I'm trying to model the flow and suspension of microcarriers (particles that are used as surfaces for cells to attach to and grow on) in a CFD application. I know some basic characteristics of the particles (they're called "Cytodex", about 180 µm big, density is 1.03g/cm^2) but I'd like to find the Stokes number to determine how strongly they are affected by turbulence and movement of the fluid. Can somebody point me to how to approach this (or at least approximate?). It's surprisingly hard to find any information for somebody like me who hasn't got a very strong background in fluid mechanics.
Here is the manufacturer's microcarrier manual. See page 62, Table 12 for Cytodex 1 physical properties.
https://www.gelifesciences.co.kr/wp-content/uploads/2016/07/023.8_Microcarrier-Cell-Culture.pdf
See this SlideShare, slide 15, for how to calculate the Stokes # for Cytodex 1 microcarriers: https://www.slideshare.net/rjrishabhjain/bs-4sedimentation?from_action=save
but for Cytodex 1 correct the d=180 um, for cell culture media=nutrient broth viscosity = 0.96 cP, media density ~ 1.007g/mL, microcarrier density 1.03 g/mL, to get settling velocity of 0.062cm/s = 3.72 cm/min. However, per the manufacturer's manual settling velocity is 12-16mL/min. Might be an error. I am seeing an answer.
For CFD modeling of microcarriers in bioreactors see: Loubière
https://pdfs.semanticscholar.org/d955/75b5c640c8268fd1ec51b2ce46862e7bbfbd.pdf
I have more related literature if you have interest.
DApple
Related
I am trying to model the interior of an epithelial space and am stuck on movement around the interior edges of a cylindrical space. Basically, I'm trying to implement StickyBorders and keep agents on those borders in a cylindrical space that I am creating.
Is there a way to use cylindrical coordinates in Repast Simphony? I found this example (https://www.researchgate.net/publication/259695792_An_Agent-Based_Model_of_Vascular_Disease_Remodeling_in_Pulmonary_Arterial_Hypertension) where they seem to have done something similar, but the paper doesn't explain methods in much depth, and I don't believe this is an example in the repast simphony models.
Currently, I have a class of epithelial cells that are set up to form a cylinder and other agents start just inside that cylinder. To move, they are choosing their most desired spot (similar to the Zombie code) then pointing to a new location in the direction of that desired location within one grid square of that original location. They check that new point before moving to it and make sure that there are at least two other epithelial cells in the immediate moore neighborhood, to ensure they stay against the wall.
GridPoint intendedpt = new GridPoint((int)Math.rint(alongX),(int)Math.rint(alongY),(int)Math.rint(alongZ));
GridCellNgh<EpithelialCell> nearEpithelium = new GridCellNgh<EpithelialCell>(mac_grid, intendedpt, EpithelialCell.class, 1,1,1);
List<GridCell<EpithelialCell>> EpiCells = nearEpithelium.getNeighborhood(false);
int nearbyEpiCellsCount=0;
for (GridCell<EpithelialCell> cell: EpiCells) {
nearbyEpiCellsCount++;
}
if (nearbyEpiCellsCount<2) {
System.out.println(this + " leaving epithelial wall /r");
RunEnvironment.getInstance().pauseRun();
//TODO: where to go if false
}
I am wondering if there is a way to either set the boundaries of the space to be a cylinder or to check which side of the agent is against the wall and restrict its movement in that direction.
The sticky border code (StickyBorders.java) essentially just checks if the point that the agent moves to is beyond any of the space's dimensions, and if so the point is clamped to that dimension. So, for example, if the space is 3x4 and an agent's movement would take it to 4,2, then that point becomes 3,2 and the agent is placed there. Can you do something like that in this case? If not, can you edit your question to explain why not and maybe that will help us understand better.
The approach we took in that model was to use a 3D grid space with custom borders and query methods. The space itself was still Cartesian - we just visualized it as a cylinder using custom display code. Using the Cartesian grid was an reasonable approximation for this application since the cell dimensions were significantly smaller that the vessel radius, so curvature effects were neglected. The boundary conditions on the vessel space were wrap around in the angular dimension, so that cells could move continuously around the circumference of the vessel, and the axial boundary conditions were also wrapped, as we assumed a long enough vessel length that this would be reasonable. The wall thickness dimension had hard boundaries at the basement membrane (y=0) and at the fluid interface (y=wall thickness).
