2016 2017 GUIDE TO GRADUATE STUDIES - DEPARTMENT OF CHEMISTRY AND BIOCHEMISTRY - Department of ...

 
UNIVERSITY OF NOTRE DAME

DEPARTMENT OF CHEMISTRY AND BIOCHEMISTRY

      GUIDE	
  TO	
  GRADUATE	
  STUDIES	
  

                 2016	
  –	
  2017	
  
CONTENTS
                                                                               	
  
Chapter	
              	
         	
          	
         	
          	
               	
     	
        	
          	
         	
        	
  	
  	
  	
  	
  	
  	
  	
  Page	
  
                                                                               	
  
1.	
          INTRODUCTION	
      	
        	
          	
      	
        	
   	
                                  	
         	
        	
                            3	
  
	
            	
  
2.	
          DEGREE	
  REQUIREMENTS	
  FOR	
  THE	
  DOCTOR	
  OF	
  PHILOSOPHY	
                                 	
         	
        	
                            3	
  
	
  
3.	
          ACADEMIC	
  AND	
  RESEARCH	
  PROGRESS	
  EXAMINATION	
                                 	
          	
         	
        	
                            6	
  
	
  
4.	
  	
      UNIVERSITY	
  ORAL	
  CANDIDACY	
  EXAMINATION	
                               	
        	
          	
         	
        	
                            9	
  
	
  
5.	
  	
      DOCTORAL	
  DISSERTATION	
                 	
          	
               	
     	
        	
          	
         	
        	
                            10	
  
                                                                               	
  
6.	
  	
      NON-­‐THESIS	
  AND	
  THESIS	
  MASTER’S	
   	
                        	
     	
        	
          	
         	
        	
                            11	
  
	
  
7.	
  	
      ACADEMIC	
  POLICIES	
   	
                	
          	
               	
     	
        	
          	
         	
        	
                            12	
  
	
  
8.	
  	
      ACADEMIC	
  REGULATIONS	
  	
              	
          	
               	
     	
        	
          	
         	
        	
                            16	
  
	
  
9.	
  	
      FINANCIAL	
  SUPPORT	
   	
                	
          	
               	
     	
        	
          	
         	
        	
                            19	
  
	
  
10.	
  	
     GRADUATE	
  STUDENT	
  GRIEVANCE	
  PROCESS	
   	
                             	
        	
          	
         	
        	
                            21	
  
	
  
11.	
  	
     ACADEMIC	
  INTEGRITY	
  	
                	
          	
               	
     	
        	
          	
         	
        	
                            25	
  
	
  
12.	
  	
     POLICIES	
  ON	
  HARASSMENT	
  AND	
  OTHER	
  ASPECTS	
  OF	
  STUDENT	
  LIFE	
                              	
        	
                            26	
  

Guide	
  to	
  Graduate	
  Studies,	
  Department	
  of	
  Chemistry	
  and	
  Biochemistry,	
  University	
  of	
  Notre	
  Dame	
                                                2	
  
1.	
  INTRODUCTION	
  
	
  
The	
   graduate	
   degree	
   programs	
   in	
   the	
   Department	
   of	
   Chemistry	
   and	
   Biochemistry	
   within	
   the	
  
College	
  of	
  Science	
  at	
  the	
  University	
  of	
  Notre	
  Dame	
  have	
  as	
  their	
  immediate	
  goal	
  the	
  development	
  
of	
  individuals	
  with	
  the	
  capability	
  of	
  initiating	
  and	
  conducting	
  independent	
  research	
  in	
  chemistry,	
  
biochemistry,	
   and	
   related	
   fields.	
   	
   The	
   granting	
   of	
   a	
   graduate	
   degree	
   is	
   a	
   formal	
   recognition	
   of	
  
achievement	
  in	
  variety	
  of	
  pursuits.	
  	
  It	
  acknowledges	
  that	
  a	
  student	
  has	
  satisfactorily	
  completed	
  a	
  
series	
   of	
   advanced	
   courses,	
   has	
   displayed	
   creative	
   and	
   original	
   thinking	
   in	
   their	
   candidacy	
  
examinations,	
   and	
   demonstrated	
   a	
   mastery	
   of	
   experimental	
   inquiry	
   as	
   expressed	
   through	
   the	
  
original	
  research	
  described	
  in	
  the	
  dissertation.	
  
	
  
The	
   general	
   features	
   and	
   relevant	
   specific	
   details	
   of	
   the	
   graduate	
   programs	
   are	
   described	
   below.	
  
Graduate	
   students	
   in	
   the	
   doctoral	
   program	
   will	
   be	
   required	
   to	
   demonstrate	
   competence	
   in	
  
preliminary	
   candidacy	
   examinations	
   and	
   in	
   oral	
   examinations	
   strategically	
   located	
   in	
   the	
  
program,	
   culminating	
   in	
   satisfactory	
   completion	
   of	
   an	
   acceptable	
   doctoral	
   thesis.	
   This	
   document	
  
is	
  updated	
  each	
  year	
  as	
  the	
  rules	
  and	
  regulations	
  of	
  the	
  program	
  evolve.	
  	
  	
  

   2.	
  REQUIREMENTS	
  FOR	
  THE	
  DOCTOR	
  OF	
  PHILOSOPHY	
  IN	
  CHEMISTRY	
  OR	
  BIOCHEMISTRY	
  
	
  
2.1.	
  Degrees	
  Offered	
  
	
  
The	
   department	
   offers	
   separate	
   PhD	
   degrees	
   in	
   Chemistry	
   and	
   in	
   Biochemistry.	
   Although	
   the	
  
overall	
  requirements	
  are	
  the	
  same,	
  the	
  two	
  degrees	
  remain	
  distinct.	
  Students	
  are	
  admitted	
  into	
  
either	
  the	
  Chemistry	
  or	
  the	
  Biochemistry	
  PhD	
  program.	
  Switching	
  programs	
  is	
  permissible	
  with	
  
approval	
  of	
  the	
  Director	
  of	
  Graduate	
  Studies	
  or	
  the	
  Department	
  Chair.	
  The	
  department	
  does	
  not	
  
admit	
  students	
  into	
  a	
  Master’s	
  degree	
  program,	
  although	
  a	
  terminal	
  Master’s	
  degree	
  is	
  available	
  
as	
  described	
  in	
  Section	
  7.	
  
