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Biophotonics - Science topic

Biophotonics considers engineering in applications of light for diagnostics and therapy
Questions related to Biophotonics
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1. The necessity of a polarization controller for single-mode fiber. Is a polarization controller necessary for single-mode fibers? What happens when you don't have a polarization controller?
2. Optical path matching problem. How to ensure that the two arms of the optical path difference match, any tips in the adjustment process? If the optical path difference exceeds the imaging distance, will interference fringes fail to appear?
Only these questions for the time being, if there are more welcome to point out.
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1. The polarization can change during propagation. This will degrade the visibility of the fringes. You need a polarization controller or a polarization-maintaining fiber.
2. By the imaging distance, do you mean the distance to the sample or the sample's dimension? In any case, if the OPD exceeds the coherence lenght of your source, the interference fringes disappear. In order to match the OPD, we typically sweep the reference arm a long distance and record the output intensity. Another method is to monitor the output spectrum using a spectrometer. The spectrum shows oscillations for non-zero OPD. When the OPD approaches zero, the spectrum oscillations tend to disappear.
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There are some interesting challenges for DAS systems in fields of agri-biophotonics and/or biophotonics - from vibration impact studies on the roots of growing plants to sea fauna acoustics monitoring, but researchers usually prefer array of single sensors or quasi-distributed sensors. Or maybe you know the examples with the DAS application? Thank you!
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There were two related talks that presented very promising results at the 2022 DCLDE workshop (see https://www.soest.hawaii.edu/ore/dclde/program/ )
Léa Bouffaut- Listening at the speed of light: baleen whale monitoring using distributed acoustic sensing
William Wilcock- A Community Test of Distributed Acoustic Sensing on the Ocean Observatories Initiative Regional Cabled Array Offshore Central Oregon
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I have recorded hologram is best on digital in-line holography technique. The distance between the objects and the sensor (CMOS sensor,taking from web cam) is typically 5 mm. The illumination source is LED ,that is placed at a distance of 5 cm from the sample and is filtered through a large pinhole having a diameter of 0.1 mm .
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Kamrul Hasan You can easily get the phase of refractive index, thickness, etc. for the desired hologram, which I edited for you.
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BER analyzer parameters meaning.
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The reliability of data transmission characterizes the probability of getting a distortion for the transmitted data bit. This indicator is often referred to as the Bit Error Rate (BER). The BER value for communication channels without additional means of error protection is 10-4 — 10-6, in optical fiber — 10-9. A ber value of 10-4 indicates that on average, one bit is distorted out of 10,000 bits. The q-factor of the receiving system Q is determined from the expression:
Q = GA/TC,
or, in logarithmic form:
Q[dB] = GA[dB] - 10lgTC[x].
It is the q-factor of the receiving system that determines the signal-to-noise ratio (C/N) at the output of the low-noise Converter (LNC or LNB). It is important to note that the final C/N value does not depend on the LNC gain.
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I'm searching a valid tutorial book to understand the principle of machine learning theory in order to apply directly to solve some problem in the field of bio-photonics to classify some species. I use Matlab and so I will prefer to use it as solver.
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Machine learning a probabilistic perspective Murphy
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If I am interested in lasers, optical communication, nanomaterials, electro-optics, and biophotonics, what organizations should I join as a student?
Edit: I am seeking an organization that would help me in my research.
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And of course my Alma Mater, Heriot-Watt University in Edinburgh!
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Hello,
there is a lot of data, opinions and the like available about Biophotons. Many papers reveal, that organic matter may emit photons and it is argued that cells communicate by this.
If this is so, than there should be evidence that cells also ABSORB biophotons which other cells emitted.
How has this been proved?
Lothar
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Dear Lothar,
I send you a link (google Scholar) :
and
and
I tried to find newer articles investigating this further.... (see above in your answer) ( citation/Lothar dixit)
2009 is better than eighties
JRG
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what does optical output scaled by photon number mean? what is the difference from normal optical output calculations, for example if we are calculating optical efficiency or relative optical efficiency for an optical system(CPV), what does scaling by photon number mean and how does the results change from the regular calculations ?