Depending on which type of space you are using, you will need to implement a PointTranslator or GridPointTranslator that performs the border functions. If you want specific examples of the code I suggest you reach out to the author's directly.
This is more of an open discussion topic than anything else. Currently I'm storing 50 Float32 values in my NSMutableArray *voltageArray before I refresh my CPTPlot *plot. Every time I obtain 50 values, I remove the previous 50 from the voltageArray and repeat the process....always displaying the 50 values in "real time" on my plot.
However, the data I'm receiving (which is voltage coming from a Cypress BLE module equipped with a pressure transducer) is so quick that any variation (0.4 V to 4.0 V; no pressure to lots of pressure) cannot be seen on my graph. It just shows up as a straight line, varying up and down without showing increased or decreased slopes.
To show overall change, I wanted to take those 50 values, store them in the first index of another NSMutableArray *stampArray and use the index of stampArray to display information. Meanwhile, the numberOfRecordsForPlot: method would look like this:
- (NSUInteger)numberOfRecordsForPlot:(CPTPlot *)plotnumberOfRecords {
return (DATA_PER_STAMP * _stampCount);
}
This would initially be 50, then after 50 pieces of data are captured from the BLE module, _stampCount would increase by one, and the number of records for plot would increase by 50 (till about 2500-10000 range, then I'd refresh the whole the thing and restart the process.)
Is this the right approach? How would I be able to make the first 50 points stay on the graph, while building the next 50, etc.? Imagine an y = x^2 graph, and what the graph looks like when applying integration (the whole breaking the area under the curve into rectangles).
Look at the "Real Time Plot" demo in the Plot Gallery example app included with Core Plot. It starts off with an empty plot, adding a new point each cycle until reaching the maximum number of points. After that, one old point is removed for each new one added so the total number stays constant. The demo uses a timer to pass random data to the plot, but your app can of course collect data from anywhere. Be sure to always interact with the graph from the main thread.
I doubt you'll be able to display 10,000 data points on one plot (does your display have enough pixels to resolve that many points?). If not, you'll get much better drawing performance if you filter and/or smooth the data to remove some of the points before sending them to the plot.
So, I searched through the documentation on AI CS6's Scripting Reference (JavaScript / though actually ECMAScript), and I cannot find anything for managing units, or unit conversion. Is it missing?
Photoshop uses ECMAScript's UnitValue object as a standard way for managing unit conversion, but I can't find anything for Illustrator. Illustrator functions do not accept UnitValue instances - they only accept doubles, in the "points" unit.
How am I supposed to manage units in AI?
Or, if nothing else, how do I run conversions from a given unit to points?
p.s. Why is it points anyway? Is that script-default? My current default unit is inches.
Answers to all your questions can be found in the Adobe Illustrator Scripting Guide (CS6 on the Adobe home page) in the Measurement units section. This section seem to remain unchanged for years.
In particular,
"Illustrator uses points when communicating with your scripts
regardless of the current ruler units"
"If your script depends on [...] units other than points, it must perform any unit conversions needed to represent your measurements as points."
Precise conversion rules: 1 inch = 72 points, 1 inch = 2.54 cm, 1 pica = 12 points
Try setting required units without conversion (replace PIXELS to probably POINTS):
//at start of script:
var originalUnit=preferences.rulerUnits;//alert(originalUnit);
preferences.rulerUnits = Units.PIXELS;//alert(preferences.rulerUnits);
//your main code here
//at the end - restore units:
preferences.rulerUnits = originalUnit;
I have a game I am working on that has homing missiles in it. At the moment they just turn towards their target, which produces a rather dumb looking result, with all the missiles following the target around.
I want to create a more deadly flavour of missile that will aim at the where the target "will be" by the time it gets there and I am getting a bit stuck and confused about how to do it.
I am guessing I will need to work out where my target will be at some point in the future (a guess anyway), but I can't get my head around how far ahead to look. It needs to be based on how far the missile is away from the target, but the target it also moving.