	
  
2.2.	
  Course	
  Work	
  Requirements	
  
	
  
In	
  order	
  to	
  remain	
  in	
  good	
  academic	
  standing	
  within	
  the	
  Department,	
  all	
  graduate	
  students	
  will	
  
be	
   required	
   to	
   have	
   completed	
   18	
   credits	
   of	
   graduate	
   coursework	
   by	
   the	
   end	
   of	
   their	
   third	
  
semester.	
   If	
   a	
   student	
   fails	
   to	
   meet	
   this	
   requirement,	
   he	
   or	
   she	
   will	
   be	
   dismissed	
   from	
   the	
  
program	
   without	
   a	
   degree	
   at	
   the	
   end	
   of	
   the	
   third	
   semester.	
   Graduate	
   courses	
   assigning	
   letter	
  
grades	
   and	
   related	
   to	
   chemistry	
   and	
   biochemistry,	
   broadly	
   defined,	
   will	
   count	
   toward	
   the	
  
requirement.	
   English	
   as	
   a	
   Second	
   Language	
   will	
   not	
   count	
   toward	
   the	
   requirement,	
   and	
   directed	
  
readings	
   and	
   graduate	
   coursework	
   from	
   other	
   institutions	
   will	
   qualify	
   only	
   with	
   explicit	
  
approval	
  of	
  the	
  Director	
  of	
  Graduate	
  Studies.	
  Exceptions	
  to	
  this	
  policy	
  will	
  be	
  considered	
  in	
  the	
  
event	
   of	
   a	
   documented	
   extenuating	
   circumstance,	
   as	
   determined	
   by	
   the	
   Director	
   of	
   Graduate	
  
Studies.	
  In	
  light	
  of	
  this	
  requirement,	
  graduate	
  students	
  are	
  strongly	
  advised	
  against	
  dropping	
  or	
  
withdrawing	
  from	
  graduate	
  courses.	
  	
  
	
  
Beyond	
   the	
   minimum	
   credit	
   requirement	
   noted	
   above,	
   the	
   Department	
   recommends	
   21	
   –	
   27	
  
credits	
  of	
  graduate	
  coursework	
  for	
  either	
  PhD	
  degree.	
  A	
  typical	
  sequence	
  is	
  three	
  courses	
  in	
  the	
  
first	
   semester,	
   two	
   courses	
   in	
   the	
   second	
   semester,	
   and	
   one	
   or	
   two	
   courses	
   in	
   each	
   of	
   the	
  

Guide	
  to	
  Graduate	
  Studies,	
  Department	
  of	
  Chemistry	
  and	
  Biochemistry,	
  University	
  of	
  Notre	
  Dame	
                         3	
  
following	
  two	
  semesters	
  (21-­‐27	
  credits).	
  Advanced	
  students	
  typically	
  audit	
  appropriate	
  classes.	
  
Before	
   reaching	
   candidacy,	
   students	
   typically	
   take	
   a	
   minimum	
   of	
   three	
   core	
   courses	
   in	
   their	
  
chosen	
   sub-­‐discipline.	
   Individual	
   thesis	
   advisors	
   may	
   require	
   a	
   student	
   to	
   take	
   additional	
  
courses	
  that	
  are	
  considered	
  appropriate.	
  
	
  
All	
  students	
  must	
  pass	
  the	
  CHEM	
  63603:	
  Research	
  Perspectives	
  in	
  Chemistry	
  and	
  Biochemistry	
  
in	
  their	
  first	
  semester.	
  
	
  
In	
  addition	
  to	
  the	
  requirements	
  above,	
  a	
  combined	
  total	
  of	
  60	
  credits	
  are	
  required	
  for	
  the	
  PhD	
  in	
  
Chemistry	
   or	
   Biochemistry.	
   This	
   total	
   includes	
   all	
   courses	
   taken,	
   including	
   not	
   only	
   instructional	
  
coursework,	
   but	
   research,	
   seminars,	
   directed	
   readings,	
   etc.	
   Students	
   should	
   ensure	
   their	
   total	
  
credit	
  counts	
  are	
  on	
  track	
  to	
  reach	
  60	
  by	
  their	
  anticipated	
  date	
  of	
  graduation.	
  In	
  the	
  first	
  three	
  
semesters,	
  the	
  total	
  credit	
  count,	
  including	
  research,	
  should	
  be	
  at	
  least	
  10.	
  
	
  
2.3.	
  Waiver	
  of	
  Course	
  Work	
  
	
  
The	
  Department	
  of	
  Chemistry	
  and	
  Biochemistry	
  may	
  accept	
  course	
  work	
  completed	
  at	
  another	
  
accredited	
   university	
   toward	
   meeting	
   the	
   requirements	
   for	
   either	
   doctoral	
   degree.	
   	
   The	
   Director	
  
of	
   Graduate	
   Studies	
   should	
   be	
   consulted,	
   and	
   may	
   agree	
   to	
   waive	
   some	
   of	
   the	
   course	
   work	
  
requirements.	
  Official	
  documentation	
  of	
  course	
  completion,	
  grades,	
  and	
  content	
  will	
  be	
  required.	
  

2.4.	
  Foreign	
  Language	
  Requirement	
  

There	
   is	
   no	
   departmental	
   foreign	
   language	
   requirement.	
   	
   However,	
   individual	
   thesis	
   advisors	
  
may	
   require	
   a	
   specific	
   language	
   course	
   if	
   that	
   language	
   is	
   deemed	
   appropriate	
   for	
   a	
   particular	
  
area	
  of	
  research.

2.5.	
  Residency	
  
	
  
The	
   minimum	
   residency	
   requirement	
   for	
   either	
   PhD	
   degree	
   is	
   full-­‐time	
   status	
   for	
   four	
  
consecutive	
  semesters	
  (including	
  the	
  summer	
  session).	
  	
