efficient data transmission technique in core networks with non-bypass and bypass routing approaches. The improvement in energy efficiency is achieved through reduction in the traffic flows passing…

The transport properties of discrete-time random walks on ring networks with deterministic shortcuts are investigated through analytical and numerical methods. The network consists of a periodic chain where each node is connected to its…

Efficient and reliable identification and optimization of transition state structures is a longstanding challenge in computational chemistry. Popular chain-of-states methods require hundreds if not thousands of ab initio calculations to…

We show that molecular dynamics based moves in the Minima Hopping (MH) method are more efficient than saddle point crossing moves which select the lowest possible saddle point. For binary systems we incorporate identity exchange moves in a…

The low-temperature driven or thermally activated motion of several condensed matter systems is often modeled by the dynamics of interfaces (co-dimension-1 elastic manifolds) subject to a random potential. Two characteristic quantitative…

The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…

Assessing the time scale of biological processes using molecular dynamics (MD) simulations with sufficient statistical accuracy is a challenging task, as processes are often rare and/or slow events, which may extend largely beyond the time…

Stable states in complex systems correspond to local minima on the associated potential energy surface. Transitions between these local minima govern the dynamics of such systems. Precisely determining the transition pathways in complex and…

The true power of computational research typically can lay in either what it accomplishes or what it enables others to accomplish. In this work, both avenues are simultaneously embraced across several distinct efforts existing at three…

The minimum action method (MAM) is to calculate the most probable transition path in randomly perturbed stochastic dynamics, based on the idea of action minimization in the path space. The accuracy of the numerical path between different…

We present an information geometric characterization of quantum driving schemes specified by su(2;C) time-dependent Hamiltonians in terms of both complexity and efficiency concepts. By employing a minimum action principle, the optimum path…

Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…

The energy cost of computation has emerged as a central challenge at the intersection of physics and computer science. Recent advances in statistical physics -- particularly in stochastic thermodynamics -- enable precise characterizations…

The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…

Transition state or minimum energy path finding methods constitute a routine component of the computational chemistry toolkit. Standard analysis involves trajectories conventionally plotted in terms of the relative energy to the initial…