vsgh khkm ghlm akhl omdk khkj mkhtr ebrS ebrp krmi ghsm:

General:

-Fluorimeter thermost
-At the beginning of each semester you can present a progress report to Dept.
-The last year report, please.

- Chemom seminar in Orumia Aban 6th to 8th (.

Khoshkam
Ebrahimi
Ghasemi
Shamseddin
-Hamedan Anal Chem Congress:
Ghlm: 2nd Part of MS proj,
Ghsm: 1st (and maybe 2nd) Part(s) of MS proj,
Akhl: SNtucker,
Mkhtr: MS proj,
Hsnz: MS Proj,
-Arak Semin of Mathem Chem

-------------------------------------------------------------------------------------------------------

- Reading a book together in a weekly meeting ()?

880208tue, 11:30 cross-val in multiw.

880215tue, 11:30 cross-val in multiw.
880222tue, 11:30 Chapter 4 (57-62) Ms Ghasemi,
880229tue, 11:30 Chapter 4 (63-68) Ms khkm,
880305tue, 11:50 Chapter 4 (69-76) Ms khkm,
880312tue, 11:50 Chapter 4 (77-83) Ms ghlm,
880326tue, 11:50 Chapter 4 (84-93) Mr aklg,
880423tue, 11:50 Chapter 4 (93-102) Ms ghlm, ???
880430tue, 11:50 Chapter 4 (102-113) Ms khkm ???,
880506tue, 11:50 Chapter 4 (93-102) Ms ghlm, 
 * progress report (Weekly).

Papers from search /

Experimental data reprting+corresp m-file+ppt file of figures

5 3:30 2 12:30 11 9.30 8

Meeting Meeting ‫آموزش‬ ‫کالس‬ ‫مطالعه‬ ‫شنبه‬
MKHT EBRS
Meeting ‫جلسه گروه‬ ‫آموزش‬ Meeting ‫یکشنبه‬
KRMI+ebrs AKLG
‫جلسه‬ ‫جلسه‬ ‫آموزش‬ ‫کالس‬ ‫مطالعه‬ ‫دوشنبه‬
Book Meeting ‫آموزش‬ Meeting ‫سه شنبه‬
VSGH GHLM
Meeting Meeting ‫آموزش‬ Group Meeting Chem Dept ‫سمينار‬ ‫چهار شنبه‬
EBRP KHKM Presentat ‫تجزيه‬
Meeting Meeting ‫پنجشنبه‬
KHJH+MKHT OMDK+AKLG

vsgh khkm ghlm akhl omdk khkj mkhtr ebrs ebrp krmi
890121 - - x x x progr
- x x x
890128 - - read pp some - - progr progr

manuscp

corr

890204 pp+
prgrdata
890211 pp prgrs prgrs PP(k
s s ubist
a
890218 prgr/2 prgr+ prgrs prgr+ prog/ pp
pp s pp 2+pp
890225 x

x: held, -: not held, prgr: progress(prgr/2:1/2 of progr), pp: paper

 * Wed meeting presentation of a paper (Weekly.
Wed(11:-12:15) Ms Mkhtr provides some cookies or fruit for motivation !!!

vsgh khkm ghlm akhl omdk khkj mkhtr ebrs ebrp krmi
omdk
vsgh 880820
GA-SOM
khkj 880827 x x x xx x x x -
aklg 880904 x xx x x x
ebrs 880911 x x x xx x
880918
880925
ebrp 881002 Not
held
ebrp 881009 x x x X x x x xx
proteom
krmi 881016 x x x x x xx
PartSwOpt
khkm 881023 xx x x x x x x
DNA+kinet
ghlm 881030 xx x x x x x x
aklg 881107 x x xx x x x
omdk 881114 x x x xx x x x
Mkhtr(McGhee 881121 X+ x xx X
khkm(rep
Mkhtr/McGhee 881128 x x x X+ xx x
omdk
Khkj BLLS 881205 x x x x xx x ?
akhg 881212 x xx x x x x
ebrp/astrochem 880118 x x x x x xx x
krmi/paper 880126 xx
880201 - - - - - - - - - -
khkm 880208 - xx x x+ - x+ x x+ x+ x
ghlm 880215 - x xx x+ - x x x x x
880222
ebrp(ct for matrix eff 880229 x+ x x x xx x

x presence
xx presentation of a paper
x+ brief progress report
 Three-month progress report at dept

Vsgh akhl khkm ghlm ebrS mkh ghsm KRMI EBRP khjh omdk
tr
83
G1.Statist(abd)4
G2.Electro(ayat)
3
S1. electroch3
G3. Reveshhaa
(hghg)3
S2.Chemom
84 3
1. Mabaahes 3
E1.Chemom(abd
)3

Seminar 1
Seminar 2
Amadegi
85 jaame
Amadegi
jaame
Seminar 3 G1.Statist(ab G1.Statist(abd)4
Proj 6(5 d)4 G2.Electro(ayat)
 G2.Electro(a 3
yat)3
Proj 6( 1. Mabaahes 1. Mabaahes
86 -Chemom(ab -Chemom(abd)3
d)3 G3. Reveshhaa
G3. (hghg)3
Reveshhaa
(hghg)3
Proj 6( 1. Mabaahes 1. Mabaahes
-Chemom(ab -Chemom(abd)3
d)3 2.Biochem(emd)
2.Biochem(e 3
md)3
Amadegi Amadegi jaame
Proj 9(10 jaame
Sabbatical?? Sabbatical?
Proj 6( Amadegi Amadegi jaame G1Statist(kmp) 1.Adv Org 3 1.Adv Inorg 3
87 jaame Seminar 1 4 2. Adv Ph Ch 3 2. Adv Ph Ch 3
Seminar 1 ComprehEx S1Mabaahes:Bi 3.Adv An Ch 3 3.Adv An Ch 3
ComprehE (azar osnsNano(hghg
x (azar )3
Chemom(abd)3
Proj 6( Chemom(abd)3 1.English 2 1.English 2
Proj 6 Proj 6 Electro(rfi)3 2.ElectochI 3 2.ElectochI 3
3. Chmm1 3 3. Chmm1 3
E1Inorg Bioch 1.AdvSpectI 3 1.AdvSpectI 3
Proj 6(10 Proj 65 Proj 65 (zkv)3 3 3 2. ElectochII 3 2. ElectochII 3
(progr rep (progr rep 3. Sepn 3 3. Sepn 3
4.English 2 4.English 2
Amadegi jaame Statist(kmp Statist(kmp) 1.Adv Org 3 1.Adv Inorg 3 1.SepnII 3 1.SepnII 3
88 Thesis Proj 65 Proj 65 ComprehEx )4 4 2. Adv Ph Ch 3 2. Adv Ph Ch 3 2. AdvSpecII 3 2. AdvSpecII 3
writing (azar Mabaahes: Mabaahes:B 3.Adv An Ch 3 3.Adv An Ch 3 3.ChemomII 3 3.ChemomII 3
Sabbatical?? BiosnsNano iosnsNano(h 4.English 4.English
Defense (hghg)3 ghg)3
Chemom(a Chemom(ab Proj 33 Proj 33
10 bd)3 d)3
MolSp 3 MolSp 3
?? Proj 65 Proj 65 Proj 65 ?? ?? ?? ?? Seminar 2?? Seminar 2??
Seminar3?? Seminar 2?? Seminar 2?? Seminar1?? Subject? Subject?
Not presented add add add
Proj 33 Proj 33

Sabbatical?? Sabbatical??
89

Defense

procedure start
ProgRep2
Defense Azar 88 Wint88 Wint 88 Wint90 khordd88 Esfand87 Farvard8 Shhriv89 Shhriv89
(4.5y  (3.0y (3.0y (3.5y (2.7y W87orSp88(3 8 (2.0y (2.0y
f88(3 (2.6y 
S88orf88(3

-----------------------------------------------------

Akhl:
- Send me the final slides of Todesch, please .
-PARAFAC on FIA data.
-Cross val on FIA data.