  

2.6.	
  Degree	
  Eligibility	
  
	
  
The	
   student	
   must	
   fulfill	
   all	
   doctoral	
   requirements,	
   including	
   the	
   dissertation	
   and	
   its	
   defense,	
  
within	
   eight	
   years	
   from	
   the	
   time	
   of	
   initial	
   enrollment.	
   The	
   department	
   will	
   generally	
   dismiss	
   a	
  
student	
  if	
  they	
  have	
  not	
  completed	
  their	
  degree	
  requirements	
  within	
  8	
  years.	
  Failure	
  to	
  complete	
  
any	
   of	
   the	
   Graduate	
   School	
   or	
   departmental	
   requirements	
   within	
   the	
   prescribed	
   period	
   may	
  
result	
   in	
   forfeiture	
   of	
   degree	
   eligibility.	
   In	
   addition,	
   each	
   student,	
   regardless	
   of	
   his/her	
   source	
   of	
  
financial	
  support,	
  must	
  spend	
  two	
  semesters	
  as	
  a	
  teaching	
  assistant.	
  Cumulative	
  GPA	
  must	
  be	
  ≥	
  
3.0	
  to	
  be	
  in	
  good	
  academic	
  standing	
  and	
  to	
  be	
  eligible	
  for	
  a	
  degree.	
  	
  

2.7.	
  Research	
  Advisors	
  and	
  Dissertation	
  Committees	
  
	
  
Entering	
   graduate	
   students	
   in	
   either	
   degree	
   program	
   participate	
   in	
   three,	
   one-­‐month	
   laboratory	
  
rotations.	
   These	
   are	
   designed	
   to	
   expose	
   students	
   to	
   the	
   research	
   and	
   culture	
   of	
   various	
  
laboratories	
   and	
   to	
   provide	
   an	
   opportunity	
   for	
   new	
   students	
   to	
   interact	
   with	
   senior	
   graduate	
  

Guide	
  to	
  Graduate	
  Studies,	
  Department	
  of	
  Chemistry	
  and	
  Biochemistry,	
  University	
  of	
  Notre	
  Dame	
                            4	
  
students	
   and	
   postdocs.	
   Rotating	
   students	
   will	
   learn	
   about	
   the	
   research	
   performed	
   in	
   each	
   lab	
  
through	
  interactions	
  with	
  lab	
  members	
  and	
  attendance	
  at	
  regular	
  group	
  meetings.	
  	
  The	
  primary	
  
goal	
  of	
  these	
  rotations	
  is	
  to	
  familiarize	
  students	
  with	
  specific	
  labs,	
  not	
  to	
  accomplish	
  research.	
  
	
  
Laboratories	
  for	
  the	
  rotations	
  will	
  be	
  selected	
  by	
  the	
  student,	
  and	
  may	
  include	
  any	
  teaching	
  and	
  
research	
  faculty	
  that	
  have	
  elected	
  to	
  participate	
  in	
  the	
  program.	
  Choices	
  are	
  not	
  guaranteed	
  but	
  
will	
  be	
  accommodated	
  as	
  best	
  as	
  possible	
  according	
  to	
  space	
  and	
  parity	
  issues.	
  Students	
  submit	
  
their	
  choices	
  of	
  labs	
  for	
  the	
  second	
  and	
  third	
  rotations	
  to	
  the	
  Graduate	
  Studies	
  office	
  prior	
  to	
  the	
  
end	
  of	
  each	
  rotation.	
  
	
  
The	
  initial	
  advisor	
  for	
  new	
  students	
  in	
  either	
  degree	
  program	
  is	
  the	
  Director	
  of	
  Graduate	
  Studies.	
  
At	
  the	
  conclusion	
  of	
  the	
  rotation	
  process	
  (typically	
  in	
  November	
  for	
  students	
  entering	
  in	
  the	
  fall),	
  
the	
  student	
  will	
  list	
  one	
  member	
  of	
  the	
  teaching	
  and	
  research	
  faculty,	
  from	
  those	
  who	
  are	
  eligible	
  
to	
   accept	
   students,	
   that	
   would	
   be	
   acceptable	
   as	
   a	
   research	
   advisor.	
   	
   The	
   completed	
   forms	
   are	
  
forwarded	
   to	
   the	
   Department	
   Chair	
   who	
   with	
   the	
   Director	
   of	
   Graduate	
   Studies	
   initiates	
   the	
  
process	
   and	
   approves	
   the	
   assignment	
   of	
   students	
   to	
   individual	
   faculty	
   members	
   according	
   to	
  
departmental	
   policies	
   regarding	
   funding	
   and	
   student	
   support.	
   Normally,	
   it	
   is	
   possible	
   to	
   match	
   a	
  
student	
   with	
   his/her	
   choice	
   for	
   a	
   research	
   advisor;	
   however,	
   circumstances	
   can	
   arise,	
   such	
   as	
  
funding,	
   space,	
   or	
   other	
   considerations,	
   that	
   will	
   prevent	
   a	
   faculty	
   member	
   from	
   accepting	
   a	
  
student	
  into	
  his/her	
  group.	
  	
  
	
  
If	
   a	
   student	
   cannot	
   be	
   assigned	
   to	
   their	
   first	
   choice,	
   the	
   process	
   must	
   be	
   restarted,	
   with	
   the	
  
student	
   choosing	
   another	
   potential	
   faculty	
   from	
   those	
   still	
   eligible	
   to	
   accept	
   students.	
   All	
  
students	
   are	
   expected	
   to	
   be	
   assigned	
   to	
   an	
   advisor	
   before	
   the	
   beginning	
   of	
   their	
   second	
  
semester;	
   in	
   exceptional	
   cases	
   the	
   Director	
   of	
   Graduate	
   Studies	
   or	
   Department	
   Chair	
   may	
  
approve	
   an	
   extension	
   of	
   the	
   advisor	
   selection	
   process	
   into	
   the	
   second	
   semester.	
   However,	
   all	
  
students	
   must	
   be	
   assigned	
   to	
   an	
   advisor	
   before	
   the	
   end	
   of	
   their	
   second	
   semester.	
   If	
   approval	
   for	
  
an	
  extension	
  into	
  the	
  second	
  semester	
  is	
  not	
  given	
  or	
  an	
  advisor	
  is	
  not	
  found	
  by	
  the	
  end	
  of	
  the	
  
second	
  semester,	
  the	
  student	
  may	
  be	
  dismissed	
  from	
  the	
  program.	
  
