1 % Year for live projects
7 @string{CC-BY-SA-3.0-US = "CC BY-SA 3.0 US"}
8 @string{CC-BY-NC-SA-3.0-US = "CC BY-NC-SA 3.0 US"}
12 @string{Drexel = "Drexel University"}
16 @string{AAPT = "American Association of Physics Teachers"}
17 @string{ASQ = "American Society for Quality"}
18 @string{Blackwell = "Blackwell Publishing Ltd."}
19 @string{DLA = "Digital Library and Archives, Virginia Polytechnic
20 Institute and State University"}
21 @string{PH = "Prentice Hall, Inc."}
22 @string{WSS = "Wiley Subscription Services, Inc., A Wiley Company"}
26 @string{Crowell-address = "2233 Loma Alta Dr., Fullerton, CA 92833"}
27 @string{UpperSaddleRiver = "Upper Saddle River, NJ 07458"}
31 @string{AJP = "American Journal of Physics"}
32 @string{ASQ:HEB = "ASQ Higher Education Brief"}
33 @string{IJBMM = "International Journal of Biological Macromolecules"}
34 @string{JEE = "Journal of Engineering Education"}
35 @string{JITE = "Journal of Industrial Teacher Education"}
36 @string{NDTL = "New Directions for Teaching and Learning"}
37 @string{Science = "Science"}
41 @string{MBelloni = "Belloni, Mario"}
42 @string{RBrent = "Brent, Rebecca"}
43 @string{WChristian = "Christian, Wolfgang"}
44 @string{SPChung = "Chung, Shih-Ping"}
45 @string{CHCrouch = "Crouch, Catherine H."}
46 @string{BCrowell = "Crowell, Benjamin"}
47 @string{LDeslauriers = "Deslauriers, Louis"}
48 @string{RMFelder = "Felder, Richard M."}
49 @string{RRHake = "Hake, Richard R."}
50 @string{SDJohnson = "Johnson, Scott D."}
51 @string{WKing = "King, W.~Trevor"}
52 @string{JLochhead = "Lochhead, Jack"}
53 @string{EMazur = "Mazur, Eric"}
54 @string{MPrince = "Prince, Michael"}
55 @string{ESchelew = "Schelew, Ellen"}
56 @string{MSu = "Su, Meihong"}
57 @string{AWhimbey = "Whimbey, Arthur"}
58 @string{CWieman = "Wieman, Carl"}
59 @string{GYang = "Yang, Guoliang"}
63 title = {Open source single molecule force spectroscopy},
67 url = {http://blog.tremily.us/Thesis/},
68 eprint = {http://blog.tremily.us/Thesis/draft.pdf},
72 author = WKing #" and "# MSu #" and "# GYang,
73 title = "{M}onte {C}arlo simulation of mechanical unfolding of proteins
74 based on a simple two-state model",
78 address = "Department of Physics, Drexel University, 3141
79 Chestnut Street, Philadelphia, PA 19104, USA.",
85 alternative_issn = "1879-0003",
86 doi = "10.1016/j.ijbiomac.2009.12.001",
87 url = "http://www.sciencedirect.com/science/article/B6T7J-
88 4XWMND2-1/2/7ef768562b4157fc201d450553e5de5e",
90 keywords = "Atomic force microscopy;Mechanical unfolding;Monte Carlo
91 simulation;Worm-like chain;Single molecule methods",
92 abstract = "Single molecule methods are becoming routine biophysical
93 techniques for studying biological macromolecules. In mechanical
94 unfolding of proteins, an externally applied force is used to induce
95 the unfolding of individual protein molecules. Such experiments have
96 revealed novel information that has significantly enhanced our
97 understanding of the function and folding mechanisms of several types
98 of proteins. To obtain information on the unfolding kinetics and the
99 free energy landscape of the protein molecule from mechanical unfolding
100 data, a Monte Carlo simulation based on a simple two-state kinetic
101 model is often used. In this paper, we provide a detailed description
102 of the procedure to perform such simulations and discuss the
103 approximations and assumptions involved. We show that the appearance of
104 the force versus extension curves from mechanical unfolding of proteins
105 is affected by a variety of experimental parameters, such as the length
106 of the protein polymer and the force constant of the cantilever. We
107 also analyze the errors associated with different methods of data
108 pooling and present a quantitative measure of how well the simulation
109 results fit experimental data. These findings will be helpful in
110 experimental design, artifact identification, and data analysis for
111 single molecule studies of various proteins using the mechanical