/////////////////////////////////

-mfiles of completing of Tucker3 [from 870630 880407], NMF [from 871001-…],

Sparseness[from 871001-], constraint on core[from 880101]

-SNTucker (R&D will be finished [till 880101 880324880328]

- The number of suggestions (which is 25 now) and number of tests (which is 10 now) for each suggestion can
be increased to improve the statistical significance. It can be done be doing additional calculation in each
condition (definit sparsness, threshold and iterations) and add the results to that you already obtained.
- A simulation of acid-base titration (estimation of chemical rank of data) 880408

-Reproducable minimum residuals is a primary criteria other than TCC to evaluate the results from sparse
models. (Proper shape of loadings is a good criterion, as well: nonnegative and no random fluctualitons…

- The method can be applied for determining the optimum number of factors.[done]

-Triviality and uniqueness of the obtained simple core arrays:

Are the obtained simple cores unique?
[To be acceptable, the simple (constrained) core should result in reproducible minimum residual. The
reproducible minimum residual should have the value not significantly different from the residual of
nonconstrained Tucker3.]
Using the fixed constraint core, if the same acceptable residual value be obtained only from the same
set of loadings, the simple constrained core is unique. (880324-880401)
Obtaining same residual using different loadings, using a fixed considered core, rejects uniqueness.

Are the obtained simple cores trivial (obtainable with rotation of another core[maybe the nonconstraint
one])?
[Simple cores including one or more rows (col.s) of zeros are nontrivial and cannot be obtained by
rotation of other cores]
Checking of method in eqn 13 for testing the triviality of our core seems fruitful [jchmm04-simplicity
and typical 18;17-21]. (880324-880403)
The benefit of the proving the triviality is making sure that the simple core is from rotation of a non-
contrained global solution, without change in fit (without increase in residual). However, the non-trivial
solution that is not from rotation of a nonconstrained solution may result in higher residual and may not
be an acceptable solution. The point is that a nontrivial solution is acceptable according to chemical
knowledge, but the necessary condition is that the residual be not significantly higher than the global
residual. So, it is critical to define an acceptable level of residual value.

SAT + SB
SAT + SBT => SATSBT (FRET)Complement(match
SAT + SBm=> SATSBm Mismatched
SAT + AuNP=> SATAuNP quenched

Progress:
Generation of Gsugg(SNTuck+adjestabl threshold)
Testing the candid simple core by TuckCoreCons(reasonable simple core)
Applying on simulated, FIA and Fluoresc data
Discussion about triviality
cross val on FIA data

Progress890215(881117data):
[At 126nM, AuNP:8.2nM,PBS:4.2mM,NaCl:42mM]
-Au+At+buff=> no aggreg (Red): this experim
(Au+buff+At=> aggreg (Blue):prev experim)
#At around each AuNP?...
Titn of At(Fluo)+AuNP with Bt(Texas):
(AuNP=>signif decrease in At(Fluo) [firstly] )
=> 1.decrease in FluoAt/[At]0 : hybridiz with non-quenched Ats (non-quenched by
AuNP)
 2. increase in FluoAt/[At]0 : probably due to desorp of At from AuNP and hybridiz
with Bt
{Fluo intensity: At free>At hybrid> AtAuNP}
3. BtFluo/[Bt] increases: because of presence of excess Bt in the last steps.
dealing with missing values:
Using PLStoolbox;mechanism?
parafac with 3 compon.s was performed.(2 and 5 compon.s)
 A simple hard model could be made(assisting soft profiles)
shift in at fluo peak should be followed. First: by two way meth(>>NMFpack), then by
PARAFAC2
Sparse NMF Tucker3 alg, assist of Ms EBRS
 experim with diff sizes of AuNP, and diff temps, diff ionic strengths.

Experimental:
-This part should be started as soon [till 870701].
Giving a report to Dr Hormozi (Advisor [moshaaver]) 870510
- QDs are fluorophores (AuNPs are not. They are just quenchers)and to determine their
complexantion affinity with single or double strands there would be no need to label the
strands with fluoresceine.

Paper:
AnCh04-DNA-Fluo-quench-AuNP.pdf
SA+SBFluo-tagged =complement=> hybridiz -> dsDNA, no interact : Fluoresc ON
SA+SCFluo-Tagged=mismatch-> no hybridiz -> 2 ssDNA, interact : Fluoresc OFF
(Fluo microscope, and fluorimiter)
Rapid (10 min)
Sensitive: no need to DNA amplification by PCR

Single mismatch detect:

25oC: 50 mer target
15 mer probe(on middle or end part)
40oC: melted mismatch and hybride mismatch => higher sensit to mismatch

Two probes (one tagged with Cy5 and the other with Rhodamine) can be applied
For investigating two or one target.

PNAS04-DNA-sequence-gold-nano-color.pdf
ssDNA+AuNP -> interact +NaCl-> no aggrig of NPs RED
dsDNA+AuNP-> no interact +NaCl-> aggreg of NPs BLUE
=> mismatch (no hybridiz, stay single):can be distinguished
SA+SBFluo-tagged =complement=> hybridiz -> dsDNA, no interact : Fluoresc ON
SA+SCFluo-Tagged=mismatch-> no hybridiz -> 2 ssDNA, interact : Fluoresc OFF
ssDNA-AuNP (complex) -> Resonance raman intensity
In distilled water : dsDNA -kinet-> ssDNA
(No ionic strength-> repulsion betw strands )
Appl: Disting the SARS virus DNA (using a Fluoroph tagged probe)

-linAlgeb09-Simplic-transform-3way.pdf ;
or LinAlgeb06_Symmetry transform-square-sliced-3way.pdf or…

- jchmm04-simplic-typicRank-tucker-core.pdf (Triviality and uniqueness of results can be

considered.
- Simplimax.

Sat 880205 seminar1 , Mon 880207 – 880220 omreh, Zanjan 880222

-----------------------------------------------------
Byd:
-
-A vacant time to complete the second part of MS project.
-----------------------------------------------------

---------------------------------------

Ebrs:

-Is there any fluorescent microscope, with ability to record the spectrum in each spot?
-Interest to travel to Denmark?! It is better to do a comprehensive search around the world to
find the best possible research group. From mehr 1389 there is a 2years interval for going to
a 6-month sabbatical.(At that time more than 3.5 years is passed for Mr Aklg).
Reading about bio nano assemblies. Hans Christian Orsted Institute, BioNano Center.
[Proposal for Dimitrius Stamu: nanoscale pH meter or nanoscale thermometers, using
Fluorescence microscope with three colors].
It is better to send the proposal after completion of search for different research groups.