	
              	
  
Research	
   advisors	
   (also	
   referred	
   to	
   as	
   dissertation	
   or	
   thesis	
   directors)	
   are	
   chosen	
   from	
   the	
  
regular	
  Teaching	
  and	
  Research	
  faculty	
  of	
  the	
  Department	
  of	
  Chemistry	
  and	
  Biochemistry.	
  There	
  
also	
  may	
  be	
  one	
  co-­‐director	
  chosen	
  from	
  affiliated	
  faculty	
  within	
  or	
  outside	
  the	
  department.	
  In	
  
exceptional	
  cases,	
  a	
  student	
  may	
  choose	
  an	
  advisor	
  director	
  from	
  the	
  Notre	
  Dame	
  teaching	
  and	
  
research	
  faculty	
  outside	
  the	
  department.	
  	
  Arrangements	
  for	
  extra-­‐departmental	
  directors	
  or	
  co-­‐
directors	
  must	
  be	
  consistent	
  with	
  departmental	
  policies	
  and	
  must	
  be	
  approved	
  by	
  the	
  Director	
  of	
  
Graduate	
  Studies.	
  
	
  
The	
  research	
  advisor	
  assists	
  the	
  student	
  in	
  identifying	
  a	
  suitable	
  research	
  problem	
  that	
  will	
  be	
  
the	
  focus	
  of	
  the	
  dissertation.	
  	
  The	
  advisor	
  consults	
  with	
  the	
  student	
  on	
  a	
  regular	
  basis	
  concerning	
  
progress	
   with	
   research.	
   	
   In	
   addition,	
   the	
   advisor	
   will	
   assist	
   the	
   student	
   in	
   designing	
   a	
   plan	
   of	
  
study	
  that	
  will	
  complement,	
  but	
  is	
  not	
  limited	
  to,	
  his/her	
  area	
  of	
  research.	
  	
  	
  
	
  
After	
   the	
   student	
   has	
   chosen	
   a	
   research	
   advisor,	
   a	
   dissertation	
   committee	
   consisting	
   of	
   a	
  
minimum	
   of	
   three	
   faculty	
   members,	
   including	
   the	
   research	
   advisor,	
   is	
   appointed	
   for	
   each	
  
student.	
   	
   This	
   committee	
   reflects	
   the	
   student's	
   research	
   interests	
   and	
   the	
   general	
   area	
   of	
   the	
  
proposed	
   dissertation.	
   	
   The	
   committee	
   need	
   not	
   be	
   made	
   up	
   of	
   members	
   of	
   a	
   single	
   sub-­‐
Guide	
  to	
  Graduate	
  Studies,	
  Department	
  of	
  Chemistry	
  and	
  Biochemistry,	
  University	
  of	
  Notre	
  Dame	
                              5	
  
discipline.	
  	
  This	
  committee	
  will	
  monitor	
  the	
  student's	
  progress	
  during	
  the	
  individual's	
  tenure	
  as	
  
a	
   student	
   in	
   the	
   department.	
   	
   They	
   will	
   serve	
   on	
   the	
   student's	
   oral	
   examinations,	
   and	
   serve	
   as	
  
readers	
   of	
   the	
   dissertation.	
   The	
   Director	
   of	
   Graduate	
   Studies	
   must	
   approve	
   the	
   appointment	
   of	
   a	
  
committee	
   member	
   from	
   outside	
   the	
   Teaching	
   and	
   Research	
   faculty	
   of	
   the	
   student's	
   department	
  
or	
  from	
  outside	
  the	
  university.	
  In	
  such	
  cases	
  a	
  majority	
  of	
  the	
  committee	
  must	
  be	
  members	
  of	
  the	
  
Department.	
   The	
   appointment	
   of	
   committee	
   members	
   who	
   are	
   not	
   Teaching	
   and	
   Research	
  
faculty	
  must	
  be	
  approved	
  by	
  the	
  Department	
  Chair.	
  	
  
	
  
It	
  is	
  the	
  responsibility	
  of	
  the	
  student	
  to	
  meet	
  frequently	
  with	
  the	
  advisor,	
  as	
  well	
  as	
  the	
  rest	
  of	
  
their	
   thesis	
   committee,	
   keeping	
   them	
   abreast	
   of	
   progress	
   with	
   research,	
   course	
   work,	
   and	
  
candidacy	
  examinations.	
  	
  
	
  
Although	
   considerable	
   effort	
   will	
   be	
   made	
   to	
   avoid	
   such	
   instances,	
   after	
   consulting	
   with	
   the	
  
Department	
  Chair	
  and/or	
  Director	
  of	
  Graduate	
  Studies,	
  an	
  advisor	
  may	
  dismiss	
  a	
  student	
  from	
  
his/her	
  laboratory	
  for	
  poor	
  progression,	
  poor	
  relationships,	
  or	
  other	
  reasons.	
  In	
  most	
  cases	
  the	
  
student	
   will	
   have	
   been	
   given	
   written	
   warning	
   and	
   sufficient	
   time	
   to	
   address	
   any	
   concerns.	
   In	
  
cases	
  when	
  an	
  advisor	
  dismisses	
  a	
  student,	
  the	
  student	
  must	
  find	
  a	
  new	
  advisor	
  as	
  described	
  in	
  
Section	
  7.	
  
	
  
2.8.	
  Diagnostic	
  Examinations	
  

Entering	
  students	
  may	
  be	
  asked	
  to	
  take	
  diagnostic	
  examinations.	
  The	
  purpose	
  of	
  the	
  exams	
  are	
  
to	
   help	
   the	
   students	
   and	
   the	
   graduate	
   studies	
   committee	
   make	
   informed	
   course	
   selection	
  
decisions.	
  
	
  
2.9.	
  Seminars	
  
	
  
All	
   students	
   must	
   enroll	
   in	
   Seminar	
   in	
   Chemistry	
   (CHEM	
   63601	
   in	
   the	
   fall,	
   CHEM	
   63602	
   in	
  
spring)	
  and	
  attend	
  all	
  lectures	
  in	
  this	
  departmental	
  series.	
  