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Interesting. PMT (photo multiplier tube) actually increases the number of photons, thus increasing the signal. So when a PMT is in use, a count is different than the input photons. However, under certain circumstances, photon counting depends upon the detector area, generated current, signal timing and other factors such as the Fermi energy of the detector material. Hence, photons are counted under controlled conditions and used for calibration/scaling. For example, the dark current before a measurement. 
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Dear community,
I do not have access in the ICRU report 46 and I am not able to retrieve complete information regarding the tissue composition of prostate, urethra and rectum for a Monte Carlo simulation of brachytherapy that I want to do. Is there any knowledge regarding the composing elements, their ratios and the density of each of these three structures? Any bibliographic reference is also well appreciated.
Thank you in advance,
Konstantinos. 
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I'd like to hear from anybody who used/developed laser scalpels: general descriptions, types of surgeries, clinicians feedback, references.
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Coagulation and ablation of biological soft tissue by quantum cascade laser with peak wavelength of 5.7 μm.
Molecules such as water, proteins and lipids that are contained in biological tissue absorb mid-infrared (MIR) light, which allows such light to be used in laser surgical treatment. Esters, amides and water exhibit strong absorption bands in the 5–7 μm wavelength range, but at present there are no lasers in clinical use that can emit in this range. Therefore, the present study focused on the quantum cascade laser (QCL), which is a new type of semiconductor laser that can emit at MIR wavelengths and has recently achieved high output power. A high-power QCL with a peak wavelength of 5.7 μm was evaluated for use as a laser scalpel for ablating biological soft tissue. The interaction of the laser beam with chicken breast tissue was compared to a conventional CO2 laser, based on surface and cross-sectional images. The QCL was found to have sufficient power to ablate soft tissue, and its coagulation, carbonization and ablation effects were similar to those for the CO2 laser. The QCL also induced comparable photothermal effects because it acted as a pseudo-continuous wave laser due to its low peak power. A QCL can therefore be used as an effective laser scalpel, and also offers the possibility of less invasive treatment by targeting specific absorption bands in the MIR region.
Read More: Keisuke Hashimura et al, J. Innov. Opt. Health Sci. 07, 1450029 (2014).
Regards, Leonid Skvortsov
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I am working on 'Quantification glistenings in IOL's using Scheimpflug images &ImageJ software', for the further analysis I need to use a macro(in Excel) to calculate the light scattering against the light scattering in the aqueous humor. Anybody can help me with the macro or any advise for analyzing?
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It is not clear what you are asking specifically. Is your analysis algorithm unclear or the implementation as a macro? Shall it be a macro in ImageJ or Excel? What did you try already and what is your specific problem?
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Also give the refractive index of flat rice and puffed rice ?
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I think this would depend greatly on the hydration level of the rice grain.  
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After time lapse imaging of live cells, I need to track single cells to analyze motility from a series of bright field images in stack. Looking for a software which does that. I found a plug in called Trackmate in Fiji (an extended ImgaeJ version) but wonder whether that plug in can track cells in images other than those obtained from fluorescence imaging. 
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Brightfield is a difficult modality for cell tracking.  Fluorescence is much more robust.  You should definitely avoid DIC and try to get the most uniform illumination possible.  CellTrack is the only program I have found to repeatably segment transmitted light images: http://bio.cse.ohio-state.edu/CellTrack/.
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Hello guys as we know Bessel Beam Microscopy (BBM)  is a near to far field microscopy, Can anyone explain its limitations and possible solutions???
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Dear Kaleem,
A maximum magnification achieved by Bessel Beam Microscopy is up to 1000X. The degree of magnification achieved by the electron Bessel beams  could be improved simply by increasing krough, due to the corresponding decrease in beam central spot size. However, increases in krough are met by corresponding increases in the focal point of the first diffracted order. In order to ensure that the beam remains focused on the sample, it then becomes necessary to compensate for this effect by reducing lens excitation, therefore decreasing the demagnification factor of the system. The compensatory measures designed to re-focus the electron beam therefore ultimately cancel any benefit that might otherwise arise from an increase in the transverse wavenumber krough, This limitation could certainly be overcome by a more flexible illumination scheme, however. increasing the size of the hologram aperture would not improve the quality of images obtained in the configuration. The beam convergence is not determined by the size of the aperture in the Fresnel regime.