117 @unpublished{ 2013-05-thesis,
118 title= {Open source single molecule force spectroscopy},
123 note= {Thesis defense, Drexel University},
124 address = {Drexel University},
125 url = {http://blog.tremily.us/posts/Thesis/talk/},
128 @unpublished{ 2013-01-columbia,
129 title= {Collaborative version control with {G}it},
133 note= {Software Carpentry boot camp, Columbia University},
134 address = {Columbia University},
137 @unpublished{ 2009-10-life-cycles,
138 title= {Software life-cycles and alphabet soup},
142 note= {Drexel Physics Graduate Student Association},
143 address = {Drexel University}
146 @unpublished{ 2008-06-locks,
147 title= {Manipulating combination locks \& Ray tracing with polarization},
151 note= {Drexel Physics Graduate Student Association},
152 address = {Drexel University}
155 @unpublished{ 2006-05-quantum-computing,
156 title= {Quantum Computing},
159 note= {Rochester Solid State final},
160 address = {University of Rochester}
166 @unpublished{ 2013-04-swc,
167 title= {Teaching Software Carpentry: Better Science through Science},
171 note= {Drexel CoAS Research Day},
172 address = {Philadelphia, Pennsylvania},
175 @unpublished{ 2012-04-calibcant,
176 title= {Thermally calibrating {AFM} cantilever spring constants},
180 note= {Drexel CoAS Research Day},
181 address = {Philadelphia, Pennsylvania},
184 @unpublished{ 2011-04-saswsim,
185 title= {Flexible parallel simulations and packaging},
189 note= {Drexel CoAS Research Day},
190 address = {Philadelphia, Pennsylvania},
193 @unpublished{ 2010-04-open-source,
194 title= {Open source software in experimental protein unfolding},
198 note= {Drexel CoAS Research Day},
199 address = {Philadelphia, Pennsylvania},
202 @unpublished{ 2009-03-roughness,
203 title= {Experimental Estimation of the Free Energy Landscape
204 Roughness of Protein Molecules},
208 note= {Biophysical Society Annual Meeting},
209 address = {Philadelphia, Pennsylvania},
212 @unpublished{ 2008-04-sawsim,
213 title= {Simulated mechanical unfolding of single proteins},
217 note= {Drexel CoAS Research Day},
218 address = {Philadelphia, Pennsylvania},
221 @unpublished{ 2008-02-stiffness,
222 title= {Effects of Cantilever Stiffness on Unfolding Force in AFM
227 note= {Biophysical Society Annual Meeting},
228 address = {Long Beach, California},
233 @article{ lochhead87,
234 author = JLochhead #" and "# AWhimbey,
235 title = {Teaching analytical reasoning through thinking aloud pair
244 url = {http://dx.doi.org/10.1002/tl.37219873007},
245 doi = {10.1002/tl.37219873007},
246 abstract = {The TAPPS technique is a useful device for the
247 teaching of problem solving because it causes learners to pay
248 attention to basic reasoning skills.},
253 title = {Interactive-engagement versus traditional methods: A
254 six-thousand-student survey of mechanics test data for
255 introductory physics courses},
264 doi = {10.1119/1.18809},
265 url = {http://ajp.aapt.org/resource/1/ajpias/v66/i1/p64_s1},
266 keywords = { teaching, education, classical mechanics},
267 abstract = {A survey of pre/post-test data using the
268 Halloun--Hestenes Mechanics Diagnostic test or more recent Force
269 Concept Inventory is reported for 62 introductory physics
270 courses enrolling a total number of students $N=6542$. A
271 consistent analysis over diverse student populations in high
272 schools, colleges, and universities is obtained if a rough
273 measure of the average effectiveness of a course in promoting
274 conceptual understanding is taken to be the average normalized
275 gain $\langle g\rangle$. The latter is defined as the ratio of
276 the actual average gain
277 ($\%\langle\text{post}\rangle-\%\langle\text{pre}\rangle$) to
278 the maximum possible average gain
279 ($100-\%\langle\text{pre}\rangle$). Fourteen ``traditional'' (T)
280 courses ($N=2084$) which made little or no use of
281 interactive-engagement (IE) methods achieved an average gain
282 $\langle g\rangle_{\text{T} - \text{ave}} = 0.23\pm0.04$ (std dev).