        	
  
2.10.	
  Admission	
  to	
  Candidacy	
  

Admission	
   to	
   candidacy	
   is	
   a	
   prerequisite	
   to	
   receiving	
   any	
   graduate	
   degree.	
   To	
   qualify	
   for	
  
admission	
  to	
  doctoral	
  candidacy,	
  a	
  student	
  must:	
  (1)	
  complete	
  18	
  credits	
  of	
  	
  instructional	
  course	
  
work	
   with	
   a	
   cumulative	
   average	
   of	
   3.0	
   or	
   better	
   (see	
   Section	
   2.2);	
   (2)	
   pass	
   the	
   Academic	
   and	
  
Research	
   Progress	
   Examination	
   (Section	
   3);	
   and	
   (3)	
   pass	
   the	
   University	
   Oral	
   Candidacy	
   Exam	
  
(Section	
   4).	
   It	
   is	
   the	
   responsibility	
   of	
   the	
   student	
   to	
   apply	
   for	
   candidacy	
   admission	
   by	
   submitting	
  
the	
  appropriate	
  form	
  to	
  the	
  Graduate	
  School.	
  Students	
  must	
  be	
  admitted	
  to	
  Candidacy	
  by	
  the	
  end	
  
of	
  their	
  fourth	
  year	
  after	
  admission.	
  

                                 3.	
  ACADEMIC	
  AND	
  RESEARCH	
  PROGRESS	
  EXAMINATION	
  

All	
   PhD	
   students	
   in	
   Chemistry	
   and	
   Biochemistry	
   must	
   pass	
   the	
   Academic	
   and	
   Research	
   Progress	
  
(ARP)	
   exam	
   in	
   their	
   third	
   semester	
   to	
   continue	
   in	
   the	
   PhD	
   program.	
   The	
   goal	
   of	
   the	
   ARP	
   exam	
   is	
  
to	
  help	
  the	
  student	
  develop	
  fundamental	
  knowledge	
  in	
  their	
  field,	
  demonstrate	
  an	
  awareness	
  of	
  
their	
   research	
   project,	
   and	
   show	
   progress	
   in	
   their	
   laboratory	
   investigations.	
   The	
   ARP	
   exam	
   is	
  
taken	
  during	
  a	
  student’s	
  third	
  semester;	
  to	
  be	
  eligible	
  for	
  the	
  exam,	
  the	
  student	
  must	
  be	
  in	
  good	
  

Guide	
  to	
  Graduate	
  Studies,	
  Department	
  of	
  Chemistry	
  and	
  Biochemistry,	
  University	
  of	
  Notre	
  Dame	
                                    6	
  
academic	
   standing	
   in	
   the	
   Department.	
   The	
   exam	
   consists	
   of	
   a	
   written	
   document	
   and	
   an	
   oral	
  
defense	
  in	
  front	
  of	
  the	
  student’s	
  committee.	
  
TIMELINE	
  
	
  
	
            Fall	
  admits	
  
                    o Research	
  summary	
  paper	
  is	
  due	
  the	
  last	
  Friday	
  in	
  September	
  of	
  the	
  third	
  semester	
  
                    o Oral	
  exams	
  are	
  scheduled	
  in	
  October,	
  retakes	
  are	
  scheduled	
  in	
  December	
  
	
  
              Spring	
  admits	
  
                    o Research	
  summary	
  paper	
  is	
  due	
  the	
  last	
  Friday	
  in	
  February	
  of	
  the	
  third	
  semester	
  
                    o Oral	
  exams	
  are	
  scheduled	
  in	
  March,	
  retakes	
  are	
  scheduled	
  in	
  May	
  
	
  
RESEARCH	
  SUMMARY	
  PAPER	
  
	
  
A	
  paper	
  summarizing	
  the	
  student’s	
  research	
  project,	
  progress,	
  and	
  effort	
  is	
  due	
  by	
  4	
  PM	
  in	
  the	
  
Graduate	
  Studies	
  office	
  on	
  the	
  last	
  Friday	
  in	
  September	
  or	
  February.	
  Excluding	
  references,	
  this	
  
paper	
  should	
  be	
  a	
  minimum	
  of	
  8	
  pages	
  in	
  length	
  (double	
  spaced,	
  1	
  inch	
  margins,	
  12	
  point	
  font),	
  
but	
   no	
   more	
   than	
   10	
   pages.	
   A	
   suggested	
   organization	
   of	
   the	
   paper	
   are	
   as	
   follows:	
   (1)	
  
Introduction,	
   (2)	
   Goals,	
   (3)	
   Results,	
   (4)	
   Future	
   Directions,	
   and	
   (5)	
   References.	
   Approximately	
  
equal	
   weight	
   should	
   be	
   devoted	
   to	
   sections	
   (1)	
   through	
   (3),	
   ensuring	
   a	
   minimum	
   of	
   one	
   page	
   for	
  
future	
  directions.	
  If	
  a	
  student	
  does	
  not	
  submit	
  the	
  research	
  summary	
  paper	
  by	
  the	
  deadline,	
  the	
  
student	
   will	
   have	
   failed	
   the	
   exam	
   and	
   must	
   leave	
   the	
   program	
   at	
   the	
   completion	
   of	
   the	
   semester.	
  
If	
  in	
  good	
  academic	
  standing,	
  the	
  student	
  may	
  opt	
  to	
  leave	
  with	
  a	
  non-­‐thesis	
  Master’s,	
  which	
  will	
  
require	
  an	
  oral	
  exam	
  before	
  the	
  end	
  of	
  the	
  semester.	
  	
  
	
  
ORAL	
  EXAM	
  
	
  
In	
  the	
  month	
  of	
  October	
  or	
  March,	
  the	
  student	
  will	
  present	
  a	
  20	
  –	
  30	
  minute	
  seminar	
  on	
  his	
  or	
  
her	
   research	
   project.	
   The	
   presentation	
   should	
   contain	
   the	
   following	
   elements:	
   (1)	
   the	
   broad	
  
scientific	
   context/motivation	
   for	
   the	
  research,	
  (2)	
  preliminary	
  results,	
  and	
  (3)	
  a	
  clear	
  one-­‐year	
  
plan	
   for	
   future	
   work.	
   Following	
   the	
   seminar,	
   there	
   will	
   be	
   two	
   rounds	
   of	
   questions.	
   Each	
  
committee	
   member	
   is	
   allowed	
   two	
   rounds	
   of	
   questions	
   (totaling	
   ~20	
   minutes)	
   that	
   address	
  
specifics	
   of	
   the	
   research	
   project,	
   as	
   well	
   as	
   pertinent	
   fundamental	
   background	
   knowledge.	
  
Following	
   questions,	
   the	
   student	
   will	
   leave	
   the	
   room	
   while	
   the	
   committee	
   deliberates.	
  
