p160 orientation bacabac 2013-2014

7/28/2019 P160 Orientation Bacabac 2013-2014

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Physics 160 and APOJT (First Semester 2013-2014)

RG BacabacCourse Requirements:

1. Approved thesis proposal- See attached proposal evaluation sheet

2. Participation in research meetingsa. Present at least one (1) literature seminar at the journal club (see literatureseminar rubric)b. Present at least one (1) progress report update before the finals week (see

progress report rubric)

3. Performance evaluation by adviser (external adviser in case the thesis isconducted outside the department)

- See attached OJT rubricDeadlines for Completing the Thesis for Graduation

Physics 160

First draft of proposal submitted to adviser/s by July 22, 2013

Final draft of proposal submitted to the panel July 29, 2013

Th i l d b (fi t d) A t 12 2013


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Thesis proposal approved by (first round) August 12 2013

University of San Carlos

Department of Physics

Date

To: Thesis Evaluation Committee Member

[ ] Adviser [ ] Reader [ ] Chair

You are kindly requested to read thoroughly the

[ ] Thesis Proposal

[ ] Thesis

of ______________________________ and ______________________________ , as part of the

requirements for the degree of BS in Applied Physics.

Please indicate if the draft is acceptable for

[ ] Proposal Hearing


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A Three-Barrier, Two-Site Analysis of Gramicidin Conductivity

in Fluorinated and Native Peptides

Tomas Cruz and Angelita Huling

Physics Department

Cebuano University, Philippines

1. Purpose

For my thesis project, I propose to utilize an enhanced 3B2S model to compare energy profile

differences between fluorinated and non-fluorinated gramicidin channels. Through this analysis, I hope to

further elucidate the effect of fluorination on gramicidin function. To carry out this analysis, I will write

and execute the computer programs needed to analyze and compare the closeness of the fit between the

model and the data. These programs include a 3B2S model that will calculate currents given an energy

profile, and non-linear least squares fit that will compare predictions from the model program to measured

data and will iterate toward the minima. In my thesis, I will discuss the success of my analysis and its

relevance to membrane biophysics.

2. Background and Significance

Ionic channels span cell membranes and allow specific ions to pass into or out of a cell. They operate

in each of our bodys cells to maintain the proper physiological gradient of ions. Notable examples of cells


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the bilayer [2,3]. Later researchers introduced channel-forming substances into these bilayers and measured

their effect on ionic permeability over a range of voltages and concentrations for a variety of ions.

One of the most commonly used channel-forming substances is gramicidin A, a peptide that forms

transmembrane channels that are selective for monovalent cations. Gramicidin A is produced by various

strains ofBacillus brevis and is used as an antibiotic [4]. A linear peptide with known primary sequence

(Val, Gly, Ala, D-Leu, Ala, D-Val, Val, D-Val, Trp. D-Leu, Trp. DLeu, Trp, D-Leu, Trp), gramicidin A is

the only small ion pore whose primary amino acid sequence is completely known. The side chains are all

hydrophobic; thus the peptide can be easily inserted into lipid bilayers. With only 15 amino acids, it is the

simplest and best characterized channel-forming peptide [5].

Kinetic and chemical experiments show that the channel consists of two gramicidin peptides

transiently dimerized head-to-head by hydrogen bonds. The secondary structure of the peptide is a right-

handed helix with a central pore stabilized by --NH- - -O-- hydrogen bonds that extend parallel to thepore between groups six residues apart. The channel forms as the two helices dimerize as discussed, and it

has a central pore of 4 in diameter and is about 25 long [6,7].

Since the discovery of ionic channels, models of ion transport have been developed to describe their

energetics, mechanics and kinetics. The movement of ions through the channel can be considered as an

electrodiffusion problem and can be modeled using Nernst-Plank continuum theory, Brownian dynamics or

Eyring rate theory [5]. Thus far, Eyring rate theory has proved the most expedient and appropriate,


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The earliest application of Eyring rate theory to channel kinetics was by Hodgkin and Keynes, who

used barrier models to explain their potassium permeability results in squid axons [13]. General theoretical

models using saturating barrier one-ion channels were developed by Heckmann [14] and Lauger [15] while

Hladky introduced a model for gramicidin that had three energy barriers and two ion binding sites [16].

