Classical Mechanics Examples

<i>Note: This application is currently designed to run on Windows and requires the 2016 LabVIEW runtime engine.  It is available free to download in the references. </i><div><i><br></i><div><b>Brachistochrone</b>- An example of how a cycloid is the solution to the shortest path between two points in a particular potential.</div><div><b>2-D Membrane Modes-</b> The first few normal modes of a 2-D membrane.</div><div><b>Coupled Harmonic Oscillators-</b> Select up to 10 masses (and 11 springs) and examine their normal modes of oscillation ordered in ascending frequency with various spring constants.  </div></div

Machine Learning Operations (MLOps) Cookiecutter Template

* - Authors contributed equally to this work This software is a cookie cutter template to expedite and streamline your next collaborative mahince learning (ML) and Artificial Intelligence (AI) project. This suite of tools integrates many principles of best-practice for developing ML and models to support development, production, debugging, package management, data traceability and more. Additional details are available at the corresponding GitHub for more information.  https://github.com/UABPeriopAI/MLOpsTemplate</p

Catdcd Interface

<p>CatDCD is a versatile tool that can be cumbersome to use for non-experienced users as it is available primarily through a command line interface. The purpose of this program is to provide an easy to use interface for CatDCD and make it much simpler to perform batch tasks to process lots of data. For questions, comments, or the source code, send an email to the developer.</p> <p>Running the Application:<br>The first time running the application, it is imperative to run the configuration editor to make sure that the folder paths are correct.<br>Configuration<br>To edit/check the configuration parameters click on the runtime menu Tools>Configuration or use the shortcut key (Command-E)<br>There are three configurable parameters:<br>CatdcdExecutableFolderLocation<br>The location of catdcd. This can either be the version distributed with VMD (show package contents - Contents/vmd/plugins/MACOSXX86/bin/catdcd5.1)<br>VMDStartupApplicationLocation<br>The location of the VMD startup.command file on Mac. The default location on a Mac is, for example /Applications/VMD\ 1.9.2.app/Contents/MacOS/startup.command<br>TCLScriptFolderLocation<br>This is really just the location of the getAtomSeelctionIndices.tcl script used to index the atom selection in that operational mode.<br>Normal Usage<br>The file path controls are all compatible with drag and drop functionality so the user can drag pdb, dcd, or other files directly into the GUI controls and it will update the file path automatically.<br>Select PDB file<br>Select DCD file(s)<br>Decide operational mode:<br>1to 1 will map an output dcd file to every input to is useful execute multiple runs at once.<br>Many to 1 will concatenate the dcd files into a single output trajectory. Useful for combining different simulations together.<br>Set frame parameters<br>Determine whether or not to index. If so, input desired VMD compatible atom selection (as seen from the command line. For example, one must escape certain characters e.g. "type C1\' "<br>Select output file(s) (Note: an additional folder with the report name will be created to contain the analysis output)<br>If desired, request a log file (it will have the same file name as the first output file with a different file extension.<br>Execute<br>Rinse & Repeat<br>Quit when complete</p> <p> </p> <p> </p> <p> </p

Villin Headpiece Simulations

3 separate simulations each of 6µs concatenated together are contained herein.  Each trajectory was run with ACEMD using a CHARMM 27 force field.  The proteins (2RJY) were first solvated to 0.15 mol/L of NaCL and set in a water box modeled as a TIP3P water model.  Proteins were then equilibrated (conjugate gradient minimization) and then heated from the crystal structure to unfold.  Folding simulations were run after a subsequent equilibration. While the simulations do not find the native folded state,  they sample many partially folded intermediates and offer insight into the folding pathway of villin headpiece.  Simulations included here have had the water and ions removed for space considerations and they have been aligned to remove translation and rotation resulting from diffusion

Melvin and Godwin Wake Forest University Physics Seminar 01/13/16

Ryan Melvin and Ryan Godwin's WFU Physics Department Seminar showing their research in the Salsbury Grou

Sufficient Sampling Correlation Code and Examples

Accompanying a pending PRE submission. Here we present a novel time-dependent correlation method that provides insight into how long a system takes to grow into its equal-time (Pearson) correlation. We also show a novel usage of an extant time-lagged correlation method that indicates the time for parts of a system to become decorrelated, relative to equal-time correlation. Given a completed simulation (or set of simulations), these tools estimate (1) how long of a simulation of the same system would be sufficient to observe the same correlated motions, (2) if patterns of observed correlated motions indicate events beyond the timescale of the simulation, and (3) how long of a simulation is needed to observe these longer timescale events. We view this method as a decision-support tool that will aid researchers in determining necessary sampling times. In principle, this tool is extendable to any multi-dimensional time series data with a notion of correlated fluctuations; however, here we limit our discussion to data from Molecular Dynamics simulations

Markov Cluster Analysis in Matlab

<p>Cluster Analysis is a set of codependent matlab functions that take cluster data as an input and outputs several plots using Markov analysis.</p> <p>CLUSTERANALYSIS will return multiple plots based on a set of clustering data. It calls the functions listed below and returns the plots described. It also returns a Markov time series and rate matrix. Cutoff is the cutoff for determining a transition from an initial pure state to another state. To simply pick the most likely state at each decision point, use 0. Steps is the maximum number of steps used by Pathways to plot transitions and TimeToEquilibrium to plot the difference in rate matrix-predicted populations from the actual cluster populations.</p> <p>Its underlying functions are</p> <p>CLUSTERPOPULATIONS calculates populations (as a whole number count) and equilibrium probability distribution.</p> <p>CLUSTERTIMESERIES takes each row and turn them into a set of vertically concatonated columns. Assign each frame a cluster number.</p> <p>MARKOVRATEMATRIX calculate a row-normalized rate matrix given a set of cluster numbers and corresponding frames in the form [frames cluster#]</p> <p>PATHWAYS Returns the pathway of a pure state over "maxTimeSteps" of a simulation using a Markov "rateMatrix." A transition out of a pure state is defined by minimum "cutoff" of how likely the system is to have left a pure state. Cutoff is the likelihood a state has transitioned OUT OF a pure state. If the cutoff is met but the original state is remains the most likely, a transition will NOT be recorded.</p> <p>TIMETOEQUILIBRIUM plots the difference between the populations predicted by the Markov rate matrix and the equilibrium probability distribution calculated from the original trajectory as a function of steps.</p

Code for Correlation Clustering with HDBSCAN

The code for the paper "Visualizing correlated motion with HDBSCAN clustering"<div><br></div><div>Users will need python 3 and the packages</div><div>mdtraj</div><div>numpy</div><div>hdbscan</div><div>pandas</div><div>signal</div><div>os</div><div>subprocess</div><div>argparse</div><div><br></div><div>Users will also need VMD installed and set as 'vmd' in their shell environment. For example, </div><div><div>alias vmd="/Applications/VMD\ 1.9.2.app/Contents/MacOs/startup.command"</div></div><div><br></div><div>in ~/.bashrc</div