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Biased diffusive transport of Brownian particles through irregularly shaped, narrow confining quasi-one-dimensional structures is investigated. The complexity of the higher dimensional diffusive dynamics is reduced by means of the so-called…
Non-equilibrium Greens function techniques (NEGF) combined with Density Functional Theory (DFT) calculations have become a standard tool for the description of electron transport through single molecule nano-junctions in the coherent…
We implement, optimize, and validate the linear-scaling Kubo-Greenwood quantum transport simulation on graphics processing units by examining resonant scattering in graphene. We consider two practical representations of the Kubo-Greenwood…
A self-consistent method for calculating electron transport through a molecular device is proposed. It is based on density functional theory electronic structure calculations under periodic boundary conditions and implemented in the…
Three one-body profiles that correspond to local fluctuations in energy, in entropy, and in particle number are used to describe the equilibrium properties of inhomogeneous classical many-body systems. Local fluctuations are obtained from…
We present an efficient implemention of a non-equilibrium Green function (NEGF) method for self-consistent calculations of electron transport and forces in nanostructured materials. The electronic structure is described at the level of…
Molecular dynamics simulations and instantaneous normal mode (INM) analysis of a fluid with core-softened pair interactions and water-like liquid-state anomalies are performed to obtain an understanding of the relationship between…
Coherent electronic transport through a molecular device is studied using non-equilibrium Green's function (NEGF) formalism. Such device is made of a short linear wire which is connected to para- and ferromagnetic electrodes. Molecule…
By viewing the non-equilibrium transport setup as a quantum open system, we propose a reduced-density-matrix based quantum transport formalism. At the level of self-consistent Born approximation, it can precisely account for the correlation…
In order to describe the dynamics of crowded ions (charged particles), we use an energetic variation approach to derive a modified Poisson-Nernst-Planck (PNP) system which includes an extra dissipation due to the effective velocity…
Understanding neural dynamics is a central topic in machine learning, non-linear physics and neuroscience. However, the dynamics is non-linear, stochastic and particularly non-gradient, i.e., the driving force can not be written as gradient…
We present a microscopic derivation of the laws of continuum mechanics of nonideal ordered solids including dissipation, defect diffusion, and heat transport. Starting point is the classical many-body Hamiltonian. The approach relies on the…
Simulations of quantum transport in coherent conductors have evolved into mature techniques that are used in fields of physics ranging from electrical engineering to quantum nanoelectronics and material science. The most efficient…
While the vast majority of calculations reported on molecular conductance have been based on the static non-equilibrium Green's function formalism combined with density functional theory, in recent years a few time-depedent approaches to…
We investigate the hydrodynamic properties of a fluid simulated with a mesoscopic solvent model. Two distinct regimes are identified, the `particle regime' in which the dynamics is gas-like, and the `collective regime' where the dynamics is…
Using molecular dynamics simulations we study the slow dynamics of a colloidal fluid annealed within a matrix of obstacles quenched from an equilibrated colloidal fluid. We choose all particles to be of the same size and to interact as hard…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
The dynamics of a closed quantum system is often studied with the direct evolution of the Schrodinger equation. In this paper, we propose that the gauge choice (i.e. degrees of freedom irrelevant to physical observables) of the Schrodinger…
Viscosity calculation from equilibrium molecular dynamics (MD) simulations relies on the traditional Green-Kubo (GK) framework, which integrates the stress autocorrelation function (SACF) over time. While the formalism is exact in the…
We present a path integral formalism for expressing matrix elements of the density matrix of a quantum many-body system between any two coherent states in terms of standard Matsubara action with periodic(anti-periodic) boundary conditions…