Deliberations	
   will	
   cover	
   performance	
   on	
   the	
   written	
   and	
   oral	
   portions	
   of	
   the	
   exam,	
   performance	
  
in	
  research	
  and	
  coursework,	
  and	
  performance	
  as	
  a	
  TA.	
  
	
  
SUPPLEMENTAL	
  INFORMATION	
  
	
  
The	
  committee	
  will	
  consider	
  the	
  following	
  supplemental	
  information	
  during	
  its	
  deliberation:	
  
	
  
              1. Coursework	
  completed	
  and	
  grades	
  
              2. TA	
  performance	
  
              3. Communication	
  sent	
  after	
  the	
  two	
  prior	
  semi-­‐annual	
  reviews	
  of	
  graduate	
  students	
  
	
  
Guide	
  to	
  Graduate	
  Studies,	
  Department	
  of	
  Chemistry	
  and	
  Biochemistry,	
  University	
  of	
  Notre	
  Dame	
                             7	
  
OUTCOMES	
  
	
  
The	
  committee	
  will	
  consider	
  the	
  following	
  outcomes	
  for	
  the	
  exam:	
  
	
  
            1. Pass	
  and	
  continuation	
  in	
  the	
  Ph.D.	
  program	
  
            2. Fail	
   and	
   movement	
   into	
   the	
   Master’s	
   program,	
   with	
   the	
   outcome	
   of	
   the	
   ARP	
   exam	
  
               serving	
  as	
  successful	
  completion	
  of	
  the	
  non-­‐thesis	
  Master’s	
  exam	
  
            3. Fail	
  and	
  removal	
  from	
  graduate	
  studies	
  with	
  no	
  degree	
  

If	
  fail	
  and	
  removal	
  from	
  graduate	
  studies	
  is	
  the	
  outcome,	
  the	
  student	
  must	
  depart	
  at	
  the	
  end	
  of	
  
the	
  third	
  semester.	
  If	
  fail	
  and	
  movement	
  to	
  the	
  Master’s	
  program	
  is	
  the	
  outcome,	
  the	
  student	
  will	
  
have	
  the	
  option	
  of	
  retaking	
  the	
  exam.	
  Situations	
  in	
  which	
  a	
  retake	
  is	
  called	
  for	
  may	
  include	
  mixed	
  
performance	
   on	
   different	
   aspects	
   of	
   the	
   exam	
   or	
   poor	
   exam	
   performance	
   together	
   with	
  
outstanding	
   performance	
   in	
   coursework.	
   The	
   student	
   will	
   make	
   this	
   decision	
   after	
   consulting	
  
with	
   the	
   committee	
   and	
   must	
   communicate	
   the	
   decision	
   to	
   the	
   Graduate	
   Studies	
   office	
   within	
  
two	
   business	
   days	
   of	
   the	
   exam.	
   If	
   the	
   student	
   chooses	
   to	
   retake	
   the	
   exam,	
   it	
   will	
   be	
   scheduled	
  
during	
  the	
  month	
  of	
  December	
  or	
  May.	
  There	
  will	
  be	
  no	
  option	
  for	
  a	
  second	
  retake.	
  
	
  
A	
  student	
  who	
  fails	
  the	
  exam	
  and	
  is	
  moved	
  into	
  the	
  Master’s	
  program,	
  whether	
  as	
  an	
  outcome	
  of	
  
the	
  first	
  attempt	
  or	
  a	
  retake,	
  will	
  have	
  the	
  option	
  of	
  leaving	
  with	
  a	
  non-­‐thesis	
  Master’s	
  at	
  the	
  end	
  
of	
   the	
   third	
   semester	
   or,	
   provided	
   the	
   student	
   is	
   in	
   good	
   academic	
   standing,	
   remaining	
   in	
   the	
  
program	
  as	
  a	
  TA	
  for	
  a	
  final	
  term.	
  In	
  the	
  latter	
  case	
  a	
  non-­‐thesis	
  Master’s	
  degree	
  will	
  be	
  conferred	
  
at	
   the	
   end	
   of	
   the	
   fourth	
   semester	
   (summer	
   for	
   spring	
   admits),	
   contingent	
   upon	
   adequate	
  
performance	
   as	
   a	
   TA	
   (TA	
   evaluations	
   to	
   be	
   provided	
   by	
   the	
   course	
   instructor	
   or	
   laboratory	
  
director	
  and	
  judged	
  by	
  the	
  Director	
  of	
  Graduate	
  Studies	
  and/or	
  Chair).	
  
	
  
Any	
   student	
   leaving	
   with	
   a	
   non-­‐thesis	
   Master’s	
   must	
   have	
   successfully	
   completed	
   all	
   other	
  
programmatic	
   requirements	
   for	
   the	
   non-­‐thesis	
   Master’s	
   degree	
   (18	
   credits	
   of	
   instruction	
   and	
   30	
  
total	
  credit	
  hours	
  with	
  a	
  GPA	
  ≥	
  3.0).	
  
	
  
At	
   the	
   discretion	
   of	
   the	
   advisor	
   and	
   only	
   with	
   the	
   advisor’s	
   financial	
   support,	
   a	
   student	
   who	
   fails	
  
the	
   exam	
   and	
   is	
   moved	
   into	
   the	
   Master’s	
   program	
   may	
   have	
   the	
   option	
   of	
   completing	
   a	
   thesis	
  
Master’s	
   in	
   the	
   advisor’s	
   laboratory.	
   In	
   such	
   a	
   case,	
   provided	
   the	
   advisor	
   is	
   willing	
   and	
   able	
   to	
  
provide	
  funding,	
  the	
  student	
  may	
  remain	
  in	
  the	
  program	
  until	
  completion	
  of	
  the	
  thesis	
  or	
  the	
  end	
  
of	
  the	
  fifth	
  year,	
  although	
  the	
  student	
  may	
  choose	
  to	
  leave	
  with	
  a	
  non-­‐thesis	
  Master’s	
  at	
  any	
  time.	
  	