My missiles have a constant thrust, combined with a weak ability to turn. The hope is they will be fast and exciting, but steer like a cow (ie, badly, for the non HitchHiker fans out there).
Anyway, seemed like a kind of fun problem for Stack Overflow to help me solve, so any ideas, or suggestions on better or "more fun" missiles would all be gratefully received.
Next up will be AI for dodging them ...
What you are suggesting is called "Command Guidance" but there is an easier, and better way.
The way that real missiles generally do it (Not all are alike) is using a system called Proportional Navigation. This means the missile "turns" in the same direction as the line-of-sight (LOS) between the missile and the target is turning, at a turn rate "proportional" to the LOS rate... This will do what you are asking for as when the LOS rate is zero, you are on collision course.
You can calculate the LOS rate by just comparing the slopes of the line between misile and target from one second to the next. If that slope is not changing, you are on collision course. if it is changing, calculate the change and turn the missile by a proportionate angular rate... you can use any metrics that represent missile and target position.
For example, if you use a proportionality constant of 2, and the LOS is moving to the right at 2 deg/sec, turn the missile to the right at 4 deg/sec. LOS to the left at 6 deg/sec, missile to the left at 12 deg/sec...
In 3-d problem is identical except the "Change in LOS Rate", (and resultant missile turn rate) is itself a vector, i.e., it has not only a magnitude, but a direction (Do I turn the missile left, right or up or down or 30 deg above horizontal to the right, etc??... Imagine, as a missile pilot, where you would "set the wings" to apply the lift...
Radar guided missiles, which "know" the rate of closure. adjust the proportionality constant based on closure (the higher the closure the faster the missile attempts to turn), so that the missile will turn more aggressively in high closure scenarios, (when the time of flight is lower), and less aggressively in low closure (tail chases) when it needs to conserve energy.
Other missiles (like Sidewinders), which do not know the closure, use a constant pre-determined proportionality value). FWIW, Vietnam era AIM-9 sidewinders used a proportionality constant of 4.
I've used this CodeProject article before - it has some really nice animations to explain the math.
"The Mathematics of Targeting and Simulating a Missile: From Calculus to the Quartic Formula":
http://www.codeproject.com/KB/recipes/Missile_Guidance_System.aspx
(also, hidden in the comments at the bottom of that article is a reference to some C++ code that accomplishes the same task from the Unreal wiki)
Take a look at OpenSteer. It has code to solve problems like this. Look at 'steerForSeek' or 'steerForPursuit'.
Have you considered negative feedback on the recent change of bearing over change of time?
Details left as an exercise.
The suggestions is completely serious: if the target does not maneuver this should obtain a near optimal intercept. And it should converge even if the target is actively dodging.
Need more detail?
Solving in a two dimensional space for ease of notation. Take \vec{m} to be the location of the missile and vector \vec{t} To be the location of the target.
The current heading in the direction of motion over last time unit: \vec{h} = \bar{\vec{m}_i - \vec{m}_i-1}}. Let r be the normlized vector between the missile and the target: \vec{r} = \bar{\vec{t} - \vec{m}}. The bearing is b = \vec{r} \dot \vec{h} Compute the bearing at each time tick, and the change thereof, and change heading to minimize that quantity.
The math is harrier in 3d because of the need to find the plane of action at each step, but the process is the same.
You'll want to interpolate the trajectory of both the target and the missile as a function of time. Then look for the times in which the coordinates of the objects are within some acceptable error.
I'm not talking about algorithmic stuff (eg use quicksort instead of bubblesort), and I'm not talking about simple things like loop unrolling.
I'm talking about the hardcore stuff. Like Tiny Teensy ELF, The Story of Mel; practically everything in the demoscene, and so on.
I once wrote a brute force RC5 key search that processed two keys at a time, the first key used the integer pipeline, the second key used the SSE pipelines and the two were interleaved at the instruction level. This was then coupled with a supervisor program that ran an instance of the code on each core in the system. In total, the code ran about 25 times faster than a naive C version.
In one (here unnamed) video game engine I worked with, they had rewritten the model-export tool (the thing that turns a Maya mesh into something the game loads) so that instead of just emitting data, it would actually emit the exact stream of microinstructions that would be necessary to render that particular model. It used a genetic algorithm to find the one that would run in the minimum number of cycles. That is to say, the data format for a given model was actually a perfectly-optimized subroutine for rendering just that model. So, drawing a mesh to the screen meant loading it into memory and branching into it.
