Related papers: Systematic errors in diffusion coefficients from l…
In molecular dynamics simulations in the NPT ensemble at constant pressure, the size and shape of the periodic simulation box fluctuate with time. For particle images far from the origin, the rescaling of the box by the barostat results in…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
We present an ``equation-free'' multiscale approach to the simulation of unsteady diffusion in a random medium. The diffusivity of the medium is modeled as a random field with short correlation length, and the governing equations are cast…
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto standard, from simple liquids to complex biomacromolecules.…
Considering the example of interacting Brownian particles we present a linear response derivation of the boundary condition for the corresponding hydrodynamic description (the diffusion equation). This requires us to identify a non-analytic…
The diffusion of particles trapped in long narrow channels occurs predominantly in one dimension. Here, molecular dynamics simulation is used to study the inertial dynamics of two-dimensional hard disks, confined to long, narrow,…
Diffusion of small particles is omnipresent in a plentiful number of processes occurring in Nature. As such, it is widely studied and exerted in almost all branches of sciences. It constitutes such a broad and often rather complex subject…
Consider a particle diffusing in a confined volume which is divided into two equal regions. In one region the diffusion coefficient is twice the value of the diffusion coefficient in the other region. Will the particle spend equal…
Brownian dynamics simulations require the connection of a small discrete simulation volume to large baths that are maintained at fixed concentrations and voltages. The continuum baths are connected to the simulation through interfaces,…
We consider the numerical integration of Langevin equations for particles in a channel, in the presence of boundary conditions fixing the concentration values at the ends. This kind of boundary condition appears for instance when…
Many stochastic processes in the physical and biological sciences can be modelled as Brownian dynamics with multiplicative noise. However, numerical integrators for these processes can lose accuracy or even fail to converge when the…
A considerable number of systems have recently been reported in which Brownian yet non-Gaussian dynamics was observed. These are processes characterised by a linear growth in time of the mean squared displacement, yet the probability…
Yeh and Hummer's simplified estimation method has often been adopted to obtain diffusion coefficients for solute molecules using molecular dynamic simulation. However, the simplified formula is not necessarily valid when a small basic cell…
We investigate the Brownian diffusion of particles in one spatial dimension and in the presence of finite regions within which particles can either evaporate or be reset to a given location. For open boundary conditions, we highlight the…
Aerial manipulators undergo rapid, configuration-dependent changes in inertial coupling forces and aerodynamic forces, making accurate dynamics modeling a core challenge for reliable control. Analytical models lose fidelity under these…
We develop two-dimensional Brownian dynamics simulations to examine the motion of disks under thermal fluctuations and Hookean forces. Our simulations are designed to be experimental-like, since the experimental conditions define the…
Quantum simulation in its current state faces experimental overhead in terms of physical space and cooling. We propose boson sampling as an alternative compact synthetic platform performing at room temperature. Identifying the capability of…
We study the diffusivity of a small particle immersed in a square box filled with a non-ideal multicomponent fluid in the presence of thermal fluctuations. Our approach is based on the numerical integration of fluctuating lattice Boltzmann…
We model the dynamics of a closed quantum system brought out of mechanical equilibrium, undergoing a non-driven, spontaneous, thermodynamic transformation. In particular, we consider a quantum particle in a box with a moving and insulating…
Extensive molecular dynamics simulation studies of particles interacting via a short ranged attractive square-well (SW) potential are reported. The calculated loci of constant diffusion coefficient $D$ in the temperature-packing fraction…