-Asmund Molecules?
-Search in "chemom" and "acs" journals for recent chemom method on GRID 3DQSAR data.
Continuosly..
- How the data can be exported from the available softwares? (MS data of ebrh)
-suggestions:
Application of peak alignment methods on GRID data for better superposition of molecules...
Application of nonlinear multiway regression methods..

There are a number of other softwares for generation of 3D molec descriptors. Gasteiger, Anal
Chem

Writing:
- writing of MS work(s)

Progress:
**Temperat DNA
Data880204:
-SSFluo+SStexas : melting curve, free cooling,Em Fluo
LabeledSSDNA:small incr in fluo as a result of Temp decrease.
FluoSSDNA+TexasSSDNA: : +T decr=> initial small incr +large decr(hybridiz +FRET)
?? for Texas Red there is no FRET to the other fluorophore (fluorescein), however a significan
decrease in fluoresce was observed. Is this, only, an intensity change or the EEM spectrum of
texas is different for the hybride and SS form? (Factors: Temp decr is increasing on fluo,
Hybridiz is decreasing)
-assigning concn of buffer.
-svd on data (two step (consecutive) mechanism of hybridization).
-Is the pattern of temp Change exponent?(replication exp a number of times+fitting of exponent).
Presence of thermometer may affect the temp change trend, So an internal fluoresce
thermometer seems required.
What is the pattern of temp change?
svd and NMF on data: Presence of intermed? Occurrence of FRET?
 fsmwfa and efa to see the components
 in some ref.s it is reported that melting and cooling include diff mechanisms. It would be nice
to compare the spectral data of them.
 in 6sec interval between spectra measurement, there is a possibility that the kinetic of hybridiz
is not completed in each temp. So it seems better to record the spectra using a thermostat.
 hybridiz can be started by addition of NaCl.at a constant temp. or during cooling.
fit of conc prof.s to melting curves.
=> increase(temp reduct)+decrease(hybridiz=> considerable Fluo decrease)
 DNA hybridization(hard model is included+changing temp)[ Anlyst09-dna-hybridiz-
kinet.pdf]

-SStexas : melting curve, free cooling,Em Fluo

=> only increase in Fluo, rank=1(sharp)

**MissingQSAR
Generation of a three way data changing the three substitutions on a series of molecules.
Papers(from contiuous search)
Keywords: DNA, Fluorescence, FRET, Hybridization,

Bioch93... .pdf
Anlyst09... .pdf

anbioch09-DNA-denatur.pdf
Sanger Method(without electrophor or chromatogr)
Temp change and following meting curves+fitting curves to hard model
F=0.5 => T=Tmelt
Extent of hybrid in each T=> K(T) => ∆H,∆S
Na effect(as complexing component), at diff temps

Making a nano thermometer. Proposal for stamu.

T=> color change (from green to red)
Working with RGB information (Mirzaee, Farrokhi kord)

NAR07-DNA-kinet-FRET.pdf
A 21base primer has melting point of 50oC. A two stage reaction. Not clear mechanism is
considered...

Angew08-dna-nano.pdf

Opening of a hairpin loop(that contains a toehold)

by a fuel strand(displacement oligomer) [fuel strand can be a catalyst and
not consumed, next example]
Duplex part in initial hairpin is smaller than that in final duplex product(final duplex is more
stable)
The single part of product duplex can be applied to open another hairpin loop (an example is
presented).
The second intermediate has different structures, but the first intermediate is only one.
A+B=>I=>I2...In=>P
(production of prod was proved by: Gel electoph +Atomic force microscopy)

What about progress of reaction without toehold?

How components can be followed fluorimetrically? Having diff ex em spectra, for each?

angew05-combin-dye.pdf (slides are provided.

Dynamic Combinatorial Libraries(DCL)of Dye Complexes as Sensors
DCL: 3 dyes +2 metal ions(Cu2+,Ni2+),pH=8.4 => a # diff complexes
+dipeptide => change in complexes composition
=>color change in DCL
R&D: testing a number of dipeptides to see the color changes.
5 diff dipeptides, each in 15 time meas (3conc.s and 5 replic.s)
=> 5x15 dipetide samples
LDA +score plot => 5 clusters (superwised classif)
predict set: from same dipeptides 100% correct: when three dyes+2M
75% correct: when 3 dyes+ 1M

As there are a number of reports on complexation of metals (Hg2+)with DNA, it seems possible
to prepare a similar DCL system using DNA.

JChmm97-MultCal-3DQSAR-NPLS.pdf + Thesis
Application of NPLS in GRID data analysis, (PARAFAC and Tucker3 were mentioned in the
thesis, but not employed).
Why after 1997 there is no other study on GRID data using multiway methods? (Specially
Tucker3, that seems to be powerful, flexiable and applicable in this area).

ChRevAnCh06-Molecular-Chemom.pdf
Aca99-molec-chemom-Wehrens.pdf

-----------------------------------------

ghlm:

-sabbatical
-Submission of proposal for "center of nono studies"...
-FRET mechanism for energy exchange is nonradiative.
-NEXT: Study of mismatch to determine if the DNA chain affect the energy transfer?(or a 50%
noncomplimentary)

-Seminar1: Fluorescence Polarization Assay(angew08)? Also in Krull works

- Ordering of chemicals (nanolet05_mnlticolor colocalization of QD.pdf) 880420sat

- Revision of symmetric constraint for JChmm,

- a reprint of JChmm paper to Ms Mousavi

Writing:
-Writing the R&D for the 2nd part of MS project paper(a summer.

m-file:
NPLS model
(Modelling: PARAFAC or Tucker or Orthog proj to latent struct (OPLS, cils08, 92, 110-117.)
and other..
-Chap 4 of Multiw Anal includes a number of regress methods.
- Applying RBF before NPLS. Applying on a set of sensory data, or
( Definition of a proper vector to illustrate the distance between two matrices (Todeschini.)
- using exp(distance^2) in RBF not good prediction was obtained by NPLS. Maybe using a
completely nonlinear data, the prediction will be performed.
- Using distance in RBF is important because of our interest to reduction of data size
(using Mahalanobis dist or leverage). In this way, application of 2 way PLS on unfolded
data seems possible and can be tested.
- Using the original data in RBF(in place of distance) good predictions were obtained. So,
the method can be applied for Wine data or others. All members of data set should be
positive.
If each matrix is n points in a m dimensional space, the distance between two matrices can be a vector including
n distances between corresponding points in two matrices.
Three objects A, B, D as three matrices result in an 3xnxm initial array. Considering 2 centers in the m dim
space [2 centers is because we are emphasizing on reduction of data volume]. The distance matrix for A would be
a matrix of size nx2 and the size of distance tensor (for A, B, and D) is 3xnx2. As the number of centers is
reduced, the volume of data is reduced. Location of centers are crtutial and can be distinguished using clustering
methods. Each center camn be a representative of a cluster of data.
Then the distance matrix can be transformed using RB functions.

-lit search for models developed using NPLS, PARAFAC,…(spectroscopic, QSAR..

[it seems possible to reduce the CV PRESS value in for example (2,2,2)
number of factors, using nonlin transf]

Data:
-QSAR modeling (similar to submitted article).
- NMR, asking Rasmus (aca05-bro-2DNMR-protein.pdf, 531(2005)209-216).
2D NMR is not a simple task in Iran,
so, an alternative is to as Flemming (Copenhagen) about reaction folllwing by NMR (cisPlatin-DNA) or
interaction studies.
Another, alternative is to make 2D from 1D using continuous wavelet transform.
-wine data
-Screening of the NIR data from chromatograms.

- Foreign supervisor (you can make contact to WANG or Krull,

(FRET in the sandwich nano-assembly?

- Comprehensive exam and a proposal : Azar 88

- Proposal of the project: day 88 QD-FRET-DNA(RBF-NPLS

- Analytical chem. Lab (Safety and ordering).

What about cleaning and oiling of the ceramics on the cabinets.

--------------

Papers:
DNA technology (For seminar1)
DNA sequencing: sanger, Fluoresc NEW
DNA hybridization; can be detected by fluo; excimer formation(pyrene labeled);
Molec beaconsNEW;
Aptamers: DNAzymes
Microbeads
Flou in-situ hybridiz (FISH)

nanotec08_Intercalating dye & QD_FRET.pdf (wed meeting)

langmuir08_QD-DNA_prepartion & hybridization.pdf
FRET between a QD and intercalated Eth Bromide.

angew06-fret-QD-synth.pdf and cocb00-fret-nucleic-acid.pdf

PCCP09_qd based FRET & apl in bio.pdf

Jacs05-QD&multiplex-fret.pdf + AnCh09-81-4831-4839
Binding of labeled(with cy3) proteinto QD => reduction in QD fluoresce
Diff sites on diff QDs and following the fluo reductions (classical least sq)=> extent of binding
to each site
Reduction of fluo could be dued to : 1. FRET , 2. Electron transfer

Lumin07-Fret-QD-QD.pdf
(CdTe (not core shell) QD: not stable at pH<6.5)
QD573-antigen(electrostatic interact [donor] + QD638-antibody (hydrophilic interact
FRET effic: 51% (GOOD effic of QD-QD energy exchange
(r=6.57nm < Forster distance(for forster dist FRET eff=50%)=6.61nm)
Study: pH is effect on interaction of antib with QD => interact is electrostat
Ionic Str=>Fluo↓ (Sepn of QD) => electrostat interact
Protein conform <=> distance <=> FRET eff
Dye: photodegradat, emission overlap with other dye (QD: stable, low overlap)
Fluo(QD573)< Fluo(QD573-antigen) :only intensity change(Fig2)

(Titn? Of) QD573-antigen-antibody (fix) + QD638 (added at diff concns) (Fig5

Backgr correct for emiss of QD638 when it was excited by external source
=> FRET was happened
(It shows that "QD638excited with extern source" is a component different from "QD638excited
by DonorQD")

Calc of J:spectral overlap= 1.787e-12 cm6/mol

<= integrat of overl region ; molar abs
; lambda (nm)
R0: forster distance <= k: dipole over of donor and acc =2/3 ; ref index=1.33
quant yield; J
r : 6.57nm <= R0 ; E (FRET eff) ;n=1
Non specific binding: QD573-antigen(mouse) + QD638-antibody(rabbit) (Fig6
=> happens a bit (NO kinetic: very repid)
[Specific interact shows a kinetic (30 min)]
Study of competitive systems

nature05_qd +dna.pdf

nanolet05_mnlticolor colocalization of QD.pdf

Two fluo probes for one target. No probe on target. Probes include QDs with different sizes.
Kinetic of 60 min also is observed. Fluorescence microscopy (Facult of pharm microscope)
angew08-AuNP-Hg-fluo-polariz-Hormozy_3.pdf
AuNP increases the sensitivity of Hg detn by Fluorescence Polarization. It is because of
increase in molec volume of the formed complex compared to the single strand containing
probe. Fluo Polariz is not available. This system can be considered using ref 11a, based on
FRET, mismatch.? Distance of AuNP and Fluoroph. Number of Hg sites?
small08-AuNP-metal-abs- Hormozy _5.pdf
(different metals different colors, complexation and agregation
angew07-phosph-AuNP-abs- Hormozy _2.pdf
(kinetic and absorb+ more than two components+absorbance
jacs07_DNA_nanoparticle & sensors.pdf
(AuNPs are at different distances, but no spectra is reported to show the effect of distance on
spectra?
Sci97_ Detection Based on the Distance-Dependent(Printed).pdf
(distance, aggregate, blue and red, kinetic
(what about effect of particle size and distance on the color of solution?

cils03-project.pdf
cils09-oliveri-classif.pdf (candidate for dept meeting
It seems that distance matrices(leverage, hyperlever, or Mahalanob dist) can be applied in place of original
data, to reduce the size of data. It should be tested for multiw data.
cils08, 92,61-70 Olivieri
BLLS+ANN, sec ord adv for PLS(detn in pres of interf
Addition of sec ord adv seems possible to NPLS which is assited by RBFN

Aca05-bro-2DNMR-protein.pdf
The data seems proper to be applied for RBF-NPLS, (can be downloaded

cils05-metabolic-bro-nmr.pdf
Maybe the RBF transform of data result in lower PRESS value in a defined number of factor in each mode, e.g.
[2,2,3]

InorgChAc09-cisplatin-DNA-Kozelka.pdf (NMR is not available now!!)

-----------------------------------------------------
ghsm:
poster
merging, ordering and delivery of m-files, Poster and Data for web, awarded 880401
 Paper : completion of R&D, Introduction, submission 880410

Thesis: corrections, converting to pdf (chapter by chapter) for web, awarded

Receiving the signed forms and awards

-----------------------------------------------------
Hsnz:
- [See the last page]

-Completion of R&D of article.

-----------------------------------------------------

khkj:

- in 25oC maybe the strands are melted !!

-deriving the equation for I0 ,I, I (from alkaloids paper
-  Analysis of ExpDATA880407(ATATATA)??
Titn of NR with DNA 880424
- normal titration.

1. Soft:svdLS:
svdLS(BLLS):could be started from scores of unfolded data and rotation of them till obtsining
rank 1 for S1 and S2 +nonneg and ...

iterative procedure
-2.hrd:Hard model (before RA. M+L?
-EXPERIM: ExpDATA880701: Reverse titn (NR with DNA(7 base pairs)):
CoNR: from 10M to 5.71M, CoDNA: 0 to 2.22M
-MFILE: same CoNR and CoDNA be applied in simulations.
- MFILE:Suggestd K -> suggest Conc prof +svdLS or BLLS=> fitting of K and detn of
n(#sites)
For simulated data: done using svdLS and BLLS (K=6000, n=4)Excess NR => diff profiles
for ExpDATA880701: ...
- (MFILE:added volume in model should be from zero. The spectrum before addn should be
recorded.)
- (MFILE:All the initial conc.s should be obtained from added vol, Vo, and Co values
Cprof(CoNR, CoDNA, Vadded(as[0 0.05 ...]), Vo, Condit(Normal or reverse)))
- EXPERIM: -Normal titration (of DNA with NR) can be informative. Initial Conc.s should be
checked by simulation and previous inform. (reverse titration is done at 880701: NR with
DNA: Excess NR resulted in higher diff in conc profiles) ]
simulations for ML hard model with n=1 to 7 was performed and plots are shown.
for CCCCCCC double strand. n=2 resulted in best fit, although not completely fitted.
doing the same for AAAAAAA data(soft and hard)
normal titration experiment.
TLD as soft method (simul; ExpCCCCCCC[NR:10,DNA:5]; ExpATATATA[NR:10,DNA:5])
HTD as multiw hard (simul; ExpCCCCCCC; ExpATATATA)

-3.hrdsft:What will be the result if we annihilate the contrib. of NR (only) fro titn data.

- m-file: RankAnnihilation
- m-file: complex formation titration M+L->ML+spectra > 2D data
- m-file: simulation for preparation of EX EM data for 1 compon(a titration [ghsm]).
-mfile: ExEm Data for a sample including 3 components
-mfile: ExEx data for a number of samples including 3 components(multiway
-m-file: EXEm data for a number of samples in complexometric titn (multiway
- Writing RankAnnihilation for determining the formation constants in multiway data(with RSD
880424

-GRAM seems to be a proper method for our system…

-BLLS seems proper

Paper:
DNA, ExEmFluo, binding
Tlnt01-55 321,
DNA in excess

SpAcA03-NR-DNA-Temp... .pdf

aca07-DNA-ExEmFluo.pdf
Competition of Cu(phen)2 with EB for complexation to DNA. svdLS soft resolute.
ExEm Fluo, soft,
Estimation of formation constant. How it is performed?
PARAFAC?
biomedch05-dna-bind... .pdf, BMC06-dna_seq-selec_bind.pdf....
Site specific groove binding of alkaloids (Not intercal). MS+Fluo investing. Exact detn of
stoichim 1:1, 1:2.

SOFT-------------------------
Cils98-blls.pdf
TLmcrALS,
cils06-kinet-fit-3w-4w-mcrals-rutan.pdf
PARAFAC,
TLD
svdLS
??
cils02-2ndOrd-blls calibr-faber.pdf
cils06-BLLS-svdNNLS.pdf, cil06-trilinLS.... .pdf
soft resolution of fluo data from DNA-Drug by svdLS
svdLS, svdNNLS(regress coeff??)
aca00-svdLS.pdf, cils06-BLLS-svdNNLS.pdf 880407-880417

Hard modeling
HARDsvdLS?
HTD,
jchmm02-maed-hard-htd.pdf
Maeder(CriRev

Hard-soft
Ghsm
cils08-RA-abd-zeinali.pdf
aca05-gram-GC-MS-jalali.pdf

-ordering the strands!!

//////////////////////////////////////////////////////////////////////////////////////////////////////////////////

khkm:

-Payment of Urmia to Miss ghsm. Sooratjaleseh maali

-upgrading the PC + Fluorimeter PC
-Keywords for search (first part of CTpaper)
-Following the purchase of thermostat for Fluo. spectrometer.
-ebrp simulation(search for data)
- paper kz submission881120(Feb10)
-CW paper (cils

Writing:
- Submission of cwpap (Todeschini)
-CT1 paper 1(urumia). ppt(figures and tables) 2. R&D writing 3. Completion.
- Submission of article from 2nd part of MS proj. 880328-880411
-pHstep paper 1. ppt(figures and tables) 880819 2. R&D writing 3. Completion.

***Theory and m-files***********:

Assume two bilinear matrices with different vectors in one mode (spectra). On the other
mode (Conc) we have a number of elements in common, which can be used calib Transfer.
We use calibration transfer to make two bilinear matrices compatible (to use calibration model
from one for other one ).
In case of kinetic or titration data with different spectra of components from one
experiment to another, also, we need a number of points with same conc in two experim.s.
Finding a number of points with same conc.s (is not a simple task):
1. 1st and last points of a 1sr order kinetic can be points with known conc
2. profiles can be obtained from Targ transf fit, for both matrices,
3. for consecutive reaction with no change in k (same temp and different days) finding
regions with same conc.s is simple.(but is not reliable)
(We can try calib transf without standards.: these methods are only helpful when dealing
with intensity changes [ref])
-checking the OSC application in CT.

Checking the simulation for calibration transfer on (equilibr or one way)880328

1. a simple 1st ord kinetic data A->B. (+a simple equilibr such as pH-metric titn)
- same temp (replication)
- diff temp
- diff pH (OH as catalysis(as in carbaryl decomposition)

PART I:..........................

More samples, better models (Frans says)

Number of parameters to be optimized(both A and deltaH?)

Inform(conf interv of param) <= Aumentat <=compatable data <= CT

(Urmia) a simple two compon.s system,
+ similar concn prof : starting and ending samples as tranf stand.s
(disadv: need to infinit time to complete the react, to
have accuracy)
+ diff concn profiles : correl coeff can be helpful in finding the transfer
samples with same conc profiles. But it is not a precise
selection method
(Interpolation can result in more similar standards, to
have higher accuracy. Using Interpol the is no need
to wait till infinity for completion)
As interpolation is not simple and correlation is not precise the
beteer suggestion is using the 1. concn profiles from hard model or
2.the epsilon spectra from hard model.

+ diff concn prof.s: without need to transf standards

to do the CT using hard model (Ea or k is optimed? Or both?)by obtained
matrices of molar responses from application of hard model on each matrix.
(Ex: unfolded ExEm from carbaryl),

1 kinet
1.1. two compon.s (Carbaryl decomposition in basic medium(k=f(pH)).
1.2. three compon.s (MS data, Bookshdata (only a fluorescent intermediate in a
consecutive react))
( Augm (reduction of conf interval))

2. equilibr
(Stacking(need trilinearity Adv: multiw anal diff spect:same conc prof )
diff conc: same spectral
pH metric titn+PARAFAC
  the effect change in intensity, in addition to peak shift
gathering all m-files into one.
(Temp fluct.

Selection of transfer samples:

1. First and last points of titn or kinet (Make sure about completion)
2. A # same time points (if rate constants are equal+ 1st order (exponent) react)
3. Time points with maximum correlation (not a precise method)
4. Hard modeling => spectra of pure compon.s => Transfer to Master

If the matrices can be resolved separately, why we are interested in augmentation?

If there is a range for acceptable estimated parameter for the model, augmentation can reduce
this range, as well as the feasible range (it can be checked by a simple grid search).

But not entering to Rank defic problem...

PART II:..........................

Ms Mokhtari's MS data are rank defic, equilibrium

Usually without augmentation of two matrices, estimation of parameters are possible,

But for Rank deficient data, augment is necessary (augmentation is the only way to resolve the
data) Could the method of using "matrix of molar responses in place of transfer standards" be
applied to a rank deficient data?

-Presence of a const interf (or a changing interf) in the data sets can be investigated. In
this way the data would be rank deficient and augmentation will be necessary.

-Appl of CT in multiway data(ExEmFluo, ghsm)

2. a consecutive 1st order 880325-880301

-same temp
-diff temp

3. a simple 2nd order (equilibr(k1 &k-1) or one way)

-same temp
-diff temp
Experim: MS data
the model can be applied for transfer of a consecutive 2nd order data using two
sets of data with different concentration and spectral profile. The goal is to solve
the problem of presence of an intermediate. 880323.
(system can be rank deficient)
To do the CT three stand soln.s are needed. Or...
 Two sets of second order kinetic data are not trilinear when stacked.
Using calibration transfer it would be possible to convert make them trilinear for
applying RA or PARAFAC modeling.!!

One standard (St1) can be the initial sample [A]=C0. For the two other standards
(St2 and St3) concn.s of B and C ([B]2 [C]2 [B]3 [C]3)are required .[A]2 and [A]3
can be estimated using mass balance. B and C concn.s can be changed using GA
and in each stage fitting of augmented data [D1;D2;D3] for estimation of total
concn profiles can be performed[C1;C2;C3]. Spectral profiles of pure components
can be estimated from C1 and D1, S1, from C2 and D2, S2, and from C3 and D3,
S3 can be obtained. Proper GA parameters result in same S1,S2 and S3 and a
zero residual (proper fit).

Checking the effect of CT on the fitting error and incert in parameters. If it is

effective we should explain it theoretically.

Extent of reaction maybe helpful by reducing the rank of data !!!!!

In the finishing point of reaction, the ratio of components are not the same for
different samples using different Co values.

4. consecutive 2nd order

(MS experim data)

Model for calib. Tranf. Without standards. (anal. Chem, 1996, 68,2987-2995.). Determining if it’s
necessary that conc. profiles are the same.

5. without clear model (DNA coupling …), searching for a trilinearity(parafac) and
possibility of augment
PART III:..........................
Calibration transfer for 3 way data(Carbaryl decomposition in basic medium.
),, for gray data(in pres of unkn interf)

PART IV:..........................
Australian data??

***Experimental data************
1- MS(master of sci, of Ms khkm) data (2nd order consecut
2- 1st order (Ru complex +DNA) asking about the synthesis stages from Dr Safaee and Dr
Ayatollahi. Mr Daneshtalab’s system (a ligand with negative charge shows a kinetic in
complex formation with DNA) 880320-880323
Binuclear complex of Ru2+ : no change in mechanism at different temperatures (angw07-kinet). The possible
problem is not simple synthesis of complex or not simple experimental system.
If we find the fluorophore base (group, Ybase) in tRNA we can order a sequence of DNA that includes
fluorescence.

3-Consecutive: cis Pt and fluo (talking with Dr Safaee

 cisPlatin has a nice reaction [consecutive, hours time scale] with G and A in DNA (InorgChimActa2009
362,651-668). It is investigated mainly by NMR and HPLC. Presence of a fleorophore on G(labeled DNA) or
Pt(fluorophiore ligand) seems proper
On the other hand, tRNA (JchemEd2008,85,5,678) includes G and includes a fluorophore group. It seems that
reaction of tRNA with cisPlatin can be investigated by ExEmFluo.
4-DNA hybridization(hard model is included) ordering 880401-880406
Anlyst09-dna-hybridiz-kinet.pdf
DNA(biological reaction or binding), (Not fast: hour), ExEm Fluorescence, and No change in mechanism at
different temperatures. Well known mechanism and easy to perform systems are preferred.
Experiments in different days can also be transferred.

Coupling of two single strands to form a double strand DNA occurs through a kinetic path. It can be
considered as a single step reaction, or as a consecutive two step reaction(by considering which side
binds first). Applying two couple of fluorophore quencher at both sides. Consecutive viewing is
possible.
The utilized experimental system in Biochemistry1993, 32, 3095-3104, are a 1 st order and 2nd
order reaction of association and dissociation of labeled 5’florsein and 3’ rodamin 20 mers and 10
mers (FRET). In paper of Anal chim Acta 536 (2005) 135-143, folding of a similar FRET system in a
31 mer oligonocleotide, in different conditions (pH and temperature) was investigated. In order to use
this system for our method (calib. Transfr), we should check the folding state of DNA in our
experimental condition and check the variation of it in different temperature.
If we have 5’florsein and 5’ rodamin 20 mers, is it possible to observe the FRET again, or not?

Papers:
Aca00 409,159-170 880215
ASA(to HASA) and AA(to HAA), UVVis, 6 diff pHs, 17 samples (17x91x6)
PARAFAC=>profiles=>pKa
??rank def of acids mixture is not considered
??decomp reaction of ASA to SA(at pH>=4) is considered as shift in wavelength.

Aca0-parafac-kinetic-fluor-....pdf (data is available) 880208

Oxidation reaction(>=2 steps), Only intermed is fluorophore, flow system, 7 samples, no hard
model
Regression model:
PARAFAC (4way: ex em time sample )+(a) one compon at a time(of load A)
(b) MLR on all compon.s of A
NPLS (4 way)
Cross val: leave sample out

Aca94,298,193-201.[glob-hard-diffA-report871124.ppt]
2nd ord globaliz => activation param.s in kinet (∆S, ∆H
NGL/M, jacobian

Aca97.....pdf
Calib transf (PDS) betw two NIR spectrometers.(Scanning and FT)
Scanning:Master, S/N (need: const temp during experim
Spectral matching: nmcm-1 + interpolation
CT=> proper precsion

Cils98-ct-osc-nir.pdf
Wold
OSC on master data before CT
OSC mech is explained

Anlyst09-dna-hybridiz-kinet.pdf
Reza Rezaee University of Arizona
Competitive Kinetic of hybridization, FRET, (Adv: no need to use labeled target)
M+Q=>MQ +T=> MQT (transient) => Q + MT =>M+T
Ordin Diff eqn (ODE), to obtain Conc Profiles
room temp, size of strands(Donor and acceptor), Sticky end of donor,
Inonic str ↑ => rate↑.
Sensitivity analysis(effect of each step on overall con prof)

Aca00 406,233, Massart

CT is a type of standardization(prediction without recalibrate). CT: select of standards.
CT: by PDS and ANN(each PDS window by NN, adv: flexiable in pres of nonlin.s)
Changing the spectra of Master(instead of slave)=> no need to change any new slave spectrum.
[Master: is the data for making the calibration model]
Multiplicative Signal correction MSC:is sometimes enough for correction of slave spectra.=> no
need to CT.
Sometimes MSC is not enough<= inaccurate predictions
1.plot of obs vs estim conc.
(plotting Slave spect vs Mastr: shows the type of
diff[syst or rand; pres of shift, offset and/or intens
diff: SLOPE or INTERC]
Considering the spectral differ of each slave sample to corresp master, outlying samples in slave
can be assigned(Fig 7). These outliers can not be selected as standard samples. There should be
a trend in the difference spectra.

Transfererred spectra by PDS is similar in noise (N/S) shape to Master, and by ANN is similar to
slave. (No of hidden nodes is crucial.) whether the slave instrument is more noisy, or the master,
each of PDS or ANN can be chosen for transfer.

ABC03-ct-osc.pdf
Cal transfer using OSC is better than PDS, Maybe there is no need to common standards in
master and slave(applicable to equil and kinet), SWNIR in different temp.s, residuals and RSEP
are compared.

ces08-kinet-hard-diffinstr.pdf
kinet, esterific, diff instrum, diff pure spect, mIR, NIR, 2nd order glob anal (local mode)
2 step mechanist( email to Puxty) NEW:CT from one type of instrum to another

cils09-ct-orthogonal-NIR.pdf
Orthogonalization methods,Calibration, NIR data, 4 instrument, intrabarnd and inter brand
calibration transfer, OSC, OPLS, EROS, DOP, TOP, Transfer sample
cils08-calibtranf-nostd.pdf (e-mail to Brown 880328-880402)
No reply..

Ac93-ct-2ndorder-kwlski.pdf
GC/MS, LC/UV, 2 dimensional PDS, a submatrix of elements instead of a vector in ordinary
PDS, intensity and shift correction, NEW: EBRP

Analyst01-kinet-varselect-tselection.pdf
Variable selection method, Time selection in kinetic system- excitation-emission-correlation
coefficient, constant interference with high overlap.

bichem87-kinet-DNA-pt-fluo.pdf
labeled oligomers, fluorophore, texas red, fluorcein, kinetic investigation, 1st order, equilibrium
studies

---------------------suggestion
A simple procedure like the application of mean centering on Kinetic (Dr Bahrams method) will
work. Running ACDsee to convert movie to frames.

-A Suggestion: Decomposition reaction of dopamine (tested by Ms Ghlm).

- Faculty of Pharm

///////////////////////////////////////////////////////////////////////////////////////////////////////////////

Mkhtr:

-Two weeks period from 880212 to find a proper subject for PhD Thesis.
- summer school..
- What is the price for a calorimeter?
-Cookies or fruits for our wed meeting, please.
-Webpage?
-summarized procedure for article writing..

- Writing simulation (m-file)for (AnBioch06-McGhee-DNA.pdf)

-Applic. of McGhee to experimental data (with multiple wavelengths)
- McGhee eqn can be applied as a hard model [L],[L]B <= <= N(#sites), l(ligand
length),CoL,CoDNA
To obtain , there is no need to solve the complex equation (forl>=3 and w>1) using roots
command. It can be solved by grid search
-McGhee for different ligands and diff sites.
-dealing with problem of different sites using the usual models of
M+L1=ML1
M+L2=ML2
Ligands are added together!!
(when dealing with l=1 problem and 1 type of sites and no interaction between ligands,
Scatchard plot is applicable which is obtained from simple equilibrium and Mass balance rules.
Hence, it seems possible to deal with similar system, including different sites, with common
models)
1. classic method can be applied., or 2. Newton-Raphson method.
- Error in parameters, MS?

Writing:
- MS work: ppt file, R&D doc, Completion

Paper:
-
intJMolSci09-cooper-isotherm-titr... .pdf
multiple binding sites.

Dna-ligand.ppt
AnBioch06-McGhee-DNA.pdf
McGhee von Hippel method: Cooperative and non cooperative binding of ligands with size l=1
or higher(in ht epresence of interaction of sites) is investigated. Scatchard plot is also mentioned.
Calorimetric data is considered.

-jappSp09-McGhee-DNA-spectroph.pdf

-abc03-bootstrap-inclusion.pdf

///////////////////////////////////////////////////////////////////////////////////////////////////////////////-

Omdk:

-Investigation of 8th workshop slides(Randomiz.

-Graphic card for MATLAB computations

Theory:
-Application of CrossModel validation to validate the 6 selected descriptors.
-mentioning that the maximum q2tot value is by introducing 11 variables.
However, as the q2tot plot levels off at 5 or 6 descriptors, we chose the
 number of selected var.s as 5. There was no significant improvement in
q2tot after 5 variab.s.
-8th workshop subjects (Chance correlation
-jchmm09-selec-qsar-inform-variab.pdf
.

-rbPLS [880430-880515] , PLSbdg [880430-880515]

-cross valid LOO, LMO and model completion [880430-880317], CDFS(hemmat)
-VIP

..Nonlinear correlation?

-Searching for a good data set for testing the programs (Todesch web page).

Papers:
QSAR+VarSel (NOT GA, NOT intellig(part swarm)

QSAR+VarSel+orthog
cils06-replacem-varSelect.pdf

QSAR+validation

Selwood data
In a folder

VarSel+ p-value
Cils09-NIR-randomizat-test.pdf

Jackknife

QSAR+Cross val

SPA+var sel

Orthogonalization (GramSchmidt

jcics03-var-sel-modeling.pdf
using q2LOO, regression r2, rint (correl betw sel descr.s) as the criteria for var selec. ,
selwood data, #var=2 to 6. Disadv: all possible sets of var.s were tested.. 5 descr is OK,
RMSE decrease as # var.s increase.

jcim08-VarSel-QSAR-Monte Carlo.pdf
MonteCarlo is very similar to jackknife, variables are resampling during resampling of
samples. A p-value is calculated from f-test (p-value in Jackknife is from t-test).
 trac03-cross val-variable selection
Leave many out (LMO) CV result in better prediction of test set compared to LOO. A nice
plot in this paper can be used.

SPA arauja

cils05-var_selec_multicolin.pdf (Dept Meeting, VIP?)

cils06-cross-model-valid-varsel-QSAR.pdf
cross model validation, p-value, Jackknife, number of iterations are higher than our method?!

AnCh98-NAS-error.pdf
Estimation of NAS for InvLS regression. The usual methods are for CLS.

jchmm09-selec-qsar-inform-variab.pdf (group meeting)

Scoring of variables by different criteria (inform vect.s: regression vect, correl vect, VIP[var
influence on projection], resid vect, NAS vect, cov proced), stepwise introduction of
variables into regression model till obtaining the best model. bidiagonalizationPLS alg.

Aca07-CDFS-Hemmat.ppt
Similar to CMV, division of data(>500 molec.s) to a number of sets, GA on each set,
common descript.s from diff models, R2 and q2, CV for each group..

Aca08-Hemmat ANN
CDFS

Cils06 81 180-187.
Replacement method, start from random set of 5 variables. Checking the first elem by
replacing with all other desc.s, to select the best first. Checking the 2nd ...

Slides of 8th workshop\ (Dr. Mehdi zadeh slides)

Chemometry.com\...validation

-----------------------------------------------------
Vsgh:

-4 chapters as before(introd, Liter, Experim,R&D

-Defense 890120 (before HAZF-O-EZAAFEH
-Thesis writing will be finished till 881220
 (Tolimo result 881221
(MCHE result 890115
-Thesis, introd: add LVQ after GA
-send the vsg5-SOMclassif to a NEW-EYE to read (MissEBRS)
Data and m-files?
-Seminar 3, presentation

Writing:
-Following the 2nd submiss to fuel.
-Correction of submiss to Tlnt

vsg3-Ternary-quatern-Mixt
??

vsg4-Talasemia
- Completion of Submission of Talassemia to ACA (accepted.

vsg5-SOMclassif
- Presentation of Simulation part to Kashan. Receive your prize
-Application of Kohonen netw on medical experimental data (diagnosis.
-Writing the initialR&D of paper
-Literature search (SOM)for completion of R&D.
-writing the Introd.

NMR-heart:
-16000 +DW(or binning)> 4000 +SOM20x20(Descr sel)> 400 variables (reduced size and noise)
-Comparison of “direct correl” and “SOMscores correl” for variab selec(using PLS pred).
(SOM scores can be from weights in CounterProp or XYfused)

CWavel-class (in Italy, todesch)

-Improvem of classif ability using CW(increase of betw-class variance/within-class var ratio.
Showing it using simulation and model data.
- testing different wavelet fuctions
-applying cross validation

- [JChmm07 21:451-458]. [Classif of Wine data,Skov]matrices are comparing. If we can

introduce a factor for this comparison (like distance of two vectors), we can use it in
Kohonens.

- Have you seen any application of Kohonen in modeling (quantit), or calibration?

-Sorting the trip to Italy June 1st.

-… Comments on preparation of the CD
1.Voices, one DVD (using Jet… software on Y: voice files can be converted to *.MP3) .
2. Movies, from 7 cassettes to 14 VCDs (by Mr Yarmohamm), and to …DVDs.
3.Presentations, m-files and photos, one CD(after getting the latest version of slides from
Roberto and Davide.

-“Classification school” at IASBS, summer!!

-Seminar2: LVQ, ordib88.

- Corrections of submission to fuel, as soon.

-----------------------------------------------------------------------------------------------------------
Krmi

-Missing values and Tucker for QSAR: hyperchem calculations 881115

-Experim Dimerization of Rhodamin in a changing temp. [at high ionic strength](ebrs: modeling)+ hard model
fitting 890122 {goal: to use RhodamB as thermometer for other system}
-ordering (finding) of some dimerizing chemicals in Jce06-lumin-thermometer.pdf [pyrinyl] 880122
+combining with other dimeriz(maybe not rank defic) or DNA melting.

-Finding a chem. React to change the pH of solution, slowly. It could be used for completion of Ms HasanZadehs
work.
-Change in ionic strength...
checking the conc profiles of dimerization at diff temp.s (SpAc05-
RhodB... .pdf)...
-
Paper:
Ms Hsnz thesis

Anch96-kubista-thermodyn.pdf
Dimerization (in diff temp.s)=> X data (+svd=> T(scores) +P (loadings))
+ closure: Ctot=Cmonom+2Cdimer + spectrum of monomer (diluted sample)
=> Conc and Spectral profiles.

SpAc05-RhodB-enthalp-dimeris.pdf
RhodamB and Rhodam6G dimeriz, diff temp=> ∆H, ∆S (Diff at diff ionic strengths and diff salts)
Sppect at diff temp.s + svd => X=SL=CRR-1V +Kubista Meth(+known Vmonom+ closure) => profiles

Jce06-lumin-thermometer.pdf
Temp change can can affect the fluorescence intensity.
-In absence of equilibr: usually decreasing (collision , intersystem cross (ST)
Intramolecular charge transfer, photodissoc
Change in fluoresce lifetime
-In presence of equil: dimerization, excimer, exiplex
Complex type(metallic
Cyclodextr complexat
increasing
 Decreasing (dep on exothermic and endothericity of react
(molar fluore of dimer and monomer
-Polymer conform chnge
-viscosity change

--------------------------------------------------------------------------------------------------------
ebrp
-linear algebra (m-file)
-calibration methods (MLR, PCR, PLS
-PDS
Data:
Thomas Skov(GC-MS data of wine

Progress:
-Simulation of calibration transfer(direct); MLR and PCR was used as calibr model (transfer
samples with same conc.s were used)
simulation: piecewise directStandardiz(PDS)
simulation: applic of PDS on peak alignment (when the other mode is not shifted)
Wine data(is the shift only in elution direction?): application of PS for alignment
modeling of 2DPDS [anch93-standardiz-2ndorder-kwlski.pdf]

experim from jce, LC+DAD.

PAPER:
anch93-standardiz-2ndorder-kwlski.pdf
GC/MS, LC/UV, 2 dimensional PDS, a submatrix of elements instead of a vector in ordinary
PDS, intensity and shift correction,
-Two transfer matrices are needed.

JPBA06-ct-NIR-pharma.pdf(after reading lin algebra+regress techn.s

JchromA04-proteomc-lc.pdf(to find the data
- Receive your awards. (Deliver your documents to Miss Khoshkam).
Publication, submission, seminar, poster, data, ppt presentation of a new paper...

- A number of your extra-prints can be paid for from grant.

- Please let me know if any of you receive Torkaman scholar, or do “kaar daaneshjooee”, or any other finance.

- It is possible for PhD students to go to an International seminar (outside iran), after passing the
comprehensive exam.
- Irannian seminar: The form of participation should be filled at the department office, one month before holding of
seminar.(once a year fees will be payed by dept)

-After acceptance of proposal, a 3-months progress report (in the start of each semester. Usually the progress
reports are only 2. The first one is three months after the proposal and the secons is before defense.
m-files:
It is very crucial for a programmer to write the programs using subprograms (as you already know
well).
And the main program should be simple and short. It should contain, for instance
1. settings of parameters
2. read data (including the data selection, as a code
3. data preprocessing
4. running a method *including method selection

sometimes running of programs are long and time consuming. In such conditions resuls from each run
ca be saved and be read by anther mfile.

I mean it is very important

A. to have access to any part of results and data, easily.
B. to be able to repeat a part of study, easily and rapidly.

A subprogram can be used to read data, once in the start (it can be commented and run by f9 once
- Continuous liter search.. (send me by e-mail
sciencedirect, wiley, scopus, web of science, ACS..
scholar.google.com
(journal: chemometrics, Analyst, Analytical, analytica, Talanta, chemical, spectroscopy, inorganic

- Writing of introduction can be started after acceptance of proposal and when there is no problem in the
system and everything is clear about the system. It needs a continuous liter search.
From the found papers the stages of work can be completed.

Progressing the project

-stages of work according to papers (Start from simplest condition and considering all different possible conditions
-Literature search should be done during progress..
- While pergressing the project, to avoid repeteations, each small step should be checked.

//////// Paper writing and submission (5 months before defense

[Literature search should be completed]
[m-files should be ordered, included subprograms]
1. Finalizing Figures file (ppt) (Fig.s and Tables
(read ref.s precisely)
Figures (from Matlab or excel, Live figures are preferred
-As small as possible,
-black and white,
- lines of plots: as thick as possible
- Fonts of axes scales: 12-14 Times new roman, regular
of axes titles: 12-14 Times new roman, regular

2. R&D *.doc file (only text (just like a detailed talk in a seminar
Tables and figures: by name and not numbers
Ref.s: by A,B,C
(Ref of Ref.s by: A1, B3, ...

3. Introduction (When R&D is finished and is sent for correction

English corrections (present or past tense ...

Final checking of quantities and abreviations
submission
m-files report
////////Thesis writing (3-5 months before defense ///////////////////////////

1. Results and discussion

2. Introduction and ...

////// Defense procedure [from 5 weeks before defense///////////////////////

Necessary
conditions: report.ppt[including explanations] : 100%
liter search : 100%
Thesis introduction : 60%
Thesis R&D : 90%
Paper : submitted
------------------------------------------------------------
start: progress report 2

Thesis :Final corrections, contents, Ref.s abstracts and print(part by part)

End of 1st week: Thesis: submission to dept,

merging,ordering and delivery of m-files, Poster and Data for web, awarded
form A,
copy of thesis (checking all together) and invitation letter to 1 foreign and 2 internal
referees

Paper : completion of R&D, Introduction, submission

Payments, accommodation and breakfast, car(arrngem +payments), [forms+payments to referees]

End of 5th week: Defense
Thesis: corrections, converting to pdf (chapter by chapter) for web, awarded

Receiving the signed forms and awards (after submiss, m-file, poster, Data, thesis
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