For more on this topic, please see the following publication:
Generation and Application of Bessel Beams in Electron Microscopy
Vincenzo Grillo, Jérémie Harris , Gian Carlo Gazzadi, Roberto Balboni
Erfan Mafakheri, Mark R. Dennis, Stefano Frabboni, Robert W. Boyd, Ebrahim Karimi
Abstract
We report a systematic treatment of the holographic generation of electron  Bessel beams, with a view to applications in electron microscopy. We describe in detail the theory underlying hologram patterning, as well as the actual electrooptical configuration used experimentally. We show that by optimizing our nanofabrication recipe, electron Bessel beams can be generated with efficiencies reaching 37±3%. We also demonstrate by tuning various hologram parameters that electron Bessel beams can be produced with many visible rings, making them ideal for interferometric applications, or in more highly localized forms with fewer rings, more suitable for imaging. We describe the settings required to tune beam localization in this way, and explore beam and hologram configurations that allow the convergences and topological charges of electron Bessel beams to be controlled. We also characterize the phase structure of the Bessel beams generated with our technique, using a simulation procedure that accounts for imperfections in the hologram manufacturing process. Finally, we discuss a specific potential application of electron Bessel beams in scanning transmission electron microscopy.
Hoping this will be helpful,
Rafik
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Hello dear researchers, I have a question as we all know that the evanescent field is a non-propagating field it die quickly with distance which means photon counting decrease , I want to ask that is polarization status still there in those photons in other words is polarization continue keeping its persistency even after 2 to 3 microns even when the field is much low. if that then it can give us the pattern of the near field? Am i right? Please give your comments? if we go with polarization status then can we get more information about near field signals and to a larger range?
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Hello Kaleem. 1st: by referring to evanescant field, do you relate to the decaying part of any mode that is outside the guiding core? if that is the case, then it decays transversely. If you relate to the continuum field that is not bounded by the waveguide, i.e. tunnels out because of zero correlation with any of he modes, then it propagates by diffraction laws. It should reduce in intensity, but should not loose power, unless you are in a lossy material.
Now regardless of both, as long as your media is isotropic, SOP (state of polarization) should not vary when passing from core to the outer layer. So, for evanescent field of an eigenmode, polarization is the same as within the oscillating part.
Only in very strong refractive index contrast, the small part where there is a change in field orientation is at the tangential points near the boundary, (Maxwel boundary laws) .
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I am currently working on non-invasive blood glucose measurement using photoacoustic spectroscopy in near IR region(905nm). While using the laser source, what optical power is advisable? Is there a limit on usage of laser on skin?
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You should calculate the Maximum Permissible Exposure of your light source, which is a metric based on wavelength and exposure time. Intense radiation can still be permissible for very short pulses for certain wavelengths.
The tables in the following link might be helpful. 
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It is obvious that biophotonic emission rate depends on various factors like age, growth factor, etc etc and the question may seem a little vague.
But I would like to know
#1: what would be the average biophotonic emission rate of a single human cell? I am mentioning it to be average, so as to temporarily compromise on the various sizes of cells in human body
#2: Available literatures broadly classify the spectral range to be 300 - 650 nm. Please let me know if data on spectrum is available on a single cell level.
Ram.   
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With single-photon detectors becoming more widely used (for quantum computing etc.) perhaps such a measurement can be taken in the near future - certainly would be an interesting result. Taking a spectrum at the few (hundreds?) of cell level would be even more time consuming, but again really interesting to publish. 
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Hi , I want to ask that if one want to study the ocean animals under the polarization microscope, then what are the animals whose skin has more anisotropic structure and one can study them( I mean their cell imaging, the scattering from their cells, imaging their cell etc.) better under polarization microscope???
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Transparent or at least half-transparent ones, of course. I think polarization microscopy will allow to reveal far more details, in particular intraannual details of annual rings.
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Are there any recent investigations carried out in connection with biophoton emissions from a dying person? or, at least, do we have investigations on various bio-emissions (which includes EM spectral emissions over various bandwidths) associated with a dying condition? Also, any recent Gas Discharge Visualization (GDV) studies on a dying person?
Suppose, if we are able to detect certain bio-emissions (having the specific bandwidth) other than in the Infra-red (IR) region (which is usually connected to the metabolic activity), then we can associate these emission frequencies to the fundamental oscillations or modes at which communication (both inter- and intra-) happens. These modes can then act as the interface between mind (non-material aspect), body (material aspect) and the environment.
