3
votes
1answer
52 views

Why is the objective function used in Nudged Elastic Band method reasonable?

In Nudged Elastic Band (NEB) method, which is used to find reaction pathways when both initial and final states are know, an objective function is first constructed and then minimized to find reaction ...
1
vote
1answer
116 views

Smoothed Particle Hydrodynamics, Chemical Reactions and Stiffness [closed]

Dear people from stackexchange physics. I have been using SPH for quite a while to simulate free boundary flow, and just recently we tried to include some kind of (simple) chemical reaction in our ...
1
vote
2answers
259 views

Where does Computer Science background students fit in Theoretical Physics [closed]

I am basically an Electronics student - background in computer science (that's where I want to work). I applied for an internship in USA in a research institute where the group is focused in ...
1
vote
2answers
951 views

How do I integrate the Poisson equation to determine the electric potential along a particular direction (e.g., $z$)?

This question is a sequel of sorts to my earlier (resolved) question about a recent paper. In the paper, the authors performed molecular dynamics (MD) simulations of parallel-plate supercapacitors, ...
5
votes
2answers
321 views

In condensed matter simulations, how is particle number density computed in practice?

I have been reading a recent paper. In it, the authors performed molecular dynamics (MD) simulations of parallel-plate supercapacitors, in which liquid resides between the parallel-plate electrodes. ...
5
votes
4answers
2k views

Why is the canonical ($NVT$) ensemble often used for (classical) molecular dynamics (MD) simulations?

Molecular dynamics (MD) simulation is a common approach to the (classical) many-body problem. It relies on integration of Newton's equations of motion to simulate the trajectories of many (e.g., ...
5
votes
1answer
231 views

What equation describes the electrostatic potential in these circumstances?

I have a solver for Poisson's equation and it works nicely. It uses finite differences. It works in the presence of multiple dielectrics. It also solves the Poisson Boltzmann equation. That is, fixed ...
4
votes
3answers
627 views

Nanorobots. What stops us from producing them yet?

If we can already predicts accuratelly motion on molecular levels, what stops us from developing small robots to, for instance, navigate through our blood vessels looking for cancerous cells and ...