These early researchers noticed concentration-dependent permeability ratios and deviations from the

Ussing [17] flux-ratio test which implied that a one-ion model would be inadequate. Hladky [16] and

Lauger [15] reported concentration-dependent shapes of gramicidin current-voltage plots; at low ion

concentrations the plot was concave toward the voltage axis (sublinear), while at high ion concentrations

the plot was convex (supralinear). This concentration dependence implied that the channel would best be

modeled with multiple barriers. Also, the flux ratio exponent observed experimentally for gramicidin

channels was greater than 1.0, which implied that there were multiple ions in the channel [18].

Due to these experimental concerns, researchers sought for a suitable multiple barrier, multiple ion,

Eyring rate model for gramicidin conductance. Further research, which showed that the channel was single-

filing with ions and water molecules unable to pass each other due to the narrowness of the pore, simplified

the formulation of a suitable model [19,20]. The three-barrier, two-site, single-filing double occupancy

model (3B2S) first proposed and developed by Hladky to describe gramicidin conductance [21,22] has

proven adequate in describing most of the conductance features of the channel and has gained acceptance

in the field as a valid model. Furthermore, NMR studies [23] and X-ray diffraction studies [24] have


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ion passage through the channel [29]. With these modifications, the three-barrier, two-site model (3B2S)

has been successful in predicting most of the features of ion conductance data in gramicidin channels.

Using gramicidin peptides, Dr. Busaths lab at Brigham Young University has collec ted a large body

of data that consists of currents measured at various concentrations, voltages and temperatures. This

conductivity data is then analyzed for precision and a statistical confidence value is calculated. Dr. Busath

and associates have taken data using fluorinated and native (nonfluorinated) gramicidin peptides in an

attempt to study the effect of fluorination on the conductivity of the channel. This course of research

appears fruitful because the addition of fluorine appears to change the electrical profile of the channel by

modulating the interaction of ions with the peptide. Analysis of this data will hopefully elucidate the

specific effect of fluorine and will lead to a better understanding of the electrical profile of the channel and

its interactions with ions.

I feel that this thesis project will advance 3B2S modeling and will be of value to other membrane

biophysicists. Besides writing my thesis, I will also submit my findings to the Biophysical Journal for

publication.

3. Methods

To complete the project, I propose to do the following:

1 Review the literature for other attempts at energy barrier modeling


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4. Preliminary References

[1] B. Alberts, et al, Molecular Biology of the Cell, 3rd ed., New York: Garland Publishing, Inc.,1994.[2] O.S. Anderson, et al, Importance of tryptophan dipoles for protein function: 5-Fluorination of

tryptophans in gramicidin A channels,J. Amer. Chem. Soc., 120, 1998, pp. 5142-5146.

[3] D. Busath and G. Szabo, Permeation characteristics of gramicidin conformers,Biophys. J., 53,1988B, pp. 697-707.

[4] H. Eyring, The activated complex in chemical reactions,J. Chem. Phys., 3, 1935, pp. 107-115.[5] B. Hille, Ionic Channels of Excitable Membranes, Sunderland, Mass, Sinauer Associates, 1984.[6] P.C. Jordan, The total electrostatic potential in a gramicidin channel,J. Membr. Biol., 78, 1984,

pp. 91-102.

[7] P. Mueller and D.O. Rudin, Translocators in biomolecular lipid membranes: Their role indissipative and conservative bioenergy transductions,Curr. Top. Bioeng. 3, 1969, pp. 157-249.

[8] P. Mueller, D.O. Rudin, H.T. Tien and W.C. Wescott, Reconstitution of cell membrane structurein vitro and its transformation into an excitable system,Nature 194, 1962, pp. 979-980.