If we want to understand how a material brain could have probably constructed a non-material mind, then we need to aim at studies of field emissions from various parts of the body at the dying condition, this in a way helps in understanding location of the self or consciousness in the body (which may or may not be fundamental to the brain). This will give a glimpse as to how one's consciousness is connected to biofield/bioelectromagnetic phenomena and its probable location.
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Prof. Jonathan,
The existence of biophotons is not in any way a fictitious concept. Modern science, at first, took a step back to accept the presence of such particles, which doesn't fit in well within its dogmatic sheath. But, since the modern school of thought goes with the book of science (where we impose certain principles to quote something scientific- like evidence based, repetitive results etc), it has to finally accept the biophoton concept based on the evidence from experiments. That's how biophotons are introduced to the modern science in the discipline of biophysics. The presence of these particles would then introduce a new way of understanding things around us. It adds in life to epigenetics, morphogenesis, biophysics and even neuropsychology.
You are right in asking what connection do biophotons have to the concept of consciousness? This is based on the studies that propose biophotons to be the informational carriers at the cellular level as well as for their interaction with exogenous fields. The concept of biofield pops out in this context. Few decades back, when science knows nothing about the electric and magnetic phenomena associated with the brain and heart, we don't have techniques like EEG, MEG etc and their possible implications. Now, when we accept such possibilities (at the fundamental level associated with discrete electrons), we devised methods to understand the qualitative pictures and their deeper implications. In an analogous way, we have biophotons and the associated biofield. Various investigations have been carried out in understanding the nature of biophotons and their role. Prof. Konstantin Korotkov, from Russia, exclusively work on these lines. He came up with the GDV technique, which helps in capturing the fields generated by these biophotons and therein qualitatively interpret such phenomenon.
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Is there any recommended standard samples for performing tracking measurements (2D)? Before going to any complicated measurements, we want to run some known samples. 
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Just try to use diluted red blood cell suspension.
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I am getting an electric field that is always positive at the different junctions of the heterojunction solar cell.
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Dear Ayesha Ali,
Manuel delivered the right answer. But i would like to remember some facts about the electric field and you yourself will get the answer.
The electric field is associated with electric charges and its intensity is the force exerted on a unit positive charge. So it is a force per unit charge. Since the force is vector having magnitude and direction, the electric field will also inherit this property.
Accordingly , so the electric field is define by magnitude and direction. Practically to to set the direction of the electric field one has to set a reference direction say positive X direction. When the real field is in chosen direction the electric field will be positive if it is in the opposite direction of the reference it will be negative. More than that it may be inclined with certain angle on that reference direction, then it is said that the field make an angle say theta with the reference direction.
Since the positive numbers are  easy to work with then one chooses the reference direction such that the electric field field is positive. This point was made clear by Manuel.
Best regards
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I am wondering what is the importance and how to interpret these experiments. Also, i noticed that i can't have background corrected (No blank subtraction) for these experiments using perkin elmer equipment. How to solve this problem?!!!! Besides, I appreciate if you could send me some resources to read about 3D experiments.
Thanks in advance, 
Muhammad
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The recent version of optical spectroscopy software Spekwin32 has quite some functions for handling EEM data. It is also able to subtract a Blank EEM dataset. This might be what you are searching for. Please start from http://spectroscopy.ninja For details on the needed functions, read the online manual, starting from here: http://effemm2.de/spekwin/spekwin_man_2d_en.html
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I performed a FCS experiment on DMPC bilayer tagged with BODIPY C12 HPC.
When I increase the power of excitation laser, I observe reduction in transit times.(see Fig 1) It is effectively like I am attaining smaller and smaller PSFs with increase in excitation laser power. We are using a LEICA TCS SP5 II microscope where power can be increased/decreased by adjusting AOTF.
I am not able to understand the reason behind this trend. Is it any form of artifact? Please give your comments.
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Thank you Dr.Peter Kapusta for your comment.
If there is bleaching, intensity versus time plot should show me that as a decay in counts. But I do not see such decay.
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I know about chlorophyll and protein. Maybe someone studied biological objects?
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Photoluminescence for body fluids like saliva,urine,blood plasma give information about the proteins like collagen elastin,oxy deoxy states of biomolecules,amino acids like tryptophan,tyrosine,phenyl alanine and DNA(Added with EDTA bcoz it does not have luminescence).