(This wasn't for a PC, but for a console that had a vector unit separate and parallel to the CPU.)
In the early days of DOS when we used floppy discs for all data transport there were viruses as well. One common way for viruses to infect different computers was to copy a virus bootloader into the bootsector of an inserted floppydisc. When the user inserted the floppydisc into another computer and rebooted without remembering to remove the floppy, the virus was run and infected the harddrive bootsector, thus permanently infecting the host PC. A particulary annoying virus I was infected by was called "Form", to battle this I wrote a custom floppy bootsector that had the following features:
Validate the bootsector of the host harddrive and make sure it was not infected.
Validate the floppy bootsector and
make sure that it was not infected.
Code to remove the virus from the
harddrive if it was infected.
Code to duplicate the antivirus
bootsector to another floppy if a
special key was pressed.
Code to boot the harddrive if all was
well, and no infections was found.
This was done in the program space of a bootsector, about 440 bytes :)
The biggest problem for my mates was the very cryptic messages displayed because I needed all the space for code. It was like "FFVD RM?", which meant "FindForm Virus Detected, Remove?"
I was quite happy with that piece of code. The optimization was program size, not speed. Two quite different optimizations in assembly.
My favorite is the floating point inverse square root via integer operations. This is a cool little hack on how floating point values are stored and can execute faster (even doing a 1/result is faster than the stock-standard square root function) or produce more accurate results than the standard methods.
In c/c++ the code is: (sourced from Wikipedia)
float InvSqrt (float x)
{
float xhalf = 0.5f*x;
int i = *(int*)&x;
i = 0x5f3759df - (i>>1); // Now this is what you call a real magic number
x = *(float*)&i;
x = x*(1.5f - xhalf*x*x);
return x;
}
A Very Biological Optimisation
Quick background: Triplets of DNA nucleotides (A, C, G and T) encode amino acids, which are joined into proteins, which are what make up most of most living things.
Ordinarily, each different protein requires a separate sequence of DNA triplets (its "gene") to encode its amino acids -- so e.g. 3 proteins of lengths 30, 40, and 50 would require 90 + 120 + 150 = 360 nucleotides in total. However, in viruses, space is at a premium -- so some viruses overlap the DNA sequences for different genes, using the fact that there are 6 possible "reading frames" to use for DNA-to-protein translation (namely starting from a position that is divisible by 3; from a position that divides 3 with remainder 1; or from a position that divides 3 with remainder 2; and the same again, but reading the sequence in reverse.)
For comparison: Try writing an x86 assembly language program where the 300-byte function doFoo() begins at offset 0x1000... and another 200-byte function doBar() starts at offset 0x1001! (I propose a name for this competition: Are you smarter than Hepatitis B?)
That's hardcore space optimisation!
UPDATE: Links to further info:
Reading Frames on Wikipedia suggests Hepatitis B and "Barley Yellow Dwarf" virus (a plant virus) both overlap reading frames.
Hepatitis B genome info on Wikipedia. Seems that different reading-frame subunits produce different variations of a surface protein.
Or you could google for "overlapping reading frames"
Seems this can even happen in mammals! Extensively overlapping reading frames in a second mammalian gene is a 2001 scientific paper by Marilyn Kozak that talks about a "second" gene in rat with "extensive overlapping reading frames". (This is quite surprising as mammals have a genome structure that provides ample room for separate genes for separate proteins.) Haven't read beyond the abstract myself.
I wrote a tile-based game engine for the Apple IIgs in 65816 assembly language a few years ago. This was a fairly slow machine and programming "on the metal" is a virtual requirement for coaxing out acceptable performance.
In order to quickly update the graphics screen one has to map the stack to the screen in order to use some special instructions that allow one to update 4 screen pixels in only 5 machine cycles. This is nothing particularly fantastic and is described in detail in IIgs Tech Note #70. The hard-core bit was how I had to organize the code to make it flexible enough to be a general-purpose library while still maintaining maximum speed.
I decomposed the graphics screen into scan lines and created a 246 byte code buffer to insert the specialized 65816 opcodes. The 246 bytes are needed because each scan line of the graphics screen is 80 words wide and 1 additional word is required on each end for smooth scrolling. The Push Effective Address (PEA) instruction takes up 3 bytes, so 3 * (80 + 1 + 1) = 246 bytes.
The graphics screen is rendered by jumping to an address within the 246 byte code buffer that corresponds to the right edge of the screen and patching in a BRanch Always (BRA) instruction into the code at the word immediately following the left-most word. The BRA instruction takes a signed 8-bit offset as its argument, so it just barely has the range to jump out of the code buffer.
Even this isn't too terribly difficult, but the real hard-core optimization comes in here. My graphics engine actually supported two independent background layers and animated tiles by using different 3-byte code sequences depending on the mode:
Background 1 uses a Push Effective Address (PEA) instruction
Background 2 uses a Load Indirect Indexed (LDA ($00),y) instruction followed by a push (PHA)
Animated tiles use a Load Direct Page Indexed (LDA $00,x) instruction followed by a push (PHA)
The critical restriction is that both of the 65816 registers (X and Y) are used to reference data and cannot be modified. Further the direct page register (D) is set based on the origin of the second background and cannot be changed; the data bank register is set to the data bank that holds pixel data for the second background and cannot be changed; the stack pointer (S) is mapped to graphics screen, so there is no possibility of jumping to a subroutine and returning.
Given these restrictions, I had the need to quickly handle cases where a word that is about to be pushed onto the stack is mixed, i.e. half comes from Background 1 and half from Background 2. My solution was to trade memory for speed. Because all of the normal registers were in use, I only had the Program Counter (PC) register to work with. My solution was the following:
Define a code fragment to do the blend in the same 64K program bank as the code buffer
Create a copy of this code for each of the 82 words
There is a 1-1 correspondence, so the return from the code fragment can be a hard-coded address
Done! We have a hard-coded subroutine that does not affect the CPU registers.
Here is the actual code fragments
code_buff: PEA $0000 ; rightmost word (16-bits = 4 pixels)
PEA $0000 ; background 1
PEA $0000 ; background 1
PEA $0000 ; background 1
LDA (72),y ; background 2
PHA
LDA (70),y ; background 2
PHA
JMP word_68 ; mix the data
word_68_rtn: PEA $0000 ; more background 1
...
PEA $0000
BRA *+40 ; patched exit code
...
word_68: LDA (68),y ; load data for background 2
AND #$00FF ; mask
ORA #$AB00 ; blend with data from background 1
PHA
JMP word_68_rtn ; jump back
word_66: LDA (66),y
...
The end result was a near-optimal blitter that has minimal overhead and cranks out more than 15 frames per second at 320x200 on a 2.5 MHz CPU with a 1 MB/s memory bus.
Michael Abrash's "Zen of Assembly Language" had some nifty stuff, though I admit I don't recall specifics off the top of my head.
Actually it seems like everything Abrash wrote had some nifty optimization stuff in it.
The Stalin Scheme compiler is pretty crazy in that aspect.
I once saw a switch statement with a lot of empty cases, a comment at the head of the switch said something along the lines of:
Added case statements that are never hit because the compiler only turns the switch into a jump-table if there are more than N cases
I forget what N was. This was in the source code for Windows that was leaked in 2004.
I've gone to the Intel (or AMD) architecture references to see what instructions there are. movsx - move with sign extension is awesome for moving little signed values into big spaces, for example, in one instruction.
Likewise, if you know you only use 16-bit values, but you can access all of EAX, EBX, ECX, EDX , etc- then you have 8 very fast locations for values - just rotate the registers by 16 bits to access the other values.
The EFF DES cracker, which used custom-built hardware to generate candidate keys (the hardware they made could prove a key isn't the solution, but could not prove a key was the solution) which were then tested with a more conventional code.
The FSG 2.0 packer made by a Polish team, specifically made for packing executables made with assembly. If packing assembly isn't impressive enough (what's supposed to be almost as low as possible) the loader it comes with is 158 bytes and fully functional. If you try packing any assembly made .exe with something like UPX, it will throw a NotCompressableException at you ;)