Related papers: Computationally Efficient Characterization of Pote…
Simulating charge and energy transfer in extended molecular networks requires an effective model to include the environment because it significantly affects the quantum dynamics. A prototypical effect known as Environment-Assisted Quantum…
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…
Today's quantum computers are comprised of tens of qubits interacting with each other and the environment in increasingly complex networks. In order to achieve the best possible performance when operating such systems, it is necessary to…
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
Efficient planning and sequence selection are central to intelligence, yet current approaches remain largely incompatible with biological computation. Classical graph algorithms like Dijkstra's or A* require global state and biologically…
The characterization of network and biophysical properties from neural spiking activity is an important goal in neuroscience. A framework that provides unbiased inference on causal synaptic interaction and single neural properties has been…
We introduce a thermodynamically consistent, minimal stochastic model for complementary logic gates built with field-effect transistors. We characterize the performance of such gates with tools from information theory and study the…
Surface hopping algorithms are popular tools to study dynamics of the quantum-classical mixed systems. In this paper, we propose a surface hopping algorithm in diabatic representations, based on time dependent perturbation theory and…
We consider partially observable Markov decision processes (POMDPs) with a set of target states and positive integer costs associated with every transition. The traditional optimization objective (stochastic shortest path) asks to minimize…
Triply periodic minimal surfaces (TPMS) are a class of metamaterials with a variety of applications and well-known primitive morphologies. We present a new method for discovering novel microscale TPMS structures with exceptional…
The minimum energy path (MEP) describes the mechanism of reaction, and the energy barrier along the path can be used to calculate the reaction rate in thermal systems. The nudged elastic band (NEB) method is one of the most commonly used…
We propose a discrete transition-based reweighting analysis method (dTRAM) for analyzing configuration-space-discretized simulation trajectories produced at different thermodynamic states (temperatures, Hamiltonians, etc.) dTRAM provides…
We review two recently developed efficient methods for calculating rate constants of processes dominated by rare events in high-dimensional complex systems. The first is transition interface sampling (TIS), based on the measurement of…
Across many fields, a problem of interest is to predict the transition rates between nodes of a network, given limited stationary state and dynamical information. We give a solution using the principle of Maximum Caliber. We find the…
We introduce a method for global optimization of the structure of atomic systems that uses additional atoms with fractional existence. The method allows for movement of atoms over long distances bypassing energy barriers encountered in the…
Variational quantum eigensolver ans\"atze hold considerable promise for ground-state energy calculations on near-term quantum hardware, yet most promising ansatz designs currently strongly depend on how well the molecular orbital basis…
Energy-efficient machine learning models that can run directly on edge devices are of great interest in IoT applications, as they can reduce network pressure and response latency, and improve privacy. An effective way to obtain…
We analyze the efficiency of different methods for the calculation of reaction rates in the case of two simple analytical benchmark systems. Two classes of methods are considered: the first are based on the free energy calculation along a…
The minimum energy path (MEP) is the most probable transition path that connects two equilibrium states of a potential energy landscape. It has been widely used to study transition mechanisms as well as transition rates in the fields of…
Given a multidimensional free-energy or potential-energy landscape, finding reaction paths that connect an initial (or reactant) state and a final (or product) state is important for biophysics and materials science. The likelihood of a…