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I would like to make acoustic lens by myself. Can anyone suggest the material required for this purpose as well as some recipe?
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You could take a look at Axicon lenses, these are used for medical and NDT (non-destructive testing) ultrasound, in the 1-20MHz range. They can be made from Rexolite, which has a speed of sound (somewhat) comparable to water.
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I would like to make clot of EDTA added blood sample using CaCl2. I have 1 ml of blood with EDTA. What proportion of CaCl2 solution I should add to make a clot? I have added one drop of (2.5 ml water + 0.5M CaCl2) solution in 1 ml of blood but clot was not formed. Please let me know any possible procedure related to CaCl2 in order to form clot.
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Hi Deblina, are you using blood collected  in EDTA or heparin/EDTA tubes?
If there is heparin in the blood collection tubes then added Ca++ will have little effect.
If there is no heparin, transfer the blood with the Ca++ to a non-treated glass tube and let it sit for ~30min at RT. If there is heparin, add 0.1% protamine (final conc.)
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Hello, as a newbie in THz measurement, I encountered something strange when I tried to remove the absorption peaks in the THz measurement by pumping nitrogen into the chamber.
I found that most of the absorption peaks can be removed, such as the ones around 0.55, 0.75, 1 THz, 1.22 THz and 1.42 THz; however, the ones around 1.11 and 1.3 THz could not be removed clean even though other peaks were already unnoticeable and they just stayed there no matter how long the nitrogen pumping was. Does anyone have similar experience and how would you solve the problem? I was surprised since if these peaks are all from water vapor in the air, why they don't disappear simultaneously? 
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Thank you Joongmok! Unfortunately the designed resonance of our sample overlaps with the H2O absorption, so probably difficult to remove the absorption peak directly. 
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Dear All,
It seems that light propagation in tissue like skin can be modeled using ray tracing softwares, though in most of references Monte Carlo method has been used for this purpose.
I need to obtain spatial intensity of light (as well as angular intensity) over the skin when it is lightened using a light source.
So need to know how it is possible?
If possible what softwares are available?
Thank you very much in advance.
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Amir,
I'd recommend you to take a look at the book "Light Propagation through Biological Tissue and Other Diffusive Media: Theory, Solutions, and Software"
Author(s): Fabrizio Martelli; Samuele Del Bianco; Andrea Ismaelli; Giovanni Zaccanti 
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When the frequency of light is equal to the natural frequency of a molecule, molecule absorbs light.
My question is whether the molecule can have only one natural frequency? If thats the case why the natural frequency should match the energy gap between the ground and excited state.
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To the first part of your question on the number of frequencies a molecule has:
A molecule will absorb light at any number of frequencies depending on its size, properties, and what aspect of the molecule is being photo-excited.
Infrared light generally matches the frequency of molecular vibrational transitions. The number of frequencies at which the molecule will absorb is therefore related to the number of atoms the molecule has, and how high you can excite it before the bonds break and the molecule dissociates.
Ultraviolet light generally matches the frequency of electronic transitions, so the number of frequencies of absorption will depend on the number of electrons and how high you can excite them before they become ionized.
Different frequencies of light can also excite other aspects of a molecule, for instance radio waves can match nuclear spin state transitions to give NMR spectra, microwaves can match rotational transitions to give rotational spectra, etc.
A molecule has many different excited states, and therefore has many different frequencies of light that match the energy gaps between them. How many, and what those gaps are will depend on the particular molecule.
I hope this answers your question,
Magnus.
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Hi Serge,
There is a sort of a "bible" of myoglobin and hemoglobin in where you will find extinction coefficients and all sorts of other data on both proteins.
Best Signe
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Is it possible from Kramers Kronig relations?
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If it is absorption free and h as a frequency independent refractive index, there is no response function other than a constant refractive index.
Like Christian said above, once you look at frequency-dependent refractive index, by definition you must also have absorption.  You cannot have one without the other.
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If so, how? Do I need to divide the volume into two parts instead?
For instance, if I need to use a sphere in a sequential mode, I should use two hemispheres in contact. For an ellipsoid, rotationally symmetric for easiness, should we also divide it in two parts in contact, with one surface in respect to the anterior vertex and the second one in respect to the posterior vertex?
