Programs Chances and Preparation for Fall 2012 Math PhD Program

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Admission to PhD programs in applied mathematics can be competitive, especially with a GPA of 3.1 in upper division math courses and a 3.38 overall. The applicant is graduating in Spring 2012 and is limited to applying for funded PhD or master's programs due to funding constraints from their undergraduate institution. They have a strong background from a top 25 undergraduate institution and have taken relevant coursework, including advanced classes in Real Analysis and Dynamical Systems, with plans for further studies in Abstract Algebra and Engineering Math.Research experience includes participation in a summer REU in Mathematical Biology and a planned undergraduate thesis on ODEs/Dynamical Systems, though the timing of the thesis completion may impact its consideration in applications. The applicant expresses a primary interest in Mathematical Biology and Ordinary Differential Equations but is open to other applied math subfields. They note the scarcity of funded master's programs and emphasize that graduate schools will not see the thesis work until after applications are submitted, which may affect their competitiveness.
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Would I be able to get into any PhD Program for applied math? Would you please recommend some PhD and/or masters (with funding) programs to apply to? I'll be graduating in Spring 2012 and unfortunately, my undergrad institution only funds for an extra semester, so my only choice is to apply to a PhD program and/or a funded masters program (if I can find a masters program that gives funding) meaning that I don't have an extra year to prepare for PhD admission.

Currently, I have a 3.1 gpa in my upper div math classes (around 3.2 if lower div math classes are included) and a 3.38 overall. My university is a top 25 undergrad and in the top 50 of math grad schools.

Classes I've taken so far:
Lower Div:
Calculus II A-
Calculus III B+
Linear Algebra B

Upper Div:
Intro to Probability Theory: C
Number Theory (Withdrew)
Statistics B+
Nonlinear Ordinary Differential Equations (Dynamical Systems) A
Real Analysis I currently taking at a UC (University of California campus)

I will take Real Analysis II, Advanced Linear Algebra, a 2 semester reading course on Dynamical Systems using a grad text (Guckenheimer and Holmes), Abstract Algebra, and an Engineering Math Course (on PDEs) at my university.

Research Experience:
Summer 2010 REU in Mathematical Biology- created research project, which was presented in undergrad research poster presentation at the Joint Math Meetings
Planned- Undergrad senior thesis on ODEs/Dynamical Systems (either applied or theoretical based) with professor during Spring 2012

Awards:
Bank of America Scholarship Recipient
Scholarship through my university
Received travel funding from the MAA to fly to the Joint Math Meetings 2011

I am mainly interested in Mathematical Biology and Ordinary Differential Equations, but I am open to other subfields of applied math.
 
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Here is a (subjective) ranking of phd programs in applied math. Its rankings are focused on programs with more funded students. http://graduate-school.phds.org/rankings/applied-mathematics/rank/funding

EDIT: I should also say that there are very few masters programs out there with funding available.
 
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Also, if you're doing your thesis Spring 2012, grad schools won't see it in time when you're applying during Fall 2012. And saying "I will complete a thesis on '...' next semester" doesn't hold as much weight as "I am currently doing a thesis on '...' this semester".

Just a heads-up. Grad schools only get to see your work in the first half of the year that you're applying to them (excluding wait-lists, etc.).
 
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