283 In sharp contrast, 48 courses ($N=4458$) which made substantial
284 use of IE methods achieved an average gain
285 $\langle g\rangle_{\text{IE}-\text{ave}} = 0.48\pm0.14$ (std dev),
286 almost two standard deviations of
287 $\langle g\rangle_{\text{IE}-\text{ave}}$ above that of the
288 traditional courses. Results for 30 ($N=3259$) of the above 62
289 courses on the problem-solving Mechanics Baseline test of
290 Hestenes--Wells imply that IE strategies enhance problem-solving
291 ability. The conceptual and problem-solving test results
292 strongly suggest that the classroom use of IE methods can
293 increase mechanics-course effectiveness well beyond that
294 obtained in traditional practice.},
298 author = SDJohnson #" and "# SPChung,
299 title = {The Effect of Thinking Aloud Pair Problem Solving
300 ({TAPPS}) on the Troubleshooting Ability of Aviation Technician
309 issn-online = {1938-1603},
310 url = {http://scholar.lib.vt.edu/ejournals/JITE/v37n1/john.html},
311 license = CC-BY-NC-SA-3.0-US,
315 author = WChristian #" and "# MBelloni,
316 title = {Physlets: Teaching Physics with Interactive Curricular Material},
319 address = UpperSaddleRiver,
321 isbn = {0-13-029341-5},
322 isbn-13 = {978-0-1302-9341-1},
323 url = {http://webphysics.davidson.edu/physletprob/},
327 author = CHCrouch #" and "# EMazur,
328 title = {Peer Instruction: Ten years of experience and results},
337 doi = {10.1119/1.1374249},
338 url = {http://ajp.aapt.org/resource/1/ajpias/v69/i9/p970_s1},
339 keywords = {teaching, problem solving, educational courses},
340 abstract = {We report data from ten years of teaching with Peer
341 Instruction (PI) in the calculus- and algebra-based introductory
342 physics courses for nonmajors; our results indicate increased
343 student mastery of both conceptual reasoning and quantitative
344 problem solving upon implementing PI. We also discuss ways we
345 have improved our implementation of PI since introducing it in
346 1991. Most notably, we have replaced in-class reading quizzes
347 with pre-class written responses to the reading, introduced a
348 research-based mechanics textbook for portions of the course,
349 and incorporated cooperative learning into the discussion
350 sections as well as the lectures. These improvements are
351 intended to help students learn more from pre-class reading and
352 to increase student engagement in the discussion sections, and
353 are accompanied by further increases in student understanding.},
358 title = {Does Active Learning Work? {A} Review of the Research},
365 publisher = Blackwell,
367 doi = {10.1002/j.2168-9830.2004.tb00809.x},
368 url = {http://dx.doi.org/10.1002/j.2168-9830.2004.tb00809.x},
369 keywords = {active, collaborative, cooperative, problem-based learning},
370 abstract = {This study examines the evidence for the effectiveness
371 of active learning. It defines the common forms of active
372 learning most relevant for engineering faculty and critically
373 examines the core element of each method. It is found that there
374 is broad but uneven support for the core elements of active,
375 collaborative, cooperative and problem-based learning.},
379 author = RMFelder #" and "# RBrent,
380 title = {Active learning: An introduction},
387 url = {http://asq.org/edu/2009/08/best-practices/active-learning-an-introduction.%20felder.html?shl=093530},
388 eprint = {http://www4.ncsu.edu/unity/lockers/users/f/felder/public/Papers/ALpaper(ASQ).pdf},
389 abstract = {Richard M. Felder and Rebecca Brent describe active
390 learning as anything course-related that all students in a class
391 session are called upon to do other than watching, listening and
392 taking notes. They provide suggestions as to what teachers and
393 professors can do to engage students in active learning and the
394 formats to use for those activities.},
397 @article{ deslauriers11,
398 author = LDeslauriers #" and "# ESchelew #" and "# CWieman,
399 title = {Improved Learning in a Large-Enrollment Physics Class},
407 doi = {10.1126/science.1201783},
408 url = {http://www.sciencemag.org/content/332/6031/862.abstract},
409 eprint = {http://www.sciencemag.org/content/332/6031/862.full.pdf},
410 abstract ={We compared the amounts of learning achieved using two
411 different instructional approaches under controlled
412 conditions. We measured the learning of a specific set of topics
413 and objectives when taught by 3 hours of traditional lecture
414 given by an experienced highly rated instructor and 3 hours of
415 instruction given by a trained but inexperienced instructor
416 using instruction based on research in cognitive psychology and
417 physics education. The comparison was made between two large
418 sections (N = 267 and N = 271) of an introductory undergraduate
419 physics course. We found increased student attendance, higher
420 engagement, and more than twice the learning in the section
421 taught using research-based instruction.},
424 @book{ crowell-light-and-matter,
426 title = {Light and Matter},
428 url = {http://www.lightandmatter.com/lm/},
429 eprint = {http://www.lightandmatter.com/lm.pdf},
430 source = {git://lightandmatter.com/physics},
431 license = CC-BY-SA-3.0-US,
434 @book{ crowell-simple-nature,
436 title = {Simple Nature},
438 url = {http://www.lightandmatter.com/area1sn.html},
439 eprint = {http://www.lightandmatter.com/simple.pdf},
440 source = {git://lightandmatter.com/physics},
441 license = CC-BY-SA-3.0-US,
444 @book{ crowell-mechanics,
448 url = {http://www.lightandmatter.com/mechanics/},
449 eprint = {http://www.lightandmatter.com/me.pdf},
450 source = {git://lightandmatter.com/physics},
451 license = CC-BY-SA-3.0-US,
454 @book{ crowell-conceptual-physics,
456 title = {Conceptual Physics},
458 url = {http://www.lightandmatter.com/cp/},
459 eprint = {http://www.lightandmatter.com/cp.pdf},
460 source = {git://lightandmatter.com/physics},
461 license = CC-BY-SA-3.0-US,
464 @book{ crowell-calculus,
468 url = {http://www.lightandmatter.com/calc/},
469 eprint = {http://www.lightandmatter.com/calc/calc.pdf},
470 source = {git://lightandmatter.com/physics},
471 license = CC-BY-SA-3.0-US,
474 @book{ crowell-general-relativity,
476 title = {General Relativity},
478 url = {http://