Any advice is welcome.
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Hi all,
I think that the mixed mode is the best way to carry out your design José Antonnio. What J.M Poyet is saying you is a good  point to start with this kind of configuration. Usually, Zemax Works perfectly in mixed mode and in the last versions, this aspect has changed each time better.
It would be interesting to know what optical phenomena are you searching for to use closed surfaces.
Finally, in Knowledge base website, I'm sure that you can find out something similar to your needs. I attach a link below, the main idea is to create the ports between sequential and non sequential "worlds".
Best regards,
Pepe
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I am modelling the oblique incident reflectance profiles using a diffusion model, but would like to examine the range in which it is valid.
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Otto, try online service http://biophotonics.otago.ac.nz/MCOnline.aspx. It might work for you.
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What is the reason that requires waveguide propagating the light used in OCT imaging to be single mode? What are the disadvantages to use multimode waveguide for OCT?
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The use of single mode waveguides has two effects: 1. coherence in the time-domain is provided, because only one optical propagation path is allowed in single-mode waveguides, in contrast to multi-mode step index fibers (graded index fibers are an exception!) 2. spatial coherence is provided because of the pinhole effect of the singlemode fiber core, which results in limited speckle-effects on your surface/ in the tissue under investigation.
Graded-index fibers preserve the coherence in time-domain, so they can be used for short lengths. As OCT is mostly using broadband sources, chromatic dispersion is a limiting factor for graded-index fibers. See my publication "Miniaturization and evaluation of fiber optic probes for low-coherence interferometry" for more details.
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I want to know in terms of degradation. I saw at few places it gets dissolved. Does the dissolvability mean degradation of collagen? What about the fluorescence spectrum? Any reference paper on this?
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Hi, AA is commonly used for extraction of collagen from native tissues. AA is of course good solvent for collagen but this is not equivalent with possibility of degradation. I am also curious if there is problem of degradation of collagen in AA solutions
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I am interested in the reasonable alternative to Qdot® 655 from Invitrogen Life Science Technologies.
Applications: Two Photon Intravital Microscopy of blood vessels (Organic dyes are not optimal).
I would appreciate any suggestions: quantum dots supplier or commercially available quantum dots for in vivo applications.
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Hi Vyacheslav,
Try this one:
Mesolight LLC
4607 W 61st St
Little Rock AR 72209 USA
Phone: 501 562 2070
Here is en example of what they have:
1. HMF-ZnSe/ZnS QDs: heavy metal free (HMF), deep blue PL emissions from at 400-440 nm, FWHM<20 nm, Quantum efficiency of up to 90%, and a high stability.
2. HMF-InP/ZnS QDs: heavy metal free (HMF), wide range PL emission from at 470-800 nm, FWHM: 50-70 nm, Quantum efficiency >50%.
3. GA-CdS/ZnS: with Gradient Alloyed (GA) structures, blue PL emission from at 440-470 nm, HWHM<25 nm, QY>80%, highly stable.
4. GA-CdSe/ZnS QDs: with Gradient Alloyed (GA) structures, PL emission cover entire wavelength range from at 520-650 nm, HWHM<30 nm, QY: 60-90%, highly stable.
5. PbS QDs, have the PL emission from at 800-2000 nm, narrow size distribution.
6. CIS(Se), CIGS(Se), and CZTS(Se) QDs that can used for solar cell applications.
Good luck!
Serge
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Gold spheres, rods and cages; unconjugated.
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I've found the answer if anybody's interested. Use aqua regia (1:3 mixture of nitric and hydrochloric acids) and a syringe with long (>3 inches) 18 Gauge needles. It cleans the capillaries perfectly and removes all the stain from gold. Since the mixture is highly corrosive, don't use the needle for purposes other than cleaning with aqua regia.
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Has anyone defined a theoretical lower limit for the concentration of bonds that CARS is able to image?
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This also depends on incident power. A big limitation of CARS is sample damage. This is less a problem for single frequency CARS than it is for broadband, but no matter what you're always working on the edge of burning up your sample to get the best signal to noise.
Are you really going to do CARS for a student lab? That's impressive. Really any dense medium will work, especially organics with a high concentration of rings. If you aren't interested in imaging, then go straight for solvents. Toluene is great.