[9] W. M. O'Leary, ed.,Practical Handbook of Microbiology, Boca Raton, CRC Press, Inc., 1989.[10] D. W. Urry, K.U. Prasad, and T.L. Trapane, Location of monovalent cation binding sites in the

gramicidin channel.Proc. Natl. Acad. Sci., 79, 1982, pp. 390-94.

5. Time line for completing the thesis

15 Jul 2050 Submit final draft of thesis proposal to adviser/s for comments


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10 Feb 2051 Submit final draft of thesis to panel members

17 Feb 2051 Finalize thesis defense schedule with panel members

2025 Feb 2051 Thesis defense

27 Feb 205102 Mar 2051 Revise thesis according to panel members comments and submit to

adviser/s for final review

05 Mar 2051 Collect reviewed thesis from adviser/s and collate document with CV

for binding

08 Mar 2051 Complete three signed hardbound copies of thesis


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University of San Carlos

Department of Physics

CERTIFICATE OF ACCEPTABILITY

Title of Thesis:

Name/s of Proponent/s:

(To be completed by the thesis evaluation committee member)

Yes No Do the proposed scope and contents of the manuscript meet the standards

expected of a BS Applied Physics thesis?[ ] [ ]

Are the methods clearly explained and is/are the proponent/s capable ofimplementing the methods?

[ ] [ ]

Are the methods appropriate to address the research questions? [ ] [ ]

I have reviewed the thesis proposal and consider it to be

[ ] acceptable.

[ ] unacceptable.

Further Comments/Suggestions:


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Physics 160: Thesis Proposal Evaluation SheetStudent Name:

Thesis:

Adviser/s:

I. Research proposal

Criteria for assessment

A. Context The motivation to study the centralsubject includes a description of whichknowledge domain it applies to, omissionsin existing literature, theoretical starting

points, assumptions, and explanation ofscientific relevance.

Score: ___ 0 ___ 1 ___ 2 ___ 3 ___ 4 ___ 5

Comments:

B. Goal The research proposal provides a cleardescription of the research goal, researchquestions, and main deliverables. The goalis also an indicator of the ambition leveland scope of the thesis project.

Score: ___ 0 ___ 1 ___ 2 ___ 3 ___ 4 ___ 5

Comments:

C. Approach The proposal includes the theoreticalframework and the research methods thatare applied to study the subject. Inaddition, there is a project outline withspecific tasks, dates, and deliverables.

Score: ___ 0 ___ 1 ___ 2 ___ 3 ___ 4 ___ 5

Comments:

II. Presentation of the proposal


A. Argument The presentation is objective, thorough,and understandable. It provides the readerwith a coherent insight into the definedresearch questions choice of methods

Score: ___ 0 ___ 1 ___ 2 ___ 3 ___ 4 ___ 5

Comments:


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III. Attitude and motivation of the student towards research


A. Analytical

capabilities

The student is aware of the relevant

methodological and practical criteria, whythey are important, and when they aremet. The student shows insight in thestrong and weak points of the currentresearch and practice, and searches forcreative solutions.

Score: ___ 0 ___ 1 ___ 2 ___ 3 ___ 4 ___ 5

Comments:

B. Attitude The student shows independence, workshard, precisely, and is eager to learn. The

student actively participates in progressreport meetings and reworks the researchplan using feedback from the adviser(s).

Score: ___ 0 ___ 1 ___ 2 ___ 3 ___ 4 ___ 5

Comments:

C. Researchprocess

The student adheres to the research planbut is also prepared to change or adaptthe plan if necessary. The student hands inmaterial on time, and keepsappointments.

Score: ___ 0 ___ 1 ___ 2 ___ 3 ___ 4 ___ 5

Comments:

IV. Summary of Scores (Please summarize the scores below)

Criteria A (5 pts) B (5 pts) C (5 pts) Total (15 pts)

Area

I. Research proposal ___ ___ ___ ___

II. Presentation ___ ___ ___ ___

III. Attitude and motivation ___ ___ ___ ___

Score: ___/45


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PHYS 160 Literature Seminar Requirements Rubric

CriteriaNo

evidence(0%)

Very littleevidence(< 50%)

Partialevidence(50-80%)

Completeevidence(> 80%)

Quality of ContentA. Ideas are developed with clear focus and audience is provided with a clear and interesting overview

0 1 2 3

B. Provides coherent insight into the defined research questions, choice of methods, results, and discussion 0 1 2 3C. Summarizes main points and places results in the context of the big picture 0 1 2 3

DeliveryA. Suitable volume, enunciates clearly, no halting/repetition of words, avoids filler phrases (e.g., um, ah, OK, like,

basically, actually, etc)

0 1 2 3

B. Uses appropriate gestures and eye contact, avoids nervous movements 0 1 2 3C. Ability to handle disruptions with ease, involves listeners by fielding questions 0 1 2 3

AttitudeA.Actively participates in literature seminars and research meetings 0 1 2 3B. Chooses articles which are interesting and relevant 0 1 2 3C. Shows familiarity with the main points stated in the references of the article being presented 0 1 2 3

Presentation SlidesA.Good contrast, pleasant color scheme, minimal text entries and no unnecessary details, suitable layout 0 1 2 3B.Number of slides is minimal and the slides are organized to provide better pacing 0 1 2 3C. Images, diagrams, animations are effectively used and serve their purpose 0 1 2 3

Score Equivalents

Excellent(72)

1.0

Above Satisfactory(68-71)

1.1

Satisfactory(61-68)

Below Satisfactory (49-58) Unsuccessful(0-47)

5.067 = 1.2 65 = 1.4 63 = 1.6 61 = 1.8 59 = 2.0 57 = 2.1 55 = 2.3 53 = 2.5 51 = 2.7 49 = 2.9

66 = 1.3 64 = 1.5 62 = 1.7 60 = 1.9 58 = 2.0 56 = 2.2 54 = 2.4 52 = 2.6 50 = 2.8 48 = 3.0

Literature Seminar # _______

CriteriaQuality ofContent

Score Delivery Score Attitude ScorePresentation

SlidesScore Total Grade

ElementA B C Sum X3 A B C Sum X2 A B C Sum X2 A B C Sum X1 72 1.0

Name of Student


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PHYS 160 Progress Report Requirements Rubric

CriteriaNo

evidence(0%)

Very littleevidence(< 50%)

Partialevidence(50-80%)

Completeevidence(> 80%)

Quality of ContentA. Objectives and parameters are well-defined, methods adequately outlined

0 1 2 3

B. Provides coherent insight into the choice of methods and techniques 0 1 2 3C. Assumptions are clearly presented in the method, results are valid, reliable, and verifiable, and conclusions are

scientifically sound0 1 2 3

Work PlanningA. Ideas are developed with clear focus and addresses most of the issues presented in past progress reports 0 1 2 3B. Adheres to the research work plan but is also prepared to change or adapt the plan when necessary 0 1 2 3C. Sets a clear and realistic work plan and presents the main deliverables 0 1 2 3

Attitude (consult with respective adviser/s)B.Actively participates in meetings and hands in material on time 0 1 2 3B. Shows insight into the strong and weak points of the research methods and searches for creative solutions 0 1 2 3C. Works hard, precisely, independently, and is eager to learn 0 1 2 3

Presentation EfficiencyC.Structure and Speech: the presenter uses appropriate words in speech and provides enough depth and emphasis

on each topic discussed; the presentation is well-organized and follows a logical sequencing of ideas0 1 2 3

D.Visual Aids: the presentation slides follow a format, layout and structure appropriate for a scientificpresentation and the font style/size and color scheme facilitate reading and promote audience focus attention

0 1 2 3

C. Delivery: the presenter uses suitable volume, speaks with correct intonation, overcomes strong accents, avoidsfiller phrases (e.g. um, ah, actually, etc.) and repetitions of words/phrases, makes good eye contact withaudience, controls nervousness, and answers questions from the audience

0 1 2 3

Score Equivalents

Excellent(72)

1.0

Above Satisfactory(68-71)

1.1

Satisfactory(61-68)

Below Satisfactory (49-58) Unsuccessful(0-47)

5.067 = 1.2 65 = 1.4 63 = 1.6 61 = 1.8 59 = 2.0 57 = 2.1 55 = 2.3 53 = 2.5 51 = 2.7 49 = 2.9

66 = 1.3 64 = 1.5 62 = 1.7 60 = 1.9 58 = 2.0 56 = 2.2 54 = 2.4 52 = 2.6 50 = 2.8 48 = 3.0

Progress Report # _______

CriteriaQuality ofContent

Score Work Planning Score Attitude ScorePresentation

EfficiencyScore Total Grade

ElementA B C Sum X3 A B C Sum X2 A B C Sum X2 A B C Sum X1 72 1.0

Name of Student


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University of San CarlosDepartment of Physics

BS Applied Physics OJT Grade Sheet

(N.B. Using the scale in the leftmost column as guide, indicate the students score in the SHADED CELLS provided for each of the SIX areas below.)

ScaleThesis / Problem /

QuestionInformation Seeking /Selecting & Evaluating

Analysis Synthesis Documentation Process / Output

3.1to4.0

Student posed athoughtful, creativequestion that engagedthem in challenging orprovocative research.The question breaks newground or contributes to

knowledge in a focused,specific area.

Student gathered informationfrom a variety of qualityelectronic and print sources,including appropriate licenseddatabases. Sources arerelevant, balanced and includecritical readings relating to the

thesis or problem. Primarysources were included.

Student carefullyanalyzed theinformation collectedand drew appropriateand inventiveconclusions supported

by evidence.

Student developedappropriate structurefor communicatingoutput, incorporatingvariety of qualitysources. Information islogically andcreatively organized.

Student documented allsources, including visuals,sounds, and animations.Sources are properly cited,both in-text and on works-cited/works-consultedsections. Documentation iserror-free.

Student effectively andcreatively used appropriatecommunication tools toconvey their conclusions anddemonstrated thorough,effective research techniques.Output displays creativity andoriginality.

2.1to3.0

Student formulated afocused question thatinvolves him inchallenging research.

Student gathered informationfrom a variety of relevantsources both print andelectronic.

Student shows goodeffort in analyzing theevidence collected.

Student logicallyorganized the outputand made goodconnections amongideas.

Student documented sourceswith some care, sources arecited, both in-text and onworks-cited/works-consultedsections. Few errors werenoted.

Student effectivelycommunicated the results ofresearch to the audience.

1.1to2.0

Student generated aquestion that lends itselfto readily available orobvious answers.

Student gathered informationfrom a limited range of sourcesand displayed minimal effort inselecting quality resources.

Student conclusionscould have beensupported by strongerevidence. Level ofanalysis could havebeen deeper.

Student could haveput greater effort intoorganizing the output.

Student needs to use greatercare in documenting sources.Documentation was poorlyconstructed or was veryminimal.

Student needs to work oncommunicating moreeffectively.

0to1.0

Student relied onsupervisor-generatedquestions or developed aquestion requiring littlecreative thought.

Student gathered informationthat lacked relevance, quality,depth and balance.

Student conclusionssimply involvedrestating information.Conclusions were notsupported by evidence.

Students work is notlogically or effectivelystructured.

Student clearly plagiarizedmaterials and/ordocumentation wasunavailable.

Student shows little evidenceof thoughtful research and isnot capable of effectivelycommunicating researchfindings.

Score:

PLEASE USE THE FOLLOWING FORMULA:

Total scoreGrade =5

6

. IFGrade 3.0, WRITE5.0Grade:

I hereby certify that the above evaluation is correct. Supervisor (please sign above printed name):

te: Supervisor / Adviser

Name of Student/Trainee:

Place of training: Duration of training (months):

Task description:


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p160 orientation bacabac 2013-2014

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