Owners (the only one with the permission to edit the main text) Antoine, Frank, Laura Preliminary work Update 10/04/24 Goal: Find the functional form of $\beta \mu(R)$ for a range of densities. Canonical simulations:

Author: Frank The units in our simulations In any simulation we run, our code normally just working with numbers: it does not keep track of units. Unlike in experiments, where a distance is clearly measured in e.g. meters, nanometers, or kilometers, in a simulation the distance between two particles is simply stored as a number, like 1.2. When writing about your simulation results, it is then important to keep in mind what these numbers actually mean. Even in simulations, distances are measured in units of something, and you have made some sort of choice of what that unit is when implementing the simulation. Let us say, for example, that we have a simple Monte Carlo code of a system of interacting particles. As an example, we can use the Lennard-Jones potential, where the pairwise potential is given by $$u(r_{ij}) = \epsilon \left(\left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^{6} \right).$$ Here, $\sigma$ is a particle size (it is a length!) and $\epsilon$ indicates the strength of the interaction (and has dimensions of energy).

Owners (the only one with the permission to edit the main text) Frank, Antoine Background We are interested in testing the Event-driven molecular dynamics (EDMD) simulation method introduced in: E. A. Peters, Rejection-free Monte Carlo sampling for general potentials., Physical Review E 85, 026703 (2012). As a testing ground, we use the WCA (Weeks-Chandler-Andersen) model at low temperature. Questions we have:

To do Fix WoL Add a queuing system for GPU and CPU use Hardware 2 Intel Xeon Gold 6234 8 cores/16 threads 3.3 GHz (4 GHz turbo) 24.75MB of cache 4 32GB DDR4 2933 Intel S4510 240GB, SATA 6Gb/s, 3D, TLC 2.5", 7.0mm, up to 2DWPD Toshiba 3.5" 8TB SATA 6Gb/s 7.2K RPM 128M 512e 4 PNYGeForce RTX 2080Ti 11Go GDDR6 1,35GHz 4352 cores

Infinite pressure phase diagram for spheres on a plane This is the phase diagram at infinite pressure for NAHD with $\Delta = \Delta_{plan}$ such that equivalent 3D spheres lie on a plane. This phase diagram does not include S4, which I could not tame (nasty NaNs). Reminder for phases Non-additivity parameter (could choose to change sign): [Frank]: Since you see the S4 phase in our JCP only for size ratios $q < 0.2$ and nonadditivity $\Delta > -0.05$, I think it is reasonable to conclude it is not a concern for this diagram?

Owners (the only one with the permission to edit the main text) Antoine, Frank 22-12-22 US code available on Github Looked at US window {$n_0 = 10$, $k = 0.15$}, HS, $\beta P \sigma^3 = {15, 16, 17}$, $\textrm{MCCycle} = 4e6$ initial configuration: $N = 10000$, $\eta = 0.49$ N = 10000, $\beta P \sigma^3 = 15$

# Raphael

tags: SoftQC self-assembly Owners (the only one with the permission to edit the main text) Frank, Giuseppe, Etienne Background We computed phase diagrams at infinite pressure for binary NAHD mixtures, and found regions where dodecagonal random tiling quasicrystals are expected to form. Using the cell approximation, and thermodynamic integration of the SHY equation of state for mixtures of NAHD, we computed finite pressure phase diagrams for those systems.

Characterizing rod packings Local nematic order parameter. See for example the definition in the SI of this paper: https://doi.org/10.1039/C6SM02162J Note that the surface-to-surface distance is already calculated in your overlap function. Distribution of orientations plotted on the surface of a sphere. For example, in this paper: https://pubs.acs.org/doi/pdf/10.1021/nn507490j?casa_token=q6RoAOG6tD4AAAAA:r0aO3JU3SEbh8LiJ2U33-u2pHgNM6sM7qhyEm-d5T66l5aUnrqV_cu_kbTi3p4AA4NOs3JkgVod9gx4 they plot orientations of bonds between neighbors in this way (e.g. Fig. 3). In your case, instead of bonds orientations you would plot particle orientations, but the principle is the same. Histogram of angles within the xy plane (0 to 180 degrees, e.g. with the x-axis).

tags: SoftQC self-assembly Owners (the only one with the permission to edit the main text) Frank, Giuseppe, Etienne Background We have computed the infinite pressure phase diagram of binary (non-)additive hard disk mixtures in the size-ratio--composition plane. This revealed several random-tiling quasicrystal regions. https://arxiv.org/abs/2003.08889

Tasks Choose a defense date. (December ?) Form a jury: make sure that they are all available and that we can cover travel expenses. Contact the doctoral school to make sure they agree with the proposed jury. Publish the manuscript of the thesis. Formally declare the jury on ADUM and send them the manuscript. Book a room for the defense. Jury ?

# Title of the new project ###### tags: --- --- ### Owners (the only one with the permission to edit the main test) Pippo, Pluto, Paperinp --- --- ## Background ## Plans ## To Do :::success green is for finished tasks ::: ### Task 1 :::success * step finised ::: * step in progrress ### Task2 :::success * step finised ::: * step in progrress ### OPEN QUESTIONS * ?

Owners (the only one with the permission to edit the main test) EF, AP, FS, GF Background Plans To Do On the setup Calibration with grains -> Be sure of the real amplitude of vibrations

# Title of the new project ###### tags: --- --- ### Owners (the only one with the permission to edit the main test) Pippo, Pluto, Paperinp --- --- ## Background ## Plans ## To Do :::success green is for finished tasks ::: ### Task 1 :::success * step finised ::: * step in progrress ### Task2 :::success * step finised ::: * step in progrress ### OPEN QUESTIONS * ?

Owners (the only one with the permission to edit the main test) Susana, Frank, Giuseppe Background Based on the paper of Tetrahedrality Dictates Dynamics in HS Mixtures, we would like to test the predictions in an experimental realization. To do so, the group of Marco Laurati from the University of Florence have been working on experimental HS particles. With those, we would like to compute the $n_{tet}$ and see how well correlated is with dynamics. [name=SMA] Specifications from the experiment--> To Do :::success green is for finished tasks

Owners (the only one with the permission to edit the main text) Frank, Giuseppe, Etienne Background Chiara is trying to perform self assembly of nano platelets of square and triangle shape. We want to have some simple simulations to compare with. The first idea is to consider hard squares and triangles in 2D. Then, we could add some edge to edge attraction between the polygons to mimick possible ligand interactions.

Owners (the only one with the permission to edit the main text) Frank, Giuseppe, Etienne This page contains side stories, related to the main one, but not specific to main research focus developped in the other pages. Automatic detection of non-equilibrated simulations [12/08/2021] Our work relies heavily on measuring equilibrium quantities from simulation snapshots. These quantities are usually averages, taken over a sequence of snapshots. Under the assumption that the system is ergodic and at equilibrium, the time averages taken from simulations are the same as ensemble averages.

Owners (the only one with the permission to edit the main test) Marielle, Etienne, Frank, Rudy, Giuseppe Background In this project we are going to build a coarse grained model of a particle system with a LJ interactions plus charge regulation term. We will implement a MC algorithm to solve the problem. The potential energy of the system is given by: $$ U({\mathbf{r}i, q_i}) = U{ LJ}({\mathbf{r}i}) + U{ fe} ({\mathbf{r}i, q_i}) $$ the first term is a standard LJ term: