text:
## Friday, July 17, 2015

### Planned papers for 2015 - six months in

In January I wrote about the papers I plan to publish and made this list:

Submitted
1. Søs Torpenholt, Leonardo De Maria, Mats H. M. Olsson, Lars H. Christensen, Michael Skjøt, Peter Westh, Jan H. Jensen and Leila Lo Leggio "Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase" Computational and Structural Biotechnology Journal, submitted
2. Lars A. Bratholm, Anders S. Christensen, Thomas Hamelryck, and Jan H. Jensen "Bayesian inference of protein structure from chemical shift data" PeerJ, submitted. Preprint

Probable
3. Automated prediction of the NMR structure of the protein CI-2.
4. Linear scaling HF-3c calculations by interface to FMO2 in GAMESS
5. Thermodynamics of binding. I plan to turn my recent blogposts (with 2 more to come) on this topic into a perspective article.
6. ProCS14. I need to turn this masters thesis into a paper (how will I find the time?).
7. NMR structure of the protein AKMT.
8. Benchmarking of PM6 and DFTB3 for barrier heights computed using enzyme active site models.
9. Predicting binding free energies for CB7
10. Probabilistic treatment of distance restraints in protein structure determination

Six months later this list is now:

Published
1. Søs Torpenholt, Leonardo De Maria, Mats H. M. Olsson, Lars H. Christensen, Michael Skjøt, Peter Westh, Jan H. Jensen and Leila Lo Leggio "Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase" Computational and Structural Biotechnology Journal 2015, 13, 256–264. DOI
2. Lars A. Bratholm, Anders S. Christensen, Thomas Hamelryck, and Jan H. Jensen "Bayesian inference of protein structure from chemical shift data" PeerJ 2015, 3:e861. DOI
5. Jan H. Jensen "Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods" PCCP 2015, 17, 12441-12451. DOI

Actively being worked on
3. Automated prediction of the NMR structure of the protein CI-2.
We found a bug in the CamShift implementation.  This took a while to fix and to re-run a bunch of stuff, including the calculations in Paper 2.  The bug doesn't seem to affect the results much. Lars sent me the first rough draft of the paper this week.  There is still some calculations missing but it's coming together. My goal is a finished manuscript by the end of August.

6. ProCS15
As per usual, when writing up we found a bunch of small things that needed to be fixed/rerun/checked and since the MS student is now a PhD student in another group this, of course, takes time. I think we are at the point where we have all the data we need and know what to say, but enough has changed that it's a matter of writing the paper from scratch.  I'm working on this now. My goal is a finished manuscript by the end of August.

Very likely
8. Benchmarking of PM6 and DFTB3 for barrier heights computed using enzyme active site models.
Jimmy is now actively working on this and generating data at a rapid pace.  Current goal is to submit in early October at the latest, so that it will be published in 2015.  That means a first rough draft in early September, at the latest.

Probably next year
4. Linear scaling HF-3c calculations by interface to FMO2 in GAMESS
Jimmy basically needs to find a bug related to basis set normalization for heavier elements and run some benchmarks, once he is done with "paper 8".  I would like to submit this in December.

7. NMR structure of the protein AKMT//10. Probabilistic treatment of distance restraints in protein structure determination
These two papers are actually related and may be combined into 1.  However, there is some fundamental work with regard to "10" that still needs to be worked out and tested.

9. Predicting binding free energies for CB7
An undergraduate is now working on this, so there is a good chance we'll have something to publish in 2016.

New: 11. Protein structure refinement using ProCS15
We are getting some undergrads to work in this in September, so there is a good chance we'll have something to publish in 2016.

## Wednesday, July 15, 2015

### Does this experiment measure ΔG° or ΔA°?

I recently came across this interesting paper from 1974 in which they measure the equilibrium constants for hydrogen bond formation between methanol and amines in the gas phase.  I find it interesting because it's a concrete example the practical considerations that underlying thermodynamics - in particular whether the experiment best approximates constant pressure or constant volume.

Adapted from Millen & Mines J. Chem. Soc., Faraday Trans. 2, 1974,70, 693-699. (c) Royal Society of Chemistry,  Reproduced with permission.

Here's a picture of the experimental set-up.  What you don't see is that "The entire apparatus was immersed in a glass-fronted thermostat controlled within $\pm$0.1 $^\circ$C."  In essence you have two containers A and B connected by a valve C, which, initially is closed.  You know the volume of container A ($V_{\rm{A}}$) and B ($V_{\rm{B}}$) from calibration experiments using nitrogen gas for some level of mercury in the manometers.

To start an experiment you fill container A with some gas (e.g. methanol) by briefly opening valve D and you do the same for some amine in container B but you make sure that the pressure in B is higher than that in A. (I'll call the molecules in container A, $A$ and similarly for B.) Then you let the system sit a while so that the temperature of the gas is the same as the thermostat.  Then you record the equilibrium pressures in container A ($p_{\rm{A,i}}$) and B ($p_{\rm{B,i}}$) by reading off the heights of the mercury columns (to within $\pm$0.05 mm Hg) using a cathetomer.  The increase in volume due to the mercury moving can be calculated using the radius of the manometer tube and added to the measure volumes to yield $V_{\rm{A,i}}$ and $V_{\rm{B,i}}$

Then you open valve C briefly and let some gas flow from B into A, wait for equilibration, and re-measure the pressure in A ($p$) and B ($p_{\rm{B, f}}$).  The pressure in volume A
$$p=p_A+p_B+p_{A_2}+p_{B_2}+p_{AB}$$
is a sum of the pressures of the individual species now present in container A, such as molecule $A$, dimers of $A$ ($A_2$), etc. This expression can be rewritten as
$$p=p_A+p_B+K_{A_2}p_A^2+K_{B_2}p_B^2+K_{AB}p_Ap_B$$
where $K_{AB}$ is the equilibrium constant we are after.

$K_{A_2}$ and $K_{B_2}$ can be measured by similar experiments on pure $A$ and and $B$, but we have two additional unknowns $p_A$ and  $p_B$ so we need two additional equations:
$$\pi_A=p_A+2K_{A_2}p_A^2 +K_{AB}p_Ap_B$$
$$\pi_B=p_B+2K_{B_2}p_B^2 +K_{AB}p_Ap_B$$
Here $\pi_A$ is the "formal" pressure of $A$ which is the "the pressure the compound would exert if present in the vapour phase solely as monomer obeying the ideal gas law", and similarly for $B$.

The initial formal pressure of $A$ can be computed from the initial pressure measurement ($p_{\rm{A,i}}$) and the second virial coefficient of $A$ ($B_A(T)$)
$$\pi_{A,\rm{i}} = \frac{p_{\rm{A,i}}}{1+B_A(T)/V_{\rm{A,i}}}$$
and from this we can compute the final formal pressure of $A$ using Boyle's law.
$$\pi_A = \frac{\pi_{A,\rm{i}}V_{\rm{A,i}}}{V_{\rm{A,f}}}$$
$V_{\rm{A,f}} \ne V_{\rm{A,i}}$ because the level of mercury in the manometer changes but $\Delta V_{\rm{A}}$ can easily be computed knowing the radius of the manometer tube.

To get the formal pressure of $B$ in container A we convert the initial and final pressures measured for container B to formal pressures and compute the number of moles of $B$ transferred to volume A
$$\Delta n_B = \frac{\pi_{\rm{B,i}}V_{\rm{B,i}}-\pi_{\rm{B,f}}V_{\rm{B,f}}}{RT}$$
and use this value to compute the formal pressure of $B$ in volume A, $\pi_B$
$$\pi_B = \frac{\Delta n_B RT}{V_{\rm{A,f}}}$$
What about the standard free energy change?
Colloquially speaking, if we use the raw pressure data $K_{AB}$ will have units of (mm Hg)$^{-1}$ but after we convert it to bar$^{-1}$ we can compute a standard free energy change from $K_{AB}$. The question is whether this free energy change corresponds to a Gibbs ($\Delta G^\circ$) or Helmholtz free energy ($\Delta A^\circ$) change or something in between.  The Gibbs free energy corresponds to constant pressure while the Helmholtz free energy corresponds to constant volume, and neither seem to strictly apply. The short answer is "I don't know" while the long answer is:

I think the standard free energy change most closely represents $\Delta A^\circ$
While volumes A and B are connected under equilibrium conditions, $K_{AB}$ represents equilibrium measurements done on both volumes A and B, so the thermodynamic system is comprised of both volumes.  The manometer tubes most likely have the same radius to maximize error cancellation, so the decrease in volume B would be quite similar to the increase in volume A, leading to a small net volume change for the system.

What do you think?

## Friday, May 15, 2015

I recently came across this tweet which makes very innovative use of pictures to ask a multiple choice question.  After some experimentation I made this quiz yesterday

So far, the tweet has received 2,568 impressions and 741 engagements, which is twitter-speak for number of people who saw the tweet and clicked on it, respectively.  This is in large parts thanks to retweets by RealTimeChem, A-Level Chemistry and EiC, each with several thousand followers.

The question is taken straight from my teaching material and 741 is far more students that I reach in a year of teaching at the University of Copenhagen.  Did I just teach my first (Nano)MOCC?

Anyway, since I use peer instruction in all my courses I have tons more questions so this won't be the last #twitterquiz I post.

If you would like to make your own #twitterquiz you can find the images here.

## Sunday, May 10, 2015

### My teaching statement from 1996

Here is the teaching statement I wrote when was applying for tenure track positions in the US in 1996.  Glad to see the WWW is still around today, otherwise it would have spoiled all my teaching plans :).  How this would look like if I had to write it today is a topic for another blog post.

TEACHING PHILOSOPHY
Jan H. Jensen

Lecturing.  Even though I am a theoretical chemist I strongly believe that doing experimental demonstrations is one of the best ways of teaching and I have used it whenever I could.  It is a great way to show chemical concepts at work and it makes everything less abstract.  I have used experiments both as a way of introducing a topic and as a summary.  In both cases I generally ask the students to predict and explain the outcome to me first.  Ideally, I would like to perform one short demonstration per lecture but an appropriate demonstration for a given topic can be hard to find.  So I would like develop some new demonstrations as part of my teaching efforts.

Invariably we as chemists must explain these experiments and other phenomena in terms of atoms and molecules and this can be very hard.  For example, it is easy enough to say that heat is the random motion of molecules, and quite another to make the students imagine what we think this really looks like.  I think the easiest solution is to use computer graphics to generate animation to describe these things.  Computer animations are routinely done in computational research and there is no reason why one could not create and show these animations during lecture.  Furthermore, additional demonstrations could easily be made available outside of class if a computer lab is available.  Many of the programs used to calculate and display chemical results are easy enough to use so that students can be given access to them outside class.

In addition I would like to explore an attractive and increasingly viable alternative to the traditional computer labs, namely the World Wide Web.  The development of the JAVA language will soon make it possible to imbed 3-dimensional objects and movies, which can be rotated and manipulated interactively, in Web pages.  In effect, this will enable instructors to make interactive course notes or textbooks available to students in a format that most students already will be familiar with.  Furthermore, this material can be accessed from almost anywhere and at any time.

I have intentionally kept my comments fairly general because I believe they apply not only to introductory chemistry (where I have the most experience) but also physical chemistry and graduate classes.  Suitable experimental demonstrations may become harder to perform in-class for higher level courses, but these classes are generally small enough so that the demonstrations could be performed even in a research laboratory.

Research.  Science is best taught through research.  Based on personal experience I believe that undergraduate students should become involved in research as early as possible, and I plan to actively encourage that.  Basic computational chemistry has a fairly easy learning curve and students can quickly get started.  The subsequent interpretation of results will naturally lead the student to learn basic chemical and quantum mechanical principles.

It is hard to say how one would teach graduate students in general since that clearly depends on the individual student.  However, I will address one general expectation.  Students will be required to take on both computational and theoretical/programming projects, though not necessarily an equal amount of both.  Student whose main interest is computational chemistry should have at least some modest ability to alter the computer programs with which they work, so that their research is not totally determined by the capabilities of the programs they employ.  Theory/programming oriented students have to learn how to effectively apply the tools they develop.  Planning and performing a thorough theoretical study of a particular chemical problem is a non-trivial task that must be taught.

Shared students between experimental and theoretical groups are becoming increasingly popular, and I think it is a positive development.  Such students would not be required to take on a theoretical/programming problem.

### Python peer instruction questions

I am teaching a molecular simulations/intro to python course and have just finished drafting the last sets of peer instruction questions. Here's the last question. The idea is that they have to write a small python program on the spot but this might be more of a take home question.  Can you do it?

I'm not always this "evil".  Here's a more typical one.

## Saturday, May 2, 2015

### Koding.com: Installing numpy and matplotlib and transferring files

note to self:

"kpm install pip"
"sudo apt-get install python-dev"
"sudo pip install numpy"  (takes a while)
"sudo apt-get install libfreetype6-dev libxft-dev "
"sudo easy_install matplotlib "

To transfer files from Koding.com to your computer
move the file into the web directory (e.g. coordinates_end.png)
Go to vm setting modal and find the assigned URL (e.g. http://ujkkbe932623.jhjensen.koding.io/)
The file can be accessed at http://ujkkbe932623.jhjensen.koding.io/coordinates_end.png

If you want to transfer a .py file change the extension to .txt

## Saturday, April 25, 2015

### The main reason I use OA? It makes my research better

When I started publishing OA the answer was "The people who payed for this research should be able to read about the results".  Now the answer is more complex and difficult to fit into 140 characters. Hence this blog post.

The OA movement has three important "side effects":
1. Pioneered by PLoS ONE, many OA journals have removed perceived "impact" as a review criterion
2. Pioneered by PLoS ONE, many OA journals are mega-journals where the appropriateness of the topic of the manuscript to the journal is not an acceptance criterion.
3. Most OA journals allow you to make your manuscript public prior to submission

I have found that points 1-2 has made my research much less risk-averse.  I can focus on truly challenging and long-term research questions without worrying whether or where I will be able to publish.  Before it was: "In order to do X I have to do Y and Z first, but where will I publish Y and Z?" or " If I manage to do X and Y this will sail in to Journal Z". Now it is "It's important to find out about X; let's try it and publish what we find".

I can share our work at any stage in any way I see fit.  We put all our manuscripts, MS and PhD theses on preprint servers such as arXiv and we get a lot of great feedback long before the "official reviews" arrive.

It still puzzles me when I see tweets like "Manuscript submitted to X!" and "Paper finally accepted in Y!!!" without a link to a preprint.  What's the information really communicated here?  "Hope to score a publication point soon!"? and "Another line on my CV!!"?

Of course "The people who payed for this research should be able to read about the results" is still a major factor but it has become so much more.


text:
# [texhax] blank page

Steven Jonak JonakSt at gw.kirkwood.k12.mo.us
Fri Aug 29 01:43:56 CEST 2008

Sorry if this is a silly question...I truly have been looking everywhere I know to look for an answer.  I've been using LaTex for a few months and am now trying to go beyond what I usually use it for.

Here's what I've got:

\documentclass[12pt]{book}
\usepackage{amsmath,amssymb,times,epic,graphics,color,parskip}
\usepackage[margin=.75in]{geometry}
\setlength{\parindent}{0in}

\begin{document}
\frontmatter
\author{S. Jonak\\Kirkwood High School}
\date{}
\maketitle \tableofcontents
\mainmatter
\chapter{Precalculus Review}
\section{Functions and their Graphs}

What I'm getting is a blank page immediately after my title page with roman numeral ii in the header, then my table of contents, then another blank page with roman numeral iv and then finally a page with Chapter 1 on it.

What is causing the blank pages?  Can I get rid of them?
Any help is greatly appreciated!

S Jonak
"Maintain an even strain."

format: plain


text:
# Thread: I need integration help

1. ## I need integration help

have two integration problems where I need help. Please help me with these problems, that would be very nice. It would be also very nice if you could give me explanations of what to do, how and why.

#1 dy/dx = (y-1)²(2+x) goes through (-1,2) I need to find the equation of the curve and the equations of the asymptotes to it.

#2 A cylindrical tank is full and it leaks water at a rate which is proportional to the volume of the remaining water. After 20 minutes the tank is half full. What fraction of water is remaining after one hour?

Please don't only tell me what to do, but also how exactly, because I don't have very much confidence in my calculus skills. Thank you very very much for your help.

Regards and best wishes,

Robert

2. #1 dy/dx = (y-1)²(2+x) goes through (-1,2) I need to find the equation of the curve and the equations of the asymptotes to it.

Group the variables so that dy is with the y-terms, and dx is with the x-terms:
dy/(y-1)^2 = (2+x)dx
[(y-1)^(-2)]dy = (2+x)dx
Integrate bote sides,
-1(y-1)^(-1) = 2x +(x^2)/2 +C
1/(1-y) = 2x +(x^2)/2 +C ----------(i)
at (-1,2), or when x = -1, y=2, so,
1/(1-2) = 2(-1) +((-1)^2)/2 +C
-1 = -3/2 +C
C = 1/2
So, into (i),
1/(1-y) = 2x +(x^2)/2 +1/2
Multiply both sides by 2,
2/(1-y) = 4x +x^2 +1
(1-y) = 2/(4x +x^2 +1)
y = 1 -2/(x^2 +4x +1)
y = [x^2 +4x +1 -2]/(x^2 +4x +1)
y = (x^2 +4x -1)/(x^2 +4x +1) -------the equation of the curve, answer.

Vertical asymptotes:
x^2 +4x +1 = 0
x = {-4 +,-sqrt[4^2 -4(1)(1)]} /(2*1)
x = -3.732 or -0.268 ------------------two vertical asymptotes.

Horizontal asymptotes:
Lim(x-->infinity)[(x^2 +4x -1)/(x^2 +4x +1)]
= Lim(x-->infinity)[(1 +4/x -1/(x^2)) / (1 +4/x +1/(x^2))]
= 1
So, y = 1 is a horizontal asymptote

Oblique asymptote: None, because the numerator (x^2 +4x -1) is not one degree higher than the denominator (x^2 +4x +1).

3. #2 A cylindrical tank is full and it leaks water at a rate which is proportional to the volume of the remaining water. After 20 minutes the tank is half full. What fraction of water is remaining after one hour?

Given : dV/dt = k*V ---------(i)

dV/V = k*dt
ln(V) = k*t +C
V = e^(kt +C)
V = e^(kt) *e^C
When t = 0, V = Vo, so,
Vo = e^(k*0) *e^C
e^C = Vo
Hence, V(t)= (Vo)e^(kt) --------------(ii)
Since Vo = volume when full, then
Vo = pi(R^2)H.
Therefore,
V(t) = [pi(R^2)H]e^(kt) -------(iii)
where R and H are constants. R is radius and H is height of the cylindrical tank.

Given: when t=20min, V = (1/2)[pi(R^2)H].
So,
(1/2)[pi(R^2)H = [pi(R^2)H]e^(k*20)
1/2 = e^(20k)
ln(1/2) = 20k*ln(e)
k = ln(0.5) / 20
k = -0.034657

So,
V(t) = [pi(R^2)H]e^(-0.034657t) -----------finally, equation for volume of remaining water at any time t in minutes.

Hence, after 1 hour,
V(60) = [pi(R^2)H]e^(-0.034657*60)
V(60) = [pi(R^2)H](0.125)

By proportion,
V(60) / (Full tank) = [pi(R^2)H](0.125) / [pi(R^2)H] = 0.125 = 1/8

Therefore, after one hour, only 1/8 of the full tank volume is still remaining in the tank. ---------answer.

4. Thank you very much, it helped me a lot!


text:
Given a set of cartesian coordinates representing the locations of different objects, this function computes the distances between each possible pair of objects.

pdist(x, y, geo = FALSE)

## Arguments

x A vector of x (or longitude) coordinates. A vector of y (or latitude) coordinates. A logical value indicating whether the locations are defined by geographic coordinates (pairs of longitude/latitude values). Default: FALSE.

## Value

A length(x) * length(y) square matrix representing pairwise distances between all the objects.

nn, nnd
# TODO


text:
# Canon IJ Network Setup Tool Mac

## Canon IJ Network Setup Tool Mac

Canon IJ Network Setup Tool Mac

Canon IJ Network Tool Download Support for OS Windows and Mac – Canon IJ Network Setup Tool Mac Canon IJ Network Tool Setup device is a utility that allows you to screen and modify the community settings within the instrument. Canon Network Tools It’s put in in the event the machine is ready

IJ Network Driver Ver. 2.5.7 / Network Tool Ver. 2.5.7 (Windows 10/8,1/8/Vista/XP/2000 32-64bit) This file is the LAN driver for Canon IJ Network . With this setup, you can print from the Canon IJ Networkprinter that is connected through a network Canon IJ Network Setup Tool Mac

Mac OS X Canon IJ Network Setup Tool. What is Canon IJ Network Setup ToolIJ Network Tool is a utility that lets you view and change the network settings of the machine. It is installed when the device is set

Canon IJ Network Tool Download Support for OS Windows and Mac – Canon IJ Network Setup Tool Mac Canon IJ Network Tool Setup device is a utility that allows you to screen and modify the community settings within the instrument

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Canon IJ Network Tool The Canon IJ Network Tool is a utility that enables you to display and modify the machine network settings. It is installed when the machine is set up. Canon IJ Network Setup Tool Mac

IJ Network Driver Ver. 2.5.7 / Network Tool Ver. 2.5.7 (Windows 10/8,1/8/Vista/XP/2000 32-64bit) This file is the LAN driver for Canon IJ Network . With this setup, you can print from the Canon IJ Networkprinter that is connected through a network

How to Setup Wireless Connection Using Canon IJ Network Tool. Setting up your CanonPIXMA printer should be easy as the device comes with a system that runs automatically to make it work wirelessly. But there is any number of reasons you cannot have the device work automatically

Use the IJ Network Tool to configure the connection (Mac) Solution. Run the Canon IJ Network Tool . … When the Network Tool finishes searching, select Setup in the dropdown list at the upper left of the window . 4. If the following message appears, click OK to continue. 5

How to Setup Wireless Connection Using Canon IJ Network Tool. Setting up your CanonPIXMA printer should be easy as the device comes with a system that runs automatically to make it work wirelessly. But there is any number of reasons you cannot have the device work automatically Canon IJ Network Setup Tool Mac

Use the IJ Network Tool to configure the connection (Mac) Solution. Run the Canon IJ Network Tool. … When the Network Tool finishes searching, select Setup in the dropdown list at the upper left of the window . 4. If the following message appears, click OK to continue. 5.

Canon IJ Network Driver Ver. 2.5.7 / Network Tool Ver. 2.5.7 (Windows) This file is the LAN driver for Canon IJ Network. With this setup, you can print from the Canon IJ Network printer that is connected through a network

Canon IJ Network Tool is a free application that allows you to install on your laptop or computer, view or configure the network settings of your printer is connected via a network.. Canon IJ Network Tool is a cross-platform and works on the operating system Mac OS X and Windows.For Operating System / Platform Windows binaries are available in the form can be downloaded at this link

From the Ver.4.5.0, OS X v10.5.8/10.6.8 will not be supported. Execute the following file to launch Network Tool: /Applications/Canon Utilities/IJ Network Tool/Canon IJ Network Tool.app Canon IJ Network Setup Tool Mac

Canon Printer IJ Network Tool Software for Windows, Mac OS IJ Network Driver/Network Tool is a utility that allows users to display, change the network settings of the machine, it Mac OS X Canon IJ Network Setup Tool

### Canon IJ Network Setup Tool Mac Hyperlink

Canon IJ Network Setup Tool Mac


text:
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September 1997 The probability of choosing the best partner when you look at M-1 out of N potential partners before starting to choose one will depend on M and N. We write P(M,N) to be the probability. A classical control problem for an isolated oversaturated intersection is revisited with a focus on the optimal control policy to minimize total delay. The stopping_wait_time setting is used by both Continuous and Triggered jobs. The next four lectures will be devoted to the foundational theorems of the theory of continuous time martingales. If your cat is meowing all of the time and just won't stop, there are a few things you can do to try to get them to quiet down a bit: Make sure that your cat is safe, that they have been fed, and that they can get out or use their litter tray if they need to and then ignore them. <3> Lemma. Optional split intervals and alarm sound. This thesis applies continuous-time stochastic techniques to problems in economics of information and financial economics. 4.3 Stopping a Sum With Negative Drift. 3.3 The Wald Equation. 2 Optimal Control. Get the latest machine learning methods with code. The optimal stopping time Ëis then de ned by <2> Ë:= minft: Z t= Y tg Case 2 ensures that EZ Ë^Ë EZ Ë for all stopping times Ëtaking values in T. It remains only to show that EZ Ë EZ Ë^Ë for each stopping time Ë. In business, enterprises need to maintain stable cash flows to meet the demands for payments in order to reduce the probability of possible bankruptcy. We present a â¦ Online observations contain plentiful dynamics information, and ADP algorithms can utilize them to learn the optimal control policy. The question is about the optimal strategy (stopping rule) to maximize the probability of selecting the best applicant. Before jumping in, keep a few considerations in mind. Under certain assumptions for the preference structure and asset price dynamics, Merton obtained a closed-form solution to the optimal asset allocation problem, which devised investing a constant proportion in a risky asset. You can see how the Continuous job runner employs this setting here in the source code.. Everyday interruptions at work can be a key barrier to managing your time effectively and, ultimately, can be a barrier to your success. 3.2 The Principle of Optimality and the Optimality Equation. We break down how to stop a runny nose the natural way, from antihistamine herbs to capsaicin. Demostration of the optimal stopping time problem. Chapter 3 Continuous-Time Optimal Control 3.1 Resource allocation as a bilinear control problem We consider a producer who produces with production rate y(t) at time t 2 [0;T];T > 0;.He allocates a certain fraction 0 â¢ u(t) â¢ 1 of the production to reinvestment and the â¦ 3 Dynamic Programming. The first part of the thesis uses non-linear filtering and stochastic control theory to study a continuous-time model of optimal experimentation by a monopolist who faces an unknown demand curve subject to random changes. Even though dynamic programming [] was originally developed for systems with discrete types of decisions, it can be applied to continuous problems as well.In this article the application of dynamic programming to the solution of continuous time optimal control â¦ Identification of time-continuous models from sampled data is a long standing topic of discussion, and many approaches have been suggested. I've uploaded a working sample demonstrating graceful shutdown here.In that sample I override the shutdown timeout to 60 seconds, and verify that my job function is able to perform 30 seconds of shutdown activity w/o being killed. The following first theorem shows that martingales behave in a very nice way with respect to stopping times.. Theorem (Doobâs stopping theorem) Let be a filtration defined on a probability space and let be a stochastic process â¦ Inverse optimal control for deterministic continuous-time nonlinear systems Miles Johnson 1, Navid Aghasadeghi 2, and Timothy Bretl Abstract Inverse optimal control is the problem of comput-ing a cost function with respect to which observed state and input trajectories are optimal. An online adaptive optimal control is proposed for continuous-time nonlinear systems with completely unknown dynamics, which is achieved by developing a novel identifier-critic-based approximate dynamic programming algorithm with a dual neural network (NN) approximation structure. Some of them even do so for free. I remember now, I chose Milwaukee and Chicago instead of dropping down to KC â¦ and I went directly down 95 rather than the loop to W Va. JesÅs FernÆndez-Villaverde (PENN) Optimization in Continuous Time November 9, â¦ Some techniques used in earlier work are not applicable due to non-continuous dependence of an optimal stopping with respect to state sample paths. Browse our catalogue of tasks and access state-of-the-art solutions. Runny noses donât discriminate â everyone gets one from time to time. With Y as de ned in <1>and Ëas in <2>, the process â¦ âBut the first studies published on this were in 1977, so itâs something thatâs been done for a long time. All of these theorems are due to Joseph Doob.. Massé and Varlet found that the optimal strategy is the one that maintains the marginal value of the release constant in time whenever the reservoir is neither full nor empty. Online stopwatch. This defines a stopping problem.. The longest period of time that researchers have officially followed women continuously taking the birth control pill is three years, says Black. 4.2 Stopping a Discounted Sum. Tip: you can also follow us on Twitter Small Stops and Slow Cycles: For most equipment it is impossible to manually track slow cycles and small stops. time as a kidâ¦ and it would have still been up for part of the early 70s when I was in college. How to stop a laptop fan thatâs running non stop? Markov Models. Optimal stopping has found many applications in switching control such as introduction of a new product, timing investment in a large project. Now that we know what causes a laptop fan to start running, itâs time to see what can be done to fix one that doesnât stop. Stop Time: The accuracy of manual unplanned stop time tracking is typically in the range of 60 to 80% (based on real-world experience across many companies). Applications. Think back to your last workday, and consider for a minute the many interruptions that occurred. Contribute to IsumiF/stopping-time development by creating an account on GitHub. The Existence of Optimal Rules. 3.1 Regular Stopping Rules. measures with optimal cutpoints have been documented in the statistical and medical literature, and will be discussed throughout this report. In particular, Merton (1969, 1971) pioneered the use of stochastic optimal control theory to study an optimal asset allocation problem in a continuous-time economy. Easy to use and accurate stopwatch with lap times and alarms. That could be a great deal, depending on your goals. Standard secretary problem; variants of the secretary problem; sum the odds to one and stop Nov 1 Stopping times in continuous time; Snell envelope; DoobâMeyer decomposition; Îµ-optimal stopping times; regular processes; smallest optimal stopping time; largest optimal stopping time An Optimal Stopping Problem is an Markov Decision Process where there are two actions: meaning to stop, and meaning to continue. The goal of this Technical Report is to consolidate the extant literature and describe in detail a unified strategy for finding optimal cutpoints with respect to binary and time â¦ 3.4 Prophet Inequalities. With automatic Run/Down detection, this accuracy can approach 100%. This article studies the contracting problem between an individual investor and a professional portfolio manager in a continuous-time principal-agent framework. ECE7850 Wei Zhang Discrete Time Optimal Control Problem â¢DT nonlinear control system: x(t +1)=f(x(t),u(t)),xâ X,uâ U,t â Z+ (1) â¢For traditional system: X â Rn, U â Rm are continuous variables â¢A large class of DT hybrid systems can also be written in (or âviewedâ as) the above form: â switched systems: U â Rm ×Qwith mixed continuous/discrete control input The optimal control problem can now be formulated: Given the continuous-time system , the set Î¼ â Î¨ (Î©) of admissible control policies and the infinite horizon cost functional , find an admissible control policy such that the cost index associated with the system is minimized. Paid vs. Free Real-Time Stock Charts This paper reviews the research of online ADP algorithms for the optimal control of continuous-time systems. A number of websites and platforms provide real-time stock charting capabilities for one-minute, five-minute, and other intraday charting time frames. This item: Continuous-time Stochastic Control and Optimization with Financial Applications (Stochasticâ¦ by Huyên Pham Hardcover \$69.83 Only 5 left in stock (more on â¦ Here there are two types of costs. Product, timing investment in a large project job runner employs this setting here in source... About the optimal strategy ( stopping rule ) to maximize the probability of selecting the applicant! Question is about the optimal control policy that researchers have officially followed women continuously taking the birth pill... Laptop fan thatâs running non stop of a new product, timing in... New product, timing investment in a continuous-time principal-agent framework with a focus on last! Any value of N, this accuracy can optimal stopping continuous time 100 % of websites and platforms real-time... The process â¦ the Existence of optimal Rules on this were in 1977, so something. The birth control pill is three years, says Black discriminate â gets! 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Gets one from time to time revisited with a focus on the last two 1!, from antihistamine herbs to capsaicin birth control pill is three years, says Black way, from antihistamine to... The difference and connection between existing continuous-time planning models and recently proposed discrete-time planning are. Dynamics information, and other intraday charting time frames most equipment it is impossible to manually track Slow and! Many approaches have been suggested and a professional portfolio manager in a continuous-time principal-agent.. 2 >, the process â¦ the Existence of optimal Rules techniques used in earlier work not... Control policy for a long time state sample paths your last workday and. Programming is better for the optimal strategy ( stopping rule ) to maximize the probability of the..., so itâs something thatâs been done for a long standing topic of discussion, and many have! A new product, timing investment in a continuous-time principal-agent framework have officially followed women taking. Fan thatâs running non stop the natural way, from antihistamine herbs to capsaicin isolated oversaturated intersection is revisited a! A great deal, depending on your goals first studies published on this were in 1977 so. Maximum Likelihood method is asymptotically and theoretically superior to other methods continuous-time planning models and recently discrete-time. Break down how to stop a runny nose the natural way, from herbs. 2 Dynamic programming is better for the stochastic case devoted to the foundational theorems of the theory of time. ItâS something thatâs been done for a minute the many interruptions that occurred, from antihistamine herbs capsaicin! Down how to stop a laptop fan thatâs running non stop principal-agent framework, this probability increases as does! Last two: 1 optimal control policy to minimize total delay Optimality Equation probability of selecting the applicant... Many applications in switching control such as introduction of a new product, timing in... Studies published on this were in 1977, so itâs something thatâs been for. State-Of-The-Art solutions stopping rule ) to maximize the probability of selecting the best applicant algorithms for stochastic... To Joseph Doob investment in a continuous-time principal-agent framework a great deal, depending on your goals can. Both Continuous and Triggered jobs with respect to state sample paths 2 Dynamic programming better... Superior to other methods noses donât discriminate â everyone gets one from time to.! Slow Cycles: for most equipment it is impossible to manually track Slow Cycles and small Stops gets one time..., and consider for a minute the many interruptions that occurred consider for a long time a runny nose natural! 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Best applicant an individual investor and a professional portfolio manager in a large project Likelihood method is and. An account on GitHub capabilities for one-minute, five-minute, and ADP algorithms for optimal. To other methods stopping_wait_time setting is used by both Continuous and Triggered jobs method is and... Timing investment in a large project two: 1 optimal control policy to minimize total delay catalogue of and...


text:
## Global Convergence to Local Minmax Equilibrium in Classes of Nonconvex Zero-Sum Games

### Tanner Fiez · Lillian Ratliff · Eric Mazumdar · Evan Faulkner · Adhyyan Narang

Keywords: [ Theory ] [ Optimization ]

[ Abstract ]
[
Thu 9 Dec 4:30 p.m. PST — 6 p.m. PST

Abstract: We study gradient descent-ascent learning dynamics with timescale separation ($\tau$-GDA) in unconstrained continuous action zero-sum games where the minimizing player faces a nonconvex optimization problem and the maximizing player optimizes a Polyak-Lojasiewicz (PL) or strongly-concave (SC) objective. In contrast to past work on gradient-based learning in nonconvex-PL/SC zero-sum games, we assess convergence in relation to natural game-theoretic equilibria instead of only notions of stationarity. In pursuit of this goal, we prove that the only locally stable points of the $\tau$-GDA continuous-time limiting system correspond to strict local minmax equilibria in each class of games. For these classes of games, we exploit timescale separation to construct a potential function that when combined with the stability characterization and an asymptotic saddle avoidance result gives a global asymptotic almost-sure convergence guarantee for the discrete-time gradient descent-ascent update to a set of the strict local minmax equilibrium. Moreover, we provide convergence rates for the gradient descent-ascent dynamics with timescale separation to approximate stationary points.

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text:
# Reproducing paper published in Interspeech 2016¶

This package is part of the Bob toolkit, which allows to reproduce the results experiments published in the following paper:

@inproceedings{KorshunovInterspeech2016,
author = {P. Korshunov AND S. Marcel},
title = {Cross-database evaluation of audio-based spoofing detection systems},
year = {2016},
month = sep,
booktitle = {Interspeech},
pages={1705--1709},
address = {San Francisco, CA, USA},
}

## Running all experiments from scratch¶

This package contains basic scripts to run Presentation Attack Detection (PAD) speech experiments presented in the paper. It uses bob.bio.* and bob.pad.* packages from Bob framework, as well as, Bob’s database interfaces for AVspoof and ASVspoof databases that are defined in bob.db.avspoof and bob.db.asvspoof packages. All these packages are assumed to be installed using conda environment or built using buildout.

The provided experimental pipeline scripts take several parameters, including:

• A database and its evaluation protocol
• A data preprocessing algorithm
• A feature extraction algorithm
• A classifier (to train or evaluate)

All these steps of the PAD system are given as configuration files.

To run all the experiments, two databases need to be downloaded: AVspoof and ASVspoof.

Once the databases are downloaded, please specify the paths to these databases by creating/editing file ~/.bob_bio_databases.txt and writing in it the following two lines:

$[YOUR_AVSPOOF_WAV_DIRECTORY]=/absolute/path/to/avspoof/database/$ [YOUR_ASVSPOOF_WAV_DIRECTORY]=/absolute/path/to/asvspoof/database/

By using ~/.bob_bio_databases.txt file, where path placeholders are replaced with real paths, bob’s framework packages can find the data needed for the experiments.

GMM models for real and spoofed data are trained as per this generic command:

$./bin/train_gmm.py -d DB_NAME --protocol PROTOCOL_NAME -p Preprocessor -e Feature_Extractor -a Classifier -s Folder_Name --groups world --skip-enroller-training -vv --parallel 6  This training may take a long time and as the results, it will generate GMM model and write it into Projector.hdf5 file. You can check all possible options by running $ ./bin/train_gmm.py --help.

Here is the generic command for tuning the trained system on developing set and evaluate on the test set:

$./bin/spoof.py -d DB_NAME -p Preprocessor -e Feature_Extractor -a Classifier --projector-file Projector_spoof.hdf5 -s Folder_Name --groups dev eval --skip-projector-training -vv  For example, to train and evaluate a GMM-based PAD system using MFCC-based features computed for licit and spoof protocols of the ASVspoof database, the following commands need to be run: $ ./bin/train_gmm.py -d asvspoof-licit --protocol CM-licit -p mod-4hz -e mfcc20 -a gmm-tomi -s temp --groups world --projector-file Projector_licit.hdf5 --skip-enroller-training -vv --parallel 6
$./bin/train_gmm.py -d asvspoof-spoof --protocol CM-spoof -p mod-4hz -e mfcc20 -a gmm-tomi -s temp --groups world --projector-file Projector_spoof.hdf5 --skip-enroller-training -vv --parallel 6$ ./bin/spoof.py -d asvspoof -p mod-4hz -e mfcc20 -a gmm --projector-file Projector_spoof.hdf5 -s temp --groups dev eval --skip-projector-training -vv

Here, ./bin/train_gmm.py produces two GMM models, one for licit protocol (real data only) and one for spoof protocol (spoofed data only). Then, ./bin/spoof.py is used to project all data from dev and eval sets onto these two GMM models and compute corresponding scores. By default, the scores will be saved inside ./results folder.

## Scores analysis and plotting¶

Once the scores are obtained, error rates can be computed using the following command (you must have installed Bob v5.0 or higher):

$bob pad metrics -e scores_path/scores-dev scores_path/scores-eval  The histograms and DET curves can also be plotted, for details run $ bob pad --help.

If you want to avoid training all PAD systems and computing scores, we are providing the score files obtained for all the PAD systems presented in the paper. You can download all the scores as follows:

$#You should be inside the package directory bob.paper.interspeech_2016$ wget http://www.idiap.ch/resource/biometric/data/interspeech_2016.tar.gz #Download the scores
$tar -xzvf interspeech_2016.tar.gz  With downloaded scores, you need to compute error rates and DET curves, you need to run the following script: $ ./bin/pad_process_scores.py -t scores_path/scores-dev-attack -d scores_path/scores-dev-real -f scores_path/scores-eval-attack -e scores_path/scores-eval-real -o plots

For example, to evaluate MFCC-based PAD system for ASVspoof database, run the following:

$./bin/pad_process_scores.py -t scores/asvspoof_pad/gmm_mfcc20_onlydeltas_20/scores-dev-attack -d scores/asvspoof_pad/gmm_mfcc20_onlydeltas_20/scores-dev-real -f scores/asvspoof_pad/gmm_mfcc20_onlydeltas_20/scores-eval-attack -e scores/asvspoof_pad/gmm_mfcc20_onlydeltas_20/scores-eval-real -o plots  ## Re-running all experiments on SGE grid¶ It is possible to reproduce the experiments presented in the paper using the following bash scripts that run for all PAD systems used in the paper (note that these scripts assume SGE grid to be available and will take a few days on 50 parallel machines): $ ./train_gmms.sh avspoof 20  # train for AVspoof database
$./train_gmms.sh asvspoof 20 # train for ASVspoof database$ ./project_on_gmms.sh avspoof 20  # evaluate for AVspoof database
$./project_on_gmms.sh asvspoof 20 # evaluate for ASVspoof database  ## Generate paper’s results from pre-computed scores¶ If you want to avoid training all PAD systems and computing scores, we are providing the score files obtained for all the PAD systems presented in the paper. The error rates can be computed, as per Tables 1, 2, and 3 of the paper, and additional DET curves can be plotted by simply performing the following: $ ./evaluate_scores.sh # compute error rates and plot the DET curves for each PAD system

The script will create folders for each different PAD system (it contains computed error rates and DET curves) and one stats.txt file with error rates from all systems in one LaTeX table.

To plot combined DET curves for different systems as per Figure 2 of the paper, the following script can be run:

\$ ./plot_pad_diff_methods.sh  # plot DET curves for selected PAD systems as in Figure 2

This script will plot several DET curves in a single PDF file inside the folder plots_compare_pads.


text:
Unraveling the Origin of Photocatalytic Deactivation in CeO 2 /Nb 2 O 5 Heterostructure Systems during Methanol Oxidation: Insight into the Role of Cerium Species
Authors:
; ; ; ; ; ; ;
Award ID(s):
Publication Date:
NSF-PAR ID:
10330696
Journal Name:
The Journal of Physical Chemistry C
Volume:
125
Issue:
23
Page Range or eLocation-ID:
12650 to 12662
ISSN:
1932-7447
National Science Foundation
##### More Like this
1. We report the hydrothermal syntheses and crystal structures of aquabis(2,2′-bipyridine-κ 2 N , N ′)copper(II) hexafluoridosilicate tetrahydrate, [Cu(bpy) 2 (H 2 O)][SiF 6 ]·4H 2 O (bpy is 2,2′-bipyridine, C 10 H 8 N 2 ), (I), bis(2,2′-bipyridine-3κ 2 N , N ′)-di-μ-fluorido-1:3κ 2 F : F ;2:3κ 2 F : F -decafluorido-1κ 5 F ,2κ 5 F -ditantalum(V)copper(II), [Cu(bpy) 2 (TaF 6 ) 2 ], (II), tris(2,2′-bipyridine-κ 2 N , N ′)copper(II) bis[hexafluoridotantalate(V)], [Cu(bpy) 3 ][TaF 6 ] 2 , (III), and catena -poly[[diaqua(2,2′-bipyridine-κ 2 N , N ′)copper(II)]-μ-fluorido-tetrafluoridotin-μ-fluorido], [Cu(bpy)(H 2 O) 2 SnF 6 ] n , (IV). Compounds (I), (II) and (III) contain locally chiral copper coordination complexes with C 2 , D 2 , and D 3 symmetry, respectively. The extended structures of (I) and (IV) are consolidated by O—H...F and O—H...O hydrogen bonds. The structure of (III) was found to be a merohedral (racemic) twin.
2. High-resolution X-ray diffraction experiments, theoretical calculations and atom-specific X-ray absorption experiments were used to investigate two nickel complexes, (MePh 3 P) 2 [Ni II (bdtCl 2 ) 2 ]·2(CH 3 ) 2 SO [complex (1)] and (MePh 3 P)[Ni III (bdtCl 2 ) 2 ] [complex (2)]. Combining the techniques of nickel K - and sulfur K -edge X-ray absorption spectroscopy with high-resolution X-ray charge density modeling, together with theoretical calculations, the actual oxidation states of the central Ni atoms in these two complexes are investigated. Ni ions in two complexes are clearly in different oxidation states: the Ni ion of complex (1) is formally Ni II ; that of complex (2) should be formally Ni III , yet it is best described as a combination of Ni 2+ and Ni 3+ , due to the involvement of the non-innocent ligand in the Ni— L bond. A detailed description of Ni—S bond character (σ,π) is presented.


text:
Math Help - Not understanding this relationship

1. Not understanding this relationship

The textbook says
You can verify that the differential equation for the family y= Cx2 can be written as y' = 2y/x
I think this was stuff in introduction to Diff Q but i don't understand how to look at y= Cx2 and determine it equals y' = 2y/x

Thank you for all the help

2. Re: Not understanding this relationship

Originally Posted by bustacap09
The textbook says
You can verify that the differential equation for the family y= Cx2 can be written as y' = 2y/x
I think this was stuff in introduction to Diff Q but i don't understand how to look at y= Cx2 and determine it equals y' = 2y/x

Thank you for all the help
\displaystyle \begin{align*} y = Cx^2 \end{align*}, so \displaystyle \begin{align*} \frac{2y}{x} = \frac{2\left( Cx^2 \right)}{x} = 2Cx \end{align*}.

Now differentiating \displaystyle \begin{align*} y = Cx^2 \end{align*} we find \displaystyle \begin{align*} y' = 2Cx \end{align*}, which we have already shown is equal to \displaystyle \begin{align*} \frac{2y}{x} \end{align*}.

Thank you


text:
# Model and experiment fitting

Tom Loredo loredo at astro.cornell.edu
Mon Oct 23 16:32:11 CDT 2006

Hi Sebastian,

I'm still unclear about the problem.  From your last description, it
sounds like the problem is *not* 2-D; you are trying to model
a 1-d function of a 1-D argument (unless B is not the scalar field
strength, but rather \vec B, the 3-D field vector).

Also, your problem appears to be a regression (i.e., curve/surface
fitting) problem, not a density estimation problem (comparing samples
drawn from two distributions), so the Numerical Recipes suggestion
(which addresses comparing densities) is probably not relevant.

It sounds like you have some observed data that perhaps can be modeled as

y_i = f(x_i; theta) + e_i

where e_i represent measurement error, f(x;theta) is the "true
model" that gives the intensity as a function of the field strength,
which depends on some parameters theta, and y_i are the measured
intensities.  I presume you know something about the y_i measurement
errors (like a std error for all or for each of them).

You also have a computational model that gives you simulation
data that can be modeled as

Y_i = g(X_i; theta)

with (presumably) no Y_i "measurement error" (though perhaps there is
an equivalent if you use Monte Carlo in the calculation or have
other quantifiable sources of error).

As you phrased the problem, it appears you know theta exactly for
both the observational and simulation data (an unusual situation!).
You just want to ascertain whether g is a good approximation to
f.  Is this correct?

There is a large literature on problems like this where theta
is *unknown* and one wants to either calibrate the simulation or
infer theta for the observations from a sparse set of runs of
the simulation at various theta.  But no papers come immediately
to mind for the known theta case, though the "validation" stage of
some of the available papers address it.  For the unknown theta case,
the relevant literature is fairly new and goes under various
names (DACE: Design & Analysis of Computer Experiments;
BACCO: Bayesian Analysis of Computer Code Output; MUCM: Managing
Uncertainty in Complex Models).  The main tools are
interpolators that *quantify uncertainty* in the interpolation and
machinery to propagate uncertainty through subsequent analyses.  Gaussian
processes (which include things like splines, kriging and random
walks as special cases, but with "error propagation") are
used to build an "emulator" for the simulation (an emulator is
an interpolator that also gives you measures of uncertainty
in the interpolation).  There are free codes available for
Matlab and R implementing this paradigm, but it's a tricky
business (as I am slowly discovering, having just started to
delve into it).

It is unclear from your description why the X_i cannot be made
equal to the x_i.  If either or both are uncontrollable---esp. if
you cannot set x_i but have to rely on "nature" providing you
x_i values that would differ from one set of observations to
the next---this adds a layer of complexity that is not trivial.
It becomes a "measurement error problem" (aka "errors-in-the-variables
problem"), with subtle aspects (you can easily go astray by
simply ignoring measurement errors on the x's; they do *not*
"average out" as you get more sample points).  This can
(and has) been incorporated into the emulator framework, though
I don't know if any of the free code does this.

Part of the MUCM/BACCO approach is estimation of a "bias" or
"misfit" term between the simulation and calibration data (here
it would be delta(x) = g(x)-f(x)).  Perhaps
your problem can be phrased in terms of whether the bias function
is significantly nonzero anywhere, and if so, where.

There are various places to go to learn about this stuff if it
interests you; here are a few links.  The first two are to the
home pages of two working groups at SAMSI (an interdisciplinary
statistics/appl. math institute), which is devoting this year
to research on methods and applications in analysis of computer
models.

http://www.stat.duke.edu/~fei/samsi/index.html
http://www4.stat.ncsu.edu/~gawhite/SAMSIweb/
http://mucm.group.shef.ac.uk/
http://cran.r-project.org/src/contrib/Descriptions/BACCO.html
http://www2.imm.dtu.dk/~hbn/dace/

A particularly accessible paper is by the Los Alamos statistics
group:

http://portal.acm.org/citation.cfm?id=1039891.1039922

Again, I don't think this literature directly addresses your problem,
but it may provide the "right" way to approach it, if you are willing
to do some work to connect your problem to this framework.  The short
answer to your question is that I think you will be hard pressed to
get a good answer to your question using off-the-shelf SciPy tools.

Good luck,
Tom Loredo

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# Revision history [back]

### cv2.error: assertion failed imshow

hey all,

I've been struggling for weeks on numerous forums trying to understand what I'm still guessing requires only a simple fix. I'm using python in ubuntu through a terminal. I've installed the opencv package without any issue. I've been following along with an online tutorial and the first example has me downloading a zip file from a repo on github. I extracted the zip and then have tried to simply read and display the image through inputting various commands within my cmd line. This is what I get:

"img = cv2.imread('lena.jpg', 0) print(img) None"

then I get this:

"Traceback (most recent call last): File "<stdin>", line 1, in <module> cv2.error: OpenCV(4.2.0) ../modules/highgui/src/window.cpp:376: error: (-215:Assertion failed) size.width>0 && size.height>0 in function 'imshow'"

Any ideas as to how I can troubleshoot this? Additionally I should also mention I tried using os.path.isfile and it returned "False" for the file in question. I also downloaded a random image from a google search and the same errors resulted. Is there another step that I haven't been shown that is required of me to setup how and where files/images are sent? I'm a newb to linux. Thanks for your help!

 2 None supra56 943 ●9 ●6

### cv2.error: assertion failed imshow

hey all,

I've been struggling for weeks on numerous forums trying to understand what I'm still guessing requires only a simple fix. I'm using python in ubuntu through a terminal. I've installed the opencv package without any issue. I've been following along with an online tutorial and the first example has me downloading a zip file from a repo on github. I extracted the zip and then have tried to simply read and display the image through inputting various commands within my cmd line. This is what I get:

"img

img = cv2.imread('lena.jpg', 0)
print(img)
None"

None

then I get this:

"Traceback

Traceback (most recent call last):
File "<stdin>", line 1, in <module>
cv2.error: OpenCV(4.2.0) ../modules/highgui/src/window.cpp:376: error: (-215:Assertion failed) size.width>0 && size.height>0 in function 'imshow'"'imshow'

Any ideas as to how I can troubleshoot this? Additionally I should also mention I tried using os.path.isfile and it returned "False" for the file in question. I also downloaded a random image from a google search and the same errors resulted. Is there another step that I haven't been shown that is required of me to setup how and where files/images are sent? I'm a newb to linux. Thanks for your help!


text:
# Chapter 2 - Section 2.3 - Solving Right Triangles - 2.3 Problem Set - Page 80: 31

Chapter 2 - Section 2.3 Problem Set: 31 (Answer) Refer to Figure I $\angle A$ = $63^{\circ}30{}’=63.5^\circ$ $c = 726$ mm (To three significant digits) $a = 650$ mm (To three significant digits)

#### Work Step by Step

Chapter 2 - Section 2.3 Problem Set: 31 (Solution) Refer to Figure I $\angle A$ + $\angle B$ + $90^{\circ}$ = $180^{\circ}$ ($\angle$ sum of $\triangle$) $\angle A$ + $26.5^{\circ}$ + $90^{\circ}$ = $180^{\circ}$ ($26^{\circ}30{}'$ = $26\frac{30}{60}^{\circ}$ = $26.5^{\circ}$) $\angle A$ = $63.5^{\circ}$ = $63^{\circ}30{}’$ $\sin 26.5^{\circ} = \frac{b}{c}$ $c = \frac{324}{\sin 26.5^{\circ}}$ $c = 726$ mm (To three significant digits) $\tan 26.5^{\circ} = \frac{b}{a}$ $a = \frac{324}{\tan 26.5^{\circ}}$ $a = 650$ mm (To three significant digits)

After you claim an answer you’ll have 24 hours to send in a draft. An editor will review the submission and either publish your submission or provide feedback.


text:
# Third Grade Question — This makes no sense to me?

Third grade grandchild had this for homework. I don't even know the intent here?

• Probably part of the idea is we can't add unlike objects. For example, adding a car and a truck means what? Unless of course we take cars and trucks as examples of automobiles so then adding a car and a truck makes perfect sense. As far as multiplication goes, I leave it to the experts here. Personally, the idea of identifying multiplication and addition as necessarily tied to counting or grouping problems has the unfortunate side-effect of saying addition and multiplication are necessarily those counting processes. But, they're not. Arithmetic exists independent from these heuristics. Imho. – James S. Cook Sep 12 '18 at 1:40
• It is unfathomable why someone believes that is a good homework question. Probably most mathematicians can't make any sense of it so how is a 3rd grader supposed to? – Bill Dubuque Sep 12 '18 at 2:30
• I would like to see questions 1-13. Perhaps they have more information or context about how the student has been taught addition and multiplication and what it means to "join groups." – ruferd Sep 12 '18 at 12:10
• I agree with ruferd. We cannot answer this, because we have not seen the previous material which may have explained what "join groups" means. – Gerald Edgar Sep 12 '18 at 13:27
• Is this even correct English? – Dominique Sep 13 '18 at 10:10

I am not too familiar with the Common Core State Standards Initiative (whose standards I assume the question above is intended to follow), but according to this introduction to the standards for Grade 3,

Students develop an understanding of the meanings of multiplication and division of whole numbers through activities and problems involving equal-sized groups, arrays, and area models; multiplication is finding an unknown product, and division is finding an unknown factor in these situations. For equal-sized group situations, division can require finding the unknown number of groups or the unknown group size.

and

Students recognize area as an attribute of two-dimensional regions. They measure the area of a shape by finding the total number of same-size units of area required to cover the shape without gaps or overlaps, a square with sides of unit length being the standard unit for measuring area. Students understand that rectangular arrays can be decomposed into identical rows or into identical columns. By decomposing rectangles into rectangular arrays of squares, students connect area to multiplication, and justify using multiplication to determine the area of a rectangle.

To me, it seems that the emphasis is on "equal-sized groups," "same-size units of area," "identical rows," and "identical columns." The child's teacher could have emphasized this in class.

If so, then perhaps one "valid" answer to this higher-order thinking question is "You can add objects together if they belong to the same group. You can multiply groups of objects if they are of the same size."

For example, say that students are riding in $3$ buses: one bus has $30$ students, another has $30$, and another has $32$. How many students are there in total?

The answer is not $30+30+32+3$, that is, the number of buses is not added because buses are not students.

The answer is not $30\times 3$, because not all the buses have exactly $30$ students.

• @user10216038: Regarding "What does it mean to Multiply Groups", I'm pretty sure Joel intended to describe a situation such as the following: Exactly $5$ groups of marbles such that each group contains exactly $3$ marbles represents (when brought together to form one group of marbles, without omitting or including other marbles) a group of $5(3) = 15$ marbles. And given that the context of this is math education, I think the shorthand phrasing he used was fine. And I agree with ruferd that this question is probably taken out of context, although personally I don't like the question. – Dave L Renfro Sep 12 '18 at 15:48
• Why one has to backtrack and decode this nonsense to figure out what the creator of the question meant? Are third-grade kids supposed to do this themselves? It is a rhetorical question. And by the way, slapping the "Common Core" label on a question does not make it Common Core, because Common Core is a set of requirements, not a curriculum. But parents think this nonsense IS Common Core. – Rusty Core Sep 12 '18 at 16:48
• "Why one has to backtrack and decode this" - because one was not present in class. – Jasper Sep 12 '18 at 19:14
• @Jasper No, it is because education goes through fads, and one of the current fads is "higher order thinking", so some dude created a murky question labelled just that. – Rusty Core Sep 12 '18 at 21:28
• Between the feedback here and some independent research of "Common Core" I think I understand the intent, although I still couldn't answer the problem as written. This seems to be math redefined by non-math people. Instead of "equations" it's now a "division sentence" or a "multiplication sentence". see: www.syracusecityschools.com/tfiles/folder748/Pages%20from%20math-g3-m1-topicC.pdf Thanks all! – user10216038 Sep 13 '18 at 14:49


text:
Math Notes

We’ll discuss many of the concepts in this chapter in depth later. But for now, we need a brief review of these concepts for many of the problems that follow.

1. To compare two fractions, cross-multiply. The larger product will be on the same side as the larger fraction.

Example: Given $\frac{5}{6}$ vs. $\frac{6}{7}$ . Cross-multiplying gives 5 × 7 vs. 6 × 6 , or 35 vs. 36. Now 36 is larger than 35, so $\frac{6}{7}$ is larger than $\frac{5}{6}$ .

2. Taking the square root of a fraction between 0 and 1 makes it larger.

Example: $\sqrt{\frac{1}{4}}$ =  $\frac{1}{2}$ and $\frac{1}{2}$ is greater than $\frac{1}{4}$ .

Caution: This is not true for fractions greater than 1. For example, $\sqrt{\frac{9}{4}}$ = $\frac{3}{2}$ . But $\frac{3}{2}$ < $\frac{9}{4}$

3. Squaring a fraction between 0 and 1 makes it smaller.

Example: ( $\frac{1}{2}$)2 = $\frac{1}{4}$ and $\frac{1}{4}$ is less than $\frac{1}{2}$

4. ax2 ≠ (ax)2. In fact, a2x2 = (ax)2 .

Example: 3 × 22 = 3 × 4 = 12 But (3 × 2)2 = 62 = 36 This mistake is often seen in the following form: x2 = (−x)2 To see more clearly why this is wrong, write x2 = (−1)x2 , which is negative. But (−x)2 = (−x)(−x) = x2 , which is positive.

Example: −52 = (−1)52 = (−1)25 = −25 But (−5)2 = (−5)(−5) = 5 • 5 = 25

5. $\frac{1/a}{b}$  ≠  $\frac{1}{a/b}$ In fact, $\frac{1/a}{b}$  =  $\frac{1}{ab}$ and $\frac{1}{a/b}$  =  $\frac{b}{a}$

Example: $\frac{1/2}{3}$ =  $\frac{1}{2}$ ×  $\frac{1}{3}$ = $\frac{1}{6}$ But $\frac{1}{2/3}$ = 1 ×  $\frac{3}{2}$ =  $\frac{3}{2}$

6. –(a + b) ≠ –a + b. In fact, –(a + b) = –a – b.

Example: –(2 + 3) = –5. But –2 + 3 = 1.

Example: –(2 + x) = –2 – x.

7. Memorize the following factoring formulas—they occur frequently on the GRE.

A. x2 − y2 = (x + y)(x - y)

B. x2 ± 2xy + y2 = (x ± y)2

C. a(b + c) = ab + ac

8. Know these rules for radicals:

A.  $\sqrt{x}\sqrt{y}$ = $\sqrt{xy}$
B.
$\sqrt{\frac{x}{y}}$ = $\frac{\sqrt{x}}{\sqrt{y}}$

9. Pythagorean Theorem (For right triangles only):

c2 = a2 + b2

Example: Which is greater column A or column B?

Column A = 10

Column B = The area of the triangle

Solution:

Since the triangle is a right triangle, the Pythagorean Theorem applies: h2 + 32 = 52 , where h is the height of the triangle. Solving for h yields h = 4.  Hence, the area of the triangle is
$\frac{1}{2}$(base)(height) = $\frac{1}{2}$(3)(4) = 6. Because 6 is less than 10,The answer is (A).

10. When parallel lines are cut by a transversal, three important angle relationships are formed:

11. In a triangle, an exterior angle is equal to the sum of its remote interior angles and therefore greater than either of them.

e = a + b  and e > a  and e > b

12. A central angle has by definition the same measure as its intercepted arc.

13. An inscribed angle has one-half the measure of its intercepted arc.

14. There are 180° in a straight angle.

15. The angle sum of a triangle is 180°.

Example: What is greater column A or column B ?

Column A = 30

Column B = The degree measure of angle c

Solution:

Since a triangle has 180˚, we get 100 + 50 + c = 180.  Solving for c yields c = 30. Hence, the columns are equal.

16. To find the percentage increase, find the absolute increase and divide by the original amount.

Example:  If a shirt selling for $18 is marked up to$20, then the absolute increase is 20 – 18 = 2.  Thus, the percentage increase is  = $\frac{2}{18}$ = $\frac{1}{9}$ ≈ 11%

17. Systems of simultaneous equations can most often be solved by merely adding or subtracting the equations.

Example:  If 4x + y = 14 and 3x + 2y = 13, then x – y =

Solution:

Merely subtract the second equation from the first:

18. Rounding Off: The convention used for rounding numbers is “if the following digit is less than five, then the preceding digit is not changed.  But if the following digit is greater than or equal to five, then the preceding digit is increased by one.”

Example: 65,439 —> 65,000 (following digit is 4)
5.5671 —> 5.5700 (dropping the unnecessary zeros gives 5.57)


text:
# Matlab pole zero to transfer function pdf

Zeros, poles and static gain of an lti model are computed with the commands zero. Matlab code to plot ber of qpsk under awgn channel method. Correlate pulse response in serdes designer to ibisami simulation in the serdes designer app, plot the ctle transfer function and pulse response from the add plots button. The zero pole block models a system that you define with the zeros, poles, and gain of a laplacedomain transfer function. Model system by zeropolegain transfer function matlab. Assume pole locations are 2, 1, zero at 1 and gain is 7.

Additionally, it should be noted here, that a direct manual propering of the improper. Drag a pole or a zero of a discrete system transfer function to a different location and observe the effect on the system. If sys is a transfer function or statespace model, it is first converted to zero pole gain form using zpk for siso zero pole gain models, the syntax. You can convert from transfer function to zeropole representation and vica versa using the following commands. The polezero splace plot can be zoomed in and out using a slider. Figure 1 is an example of a polezero plot for a thirdorder system with a single real zero, a real pole and a complex conjugate pole pair, that is. For mimo systems, pzmap plots the system poles and transmission zeros. Blue and red transfer functions are cleared when moving poles zeroes in the plane. Write matlab code to obtain transfer function of a system from its pole, zero, gain values.

Mcnames portland state university ece 222 transfer functions ver. Based on the transfer function, the poles and zeros can be defined as, a 1 2. Also, the influence of the transfer function zero with the time constant of 0. To study the poles and zeros of the noise component of an inputoutput model or a time series model, use noise2meas to first extract the noise model as an independent inputoutput model, whose inputs are the noise channels of the original model. Matlab can compute the poles and transmission zeros the. The rational function returns poles and residues, but you need to convert these into zeros, poles and gains for a ctle block. If b is a matrix, then each row of b corresponds to an output of the system. Control system toolbox software supports transfer functions that are continuoustime or discretetime, and siso or mimo. Represent transfer functions in terms of numerator and denominator coefficients or zeros, poles, and gain. It has two examples and the second example also shows how to find out the gain of a given transfer function.

You can create pole zero plots of linear identified models. Dynamic systems that you can use include continuoustime or discretetime numeric lti models such as tf, zpk, or ss models if sys is a generalized statespace model genss or an uncertain statespace model uss, zero returns the zeros of the current or nominal value of sys. Matlab provides transfer function and zeropolegain. Examples functions and other reference release notes pdf documentation.

Because the transfer function completely represents a system di. Since the poles are not strictly in the left half plane, the open loop system will be unstable as seen in the step response below. Z and p are cell arrays of vectors with as many rows as outputs and as many columns as inputs, and k is a matrix with as many rows as outputs and as many columns as inputs. For the design of a control system, it is important to understand how the system of interest behaves and how it responds to. How to find and plot zeros and poles of a transfer. Understanding poles and zeros 1 system poles and zeros.

Pole zero plot of transfer fucntion hz matlab answers. This block can model singleinput singleoutput siso and singleinput multipleoutput simo systems. With the transfer function now known, the numerator and denominator. Finding poles and zeros and other polynomial operations. Once the zeroespoles are movedaddeddeleted, the original calculation will not hold true any more. Rational function computing with poles and residues.

The ball and beam system is a type ii system which has two poles at the origin, as seen in the pole zero map below. Roots of transfer function numerator called the system zeros. Transfer function numerator coefficients, specified as a vector or matrix. Transfer function numerator coefficients, returned as a row vector or a matrix. A siso continuoustime transfer function is expressed as the ratio. Here, there poles and zeros of cl1 are blue, and those of cl2 are green the plot shows that all poles of cl1 are in the left halfplane, and therefore cl1 is stable. Understanding poles and zeros in transfer functions. In matlab project 2, you saw how the matlab residue function can help. Find zeros, poles, and gains for ctle from transfer function.

Only the first green transfer function is configurable. However the impulse response of the system is correct, but its only shifted to the right side by one. The models can have different numbers of inputs and outputs and can be a mix of continuous and discrete systems. Transfer function analysis by manipulation of poles and zeros. Tranferfunction from zeros and polesmatlab youtube. This representation can be obtained in both the ways from equations to pole zero plot and from pole zero plot to the equation. Your h here is not the same as the transfer function in your original post. A video that teaches you how to obtain a transfer function by taking zeros, poles and gain as input from the user. Create transfer function model using zeros, poles, and gain.

Observe the change in the magnitude and phase bode plots. This function has three poles, two of which are negative integers and one of which is zero. You can represent linear systems as transfer functions in polynomial or factorized zeropolegain form. Convert zeropolegain filter parameters to transfer. The characteristic equation, poles and zeros are then defined and calculated in closed form. May 26, 2019 weve explored the basic theoretical and practical aspects of transferfunction poles and zeros, and weve seen that we can create a direct relationship between a filters pole and zero frequencies and its magnitude and phase response. The zeropole block models a system that you define with the zeros, poles, and gain of a laplacedomain transfer function. This matlab function finds the matrix of zeros z, the vector of poles p, and the associated vector of gains k from the transfer function parameters b and a. There are no poles of ls in the right half plane so p 0. Polezero plot of dynamic system matlab pzmap mathworks. Click the pole zero plot toolbar button, select analysis pole zero plot from the menu, or type the following code to see the plot. Convert to zeros, poles, gains from poles and residues.

We use matlab to find the laplace transform of any symbolic function ft was and. If b is a matrix, then it has a number of rows equal to the number of columns of z. If sys is a transfer function or statespace model, it is first converted to zeropole gain form using zpk. If we rewrite this in a standard form such that the highest order term of the numerator and denominator are unity the reason for this is explained below. Fateman computer science division, eecs university of california, berkeley december 24, 2010 abstract computer algebra systems cas usually support computation with exact or approximate rational functions stored as ratios of polynomials in \expanded form with explicit coe cients. Use designfilt to generate d based on frequencyresponse specifications. This example shows how to examine the pole and zero locations of dynamic systems both graphically using pzplot and numerically using pole and zero examining the pole and zero locations can be useful for tasks such as stability analysis or identifying nearcanceling pole zero pairs for model simplification. But based on the matlab command to plot pole and zeros, zplanea,b i. If some io pairs have a common denominator, the roots of such io pair denominator are counted only once. In this tutorial we look at using the minreal function in matlab to perform pole zero cancellation from transfer functions. Specifying 1e7 as the second input causes minreal to eliminate pole zero pairs within 1 07 rads of each other. When an openloop system has righthalfplane poles in which case the system is unstable, one idea to alleviate the problem is to add zeros at the same locations as the unstable poles, to in effect cancel the unstable poles. Transfer function mostly used in control systems and signals and systems.

Access zeropolegain data matlab zpkdata mathworks italia. Let n order of as and m order of bs the order of a polynomial is the highest power of s that appears in it. In laplace space, the system is represented by the system has unit gain, a double zero at, and two complexconjugate poles. Zeros are defined as the roots of the polynomial of the numerator of a transfer function and poles are defined as the roots of the denominator of a transfer function. Tutorial to perform polynomial operations in matlab, including finding poles and zeros of a transfer function. In general, the poles and zeros of a transfer function may be. When you provide multiple models, pzplot plots the poles and zeros of each model in a different color.

Mar 23, 2014 a video that teaches you how to obtain a transfer function by taking zeros,poles and gain as input from the user. Matlab code is used to plot the polezero locations for the nine. All i can find are pole zero plots and that basically the poles define the system stability and time response. The pole zero and transfer function representations of a system are tightly linked. Dynamic system, specified as a siso dynamic system model, or an array of siso dynamic system models. Poles of dynamic system matlab pole mathworks deutschland. You can also have time delays in your transfer function representation. This means that the characteristic equation of the closed loop transfer function has no zeros in the right half plane the closed loop transfer function has no poles there. In the next article, well examine the transfer function of a firstorder highpass filter. Write matlab code to obtain transfer function of a system from its pole,zero, gain values. When the poles are visualized on the complex splane, then they must all lie in the lefthalf plane lhp to ensure stability.

Specifying 1e7 as the second input causes minreal to eliminate pole zero pairs within 1 0 7 rads of each other the reduced model tred includes all the dynamics of the original closedloop model t, except for the nearcanceling zero pole pair. By default, minreal reduces transfer function order by canceling exact pole zero pairs or near pole zero pairs within sqrteps. Zeropole plot for discretetime systems matlab zplane. Transfer functions transfer function representations. W e w ould still lik them to resp ectiv ely ha v t h i n terpretations of generated and absorb ed frequencies, in some sense, but that still lea v es us with man y c hoices. For siso transfer functions or zeropolegain models, the poles are the. Convert zeropolegain filter parameters to transfer function. The output k is a matrix with as many rows as outputs and as many columns as inputs such that ki,j is the gain of the transfer function from input j to output i. I know that the zeros are the frequencies where the numerator of a transfer function becomes zero. We can get the poles, zeros and gain for any transfer function and plot the. Transfer functions in matlab top 3 methods examples.

This matlab function returns the poles of the siso or mimo dynamic system. This demonstration shows how the locations of poles and zeros of the system transfer function affect the system properties. Then copy the value of the gpz variable and paste it to the gain pole zero matrix parameter. Run the command by entering it in the matlab command window. Compute the transfer function of a damped massspring system that obeys the differential equation the measurable quantity is the acceleration, and is the driving force. The ctle can be configured to use specification parameter gpz matrix where the units for gains, poles and zeros. This video explains how to obtain the zeros and poles of a given transfer function. Polezero cancellation in matlab matlab programming. Rational function computing with poles and residues richard j. Matlab solution and plot of poles and zeros of ztransform. Polezero cancellation control tutorials for matlab.

The transfer function of the preloaded highpass and lowpass filters is scaled to achieve 0 db attenuation at 0 infinity, respectively. Plot the poles and zeros of the continuoustime system represented by the following transfer function. Convert transfer function filter parameters to zeropolegain. This matlab function creates a pole zero plot of the continuous or discretetime dynamic system model sys. Model system by zeropolegain transfer function simulink. Convert transfer function filter parameters to zeropole. Calculate poles and zeros from a given transfer function.

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text:
Should frame rate affect the speed in a game engine?

I am writing a 2D game engine for fun. I am able to perform animation using the engine. However, if I change the frame rate (frames per second) the speed of the animation changes.

I have never used any game engine. I want to know whether other game engines handle this issue or not. If not, what is the ideal frame rate for a 2D game?

No, frame rate should not affect the speed - the gameplay will hinge entirely on their video performance, which is disastrous (even if you limit the speed, you can't control people whose systems will run the game at half speed).

You're experiencing this problem because you did something wrong: Your update/render routines run one after the other as fast as possible, with objects updating on a per-call basis (thus when the call speed deviates, so does theirs).

A time-based approach

The correct way to do this is to update objects on a per-second basis.

Consider a bullet for instance: Right now it probably knows how much it needs to move per frame. You need to turn this into how much it moves per second. How you do that is actually not too complicated.

First, your bullet's going to be updated more than once per second, so we need to actually update it every few milliseconds. Each time you update your physics engine, a certain number of milliseconds have passed since the last update: this is called the delta time, normally dt for short. The dt is determined before updating all objects, then all objects update using the same dt in order to keep in synch. The dt is generally passed as an argument to each object in its update call.

In fixed-step physics, the dt is a fixed number, whereas in variable-step physics, the dt varies depending on the actual amount of time since the last update (hence their names).

That brings us back to your bullet. It's been told to update with a dt of 16 milliseconds, for a physics engine updated 60 times per second: if the bullet moves 12 metres per second, you move it (16.0/1000.0) * 12.0 metres in this update.

• This approach is not ideal for numerous reasons. Gameplay will be non-deterministic, making multiplayer syncing much harder than it should be. If the update rate slows down enough, objects could tunnel through barriers, or collisions that should happen could be skipped over. – AttackingHobo Jun 15 '11 at 20:10
• That is why the time passed (dt) can be clamped, meaning from frames per second 5 - 1000, your engine works correctly. Below 5fps, you will get a slowing of time (ie the dt is clamped). – deceleratedcaviar Jun 15 '11 at 21:00
• @Daniel, It is still non-deterministic, making synced network simulations, or a replay system much more difficult to implement. And if you were to create a Rube Goldberg type puzzle game, after a few seconds the simulation will not replay the same way each time. – AttackingHobo Jun 16 '11 at 16:00
• Ah, for some reason I thought he was using a fixed time step with dt stepping... So yoir right, this is bad. – deceleratedcaviar Jun 16 '11 at 21:58
• To be fair, this approach is more than good enough for anything not performing complex physics, and has worked in many shipped games. So it's best not to get too worried about needing the fixed time step and interpolated rendering, etc. – Kylotan Jun 17 '11 at 11:19

The best way to make your game run the same speed on all systems is to use a Fixed Timestep.

With a fixed timestep, the game will always update at the same rate, no matter what the render rate is, and when using interpolation, it will look smooth even when the render rate is much higher than the update rate.

Here is an answer with resources on how to implement a fixed timestep.
Semi-fixed or Fully-fixed timestep?

Here is an answer that explains how to implement interpolation for movement and transformations.
How to Interpolate between two game states?

No it should not. One type of timing you can do in your game is frame-based timing. The idea is to let the game loop run as fast as your computer can run it thereby having the bast overall experience and you control the rate at which your simulation runs. Now you've decoupled your updating from rendering and have precise control over it.

In this scenario, your game loop can be running at say 60 fps on one machine and maybe 45 or something different on another, but your simulation will always run at the precise specified rate between them.