  
	
  
FEEDBACK	
  AND	
  EXPECTATIONS	
  
	
  
The	
  student	
  will	
  be	
  provided	
  written	
  feedback	
  for	
  the	
  written	
  document,	
  oral	
  performance,	
  and	
  
overall	
   progression	
   in	
   the	
   program,	
   including	
   coursework	
   and	
   TA	
   performance.	
   Scores	
   will	
   be	
  
entered	
   on	
   the	
   following	
   scale:	
   Excellent	
   (5),	
   Good	
   (4),	
   Satisfactory	
   (3),	
   Substantial	
   Weakness	
  
(2),	
  and	
  Poor	
  (1).	
  
	
  
In	
  scoring	
  the	
  written	
  proposal	
  the	
  committee	
  will	
  consider:	
  
	
          	
  

       o    Formatting	
  and	
  correct	
  use	
  of	
  grammar	
  and	
  style	
  
       o    Appropriate	
  and	
  adequate	
  use	
  of	
  references	
  
       o    Organization	
  and	
  clarity	
  
       o    Adequate	
  introduction	
  and	
  motivation	
  for	
  the	
  project	
  
       o    Clear	
  articulation	
  of	
  project	
  objectives	
  
Guide	
  to	
  Graduate	
  Studies,	
  Department	
  of	
  Chemistry	
  and	
  Biochemistry,	
  University	
  of	
  Notre	
  Dame	
                                 8	
  
o Description	
  of	
  techniques	
  and	
  methods	
  to	
  be	
  used	
  to	
  achieve	
  project	
  objectives	
  
       o Description	
  of	
  future	
  plans	
  
	
  
In	
  scoring	
  the	
  oral	
  performance	
  the	
  committee	
  will	
  consider:	
  
	
  
       o Formatting	
  and	
  correct	
  use	
  of	
  grammar	
  and	
  style	
  
       o Appropriate	
  and	
  adequate	
  use	
  of	
  references	
  
       o Organization	
  and	
  clarity	
  
       o Quality	
  of	
  the	
  research	
  effort	
  
       o Appropriate	
  interpretation	
  of	
  data	
  presented	
  
       o Ability	
  to	
  explain	
  the	
  relevance	
  and	
  context	
  of	
  the	
  work	
  
       o Ability	
  to	
  explain	
  and	
  defend	
  the	
  project	
  aims	
  and	
  investigative	
  approach	
  
       o Knowledge	
  of	
  techniques	
  and	
  equipment	
  used	
  
       o Understanding	
  of	
  fundamental	
  principles	
  and	
  concepts	
  
       o Ability	
  to	
  articulate	
  clearly	
  and	
  defend	
  a	
  plan	
  for	
  future	
  work	
  

                                     4.	
  UNIVERSITY	
  ORAL	
  CANDIDACY	
  EXAMINATION	
  

The	
  Oral	
  Candidacy	
  Exam	
  (OCE)	
  is	
  required	
  by	
  the	
  Graduate	
  School.	
  	
  The	
  purpose	
  of	
  the	
  OCE	
  is	
  
for	
  the	
  student’s	
  committee	
  to	
  make	
  a	
  determination	
  regarding	
  their	
  scientific	
  preparedness	
  for	
  
admission	
   to	
   candidacy.	
   The	
   OCE	
   must	
   be	
   completed	
   before	
   the	
   end	
   of	
   the	
   student's	
   eighth	
  
semester	
   in	
   the	
   PhD	
   program.	
   Students	
   who	
   do	
   not	
   complete	
   their	
   Graduate	
   School	
   Oral	
  
requirement	
  by	
  the	
  end	
  of	
  their	
  eighth	
  semester	
  are	
  not	
  eligible	
  for	
  Departmental	
  or	
  University	
  
Funding	
  (including	
  tuition	
  support).	
  	
  
	
  
Prior	
  to	
  the	
  OCE,	
  the	
  student	
  will	
  submit	
  a	
  brief	
  (10	
  –	
  20	
  page)	
  written	
  summary	
  of	
  the	
  proposed	
  
thesis	
  research,	
  including	
  a	
  description	
  of	
  the	
  thesis	
  problem	
  and	
  its	
  significance,	
  a	
  review	
  of	
  the	
  
relevant	
   scientific	
   literature	
   with	
   bibliography,	
   a	
   discussion	
   of	
   the	
   methods	
   to	
   be	
   used	
   in	
  
attacking	
  the	
  problem,	
  and	
  a	
  description	
  of	
  the	
  research	
  work	
  already	
  accomplished.	
  
	
  
At	
   the	
   OCE,	
   the	
   student	
   will	
   present	
   a	
   public	
   research	
   seminar	
   (30	
   –	
   40	
   minutes	
   in	
   length)	
  
Following	
  the	
  seminar,	
  each	
  committee	
  member	
  will	
  have	
  the	
  opportunity	
  to	
  ask	
  two	
  rounds	
  of	
  
questions	
  (totaling	
  approximately	
  20	
  minutes).	
  
	
  
After	
  completion	
  of	
  the	
  OCE,	
  the	
  chair	
  of	
  the	
  committee	
  (typically	
  the	
  student’s	
  research	
  advisor)	
  
calls	
  for	
  a	
  discussion	
  followed	
  by	
  a	
  vote	
  of	
  the	
  examiners.	
  With	
  a	
  committee	
  of	
  three,	
  two	
  votes	
  
are	
  required	
  to	
  pass.	
  If	
  the	
  committee	
  has	
  four	
  members,	
  three	
  votes	
  are	
  required	
  to	
  pass.	
  The	
  
chair	
  sends	
  a	
  written	
  report	
  of	
  the	
  overall	
  quality	
  of	
  the	
  oral	
  examination	
  and	
  the	
  results	
  of	
  the	
  
voting	
   immediately	
   to	
   the	
   Graduate	
   School.	
   The	
   Graduate	
   School	
   officially	
   notifies	
   the	
   student	
   of	
  
the	
  results	
  of	
  the	
  candidacy	
  examination.	
  
	
  
In	
   case	
   of	
   failure	
   in	
   candidacy	
   examinations,	
   the	
   Director	
   of	
   Graduate	
   Studies,	
   on	
   the	
  
recommendation	
  of	
  a	
  majority	
  of	
  the	
  examiners,	
  may	
  authorize	
  a	
  retake	
  of	
  the	
  examination.	
  An	
  
authorization	
   for	
   retake	
   must	
   be	
   approved	
   by	
   the	
   Graduate	
   School.	
   A	
   second	
   failure	
   results	
   in	
  
forfeiture	
  of	
  degree	
  eligibility	
  and	
  is	
  recorded	
  on	
  the	
  candidate's	
  permanent	
  record.	
  

