Sarkas: A fast pure-python molecular dynamics suite for plasma physics

Ii. Plasma Dynamics A. Plasma Physics

subject to the boundary conditions: U = Umax , at z = 0; and U 1, dU/dzo 0 as z -) oo. Here U = U/U ; U is the mean energy, 3/2 kT, of an electron; and Ue is the equilibrium energy to which the electron decays at an infinite distance z from the region of excitation. The dimensionless parameter z 0 is equal to pz, where p is the reciprocal of the free diffusion length in the radial direction of ...

MD-TASK: a software suite for analyzing molecular dynamics trajectories

Summary Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations. Here, we present MD-TASK, ...

Fast molecular tracking maps nanoscale dynamics of plasma membrane lipids.

We describe an optical method capable of tracking a single fluorescent molecule with a flexible choice of high spatial accuracy (approximately 10-20 nm standard deviation or approximately 20-40 nm full-width-at-half-maximum) and temporal resolution (< 1 ms). The fluorescence signal during individual passages of fluorescent molecules through a spot of excitation light allows the sequential local...

Molecular dynamics simulations for plasma-surface interactions

“Fundamental” Physics: Molecular Dynamics vs. Hydrodynamics

Condensed matter physics concerns the “study of matter at everyday length and energy scales.” [12] The physics of such systems is by and large decoupled from the more “fundamental” physics at small lengths and higher energies. The nature of this decoupling is of great interest and brings with it the possibility of understanding aspects of how certain phenomena can be emergent. I believe there a...