Guide	
  to	
  Graduate	
  Studies,	
  Department	
  of	
  Chemistry	
  and	
  Biochemistry,	
  University	
  of	
  Notre	
  Dame	
                        9	
  
5.	
  DOCTORAL	
  DISSERTATION	
  

The	
   candidate	
   delivers	
   paper	
   or	
   electronic	
   copies	
   of	
   the	
   finished	
   dissertation,	
   signed	
   by	
   the	
  
research	
   advisor,	
   to	
   the	
   Graduate	
   Studies	
   office	
   for	
   distribution	
   to	
   the	
   other	
   members	
   of	
   the	
  
dissertation	
  committee.	
  	
  The	
  dissertation	
  should	
  follow	
  the	
  guidelines	
  in	
  the	
  Graduate	
  School's	
  
Guide	
   for	
   Formatting	
   and	
   Submitting	
   Dissertations	
   and	
   Theses,	
   even	
   if	
   the	
   candidate	
   has	
  
previously	
   published	
   the	
   substance	
   of	
   the	
   dissertation	
   in	
   scholarly	
   journals.	
   The	
   Guide	
   is	
  
available	
  at	
  the	
  Graduate	
  School	
  website:	
  http://graduateschool.nd.edu.	
  
	
  
Readers	
  normally	
  have	
  two	
  to	
  four	
  weeks	
  to	
  read	
  the	
  dissertation,	
  decide	
  whether	
  it	
  is	
  ready	
  to	
  
be	
  defended,	
  and	
  so	
  indicate	
  on	
  the	
  appropriate	
  form	
  to	
  the	
  Graduate	
  School.	
  Reader	
  approval	
  of	
  
the	
   dissertation	
   for	
   defense	
   does	
   not	
   imply	
   reader	
   agreement	
   or	
   support;	
   it	
   implies	
   reader	
  
acknowledgment	
   that	
   the	
   dissertation	
   is	
   an	
   academically	
   sound	
   and	
   defensible	
   scholarly	
  
product.	
  Only	
  a	
  dissertation	
  which	
  has	
  been	
  unanimously	
  approved	
  for	
  defense	
  by	
  the	
  committee	
  
may	
  be	
  defended.	
  
	
  
Even	
   though	
   the	
   dissertation	
   has	
   been	
   approved	
   for	
   defense,	
   revisions	
   may	
   be	
   required.	
   If	
  
defects	
   in	
   the	
   dissertation	
   come	
   to	
   light	
   at	
   the	
   defense,	
   the	
   candidate	
   may	
   be	
   asked	
   to	
   revise	
   the	
  
dissertation	
  before	
  it	
  is	
  accepted	
  by	
  the	
  Graduate	
  School	
  and	
  the	
  degree	
  is	
  conferred.	
  In	
  that	
  case,	
  
it	
   will	
   be	
   the	
   responsibility	
   of	
   the	
   dissertation	
   director,	
   or	
   such	
   person	
   as	
   the	
   committee	
   may	
  
appoint,	
  to	
  report	
  to	
  the	
  Graduate	
  School	
  that	
  such	
  revisions	
  have	
  been	
  completed	
  satisfactorily.	
  

5.1.	
  Dissertation	
  Defense	
  

In	
   defending	
   the	
   dissertation,	
   the	
   doctoral	
   candidate	
   supports	
   its	
   claims,	
   procedures	
   and	
   results.	
  
The	
   defense	
   is	
   the	
   traditional	
   instrument	
   that	
   enables	
   the	
   candidate	
   to	
   explore	
   with	
   the	
  
dissertation	
  committee	
  the	
  dissertation's	
  substantive	
  and	
  methodological	
  force.	
  In	
  this	
  way,	
  the	
  
candidate	
   and	
   the	
   committee	
   confirm	
   the	
   candidate's	
   scholarly	
   grasp	
   of	
   the	
   chosen	
   research	
  
area.	
  
	
  
The	
  defense	
  of	
  the	
  dissertation	
  begins	
  with	
  a	
  40	
  –	
  50	
  minute	
  public	
  presentation	
  that	
  addresses	
  
the	
   major	
   results	
   of	
   the	
   thesis	
   research.	
   	
   Immediately	
   following	
   questions	
   from	
   the	
   general	
  
audience,	
   the	
   examination	
   committee	
   meets	
   with	
   the	
   candidate	
   in	
   a	
   closed	
   session.	
   	
   This	
  
provides	
   the	
   opportunity	
   for	
   clarification	
   and,	
   if	
   necessary,	
   rectification	
   of	
   potential	
   problems	
   in	
  
the	
  dissertation.	
  	
  After	
  the	
  examination	
  is	
  completed,	
  the	
  advisor	
  calls	
  for	
  a	
  discussion	
  followed	
  
by	
   a	
   vote	
   of	
   the	
   dissertation	
   committee.	
   A	
   majority	
   vote	
   is	
   required	
   to	
   pass	
   a	
   candidate.	
   The	
  
advisor	
  sends	
  a	
  written	
  report	
  of	
  the	
  voting	
  results	
  immediately	
  to	
  the	
  Graduate	
  School.	
  

5.2.	
  Formal	
  Submission	
  of	
  the	
  Final	
  Dissertation	
  	
  
	
  
To	
   receive	
   the	
   degree	
   at	
   the	
   next	
   commencement,	
   the	
   doctoral	
   student	
   who	
   has	
   successfully	
  
defended	
  his	
  or	
  her	
  dissertation	
  must	
  complete	
  the	
  requirements	
  for	
  submission	
  of	
  their	
  thesis,	
  
including	
   a	
   format	
   check	
   by	
   the	
   Graduate	
   School.	
   The	
   formatting	
   check	
   and	
   submission	
   deadline	
  
for	
  a	
  given	
  commencement	
  date	
  is	
  published	
  in	
  the	
  Graduate	
  School	
  Calendar.	
  	
  
              	
  
Guide	
  to	
  Graduate	
  Studies,	
  Department	
  of	
  Chemistry	
  and	
  Biochemistry,	
  University	
  of	
  Notre	
  Dame	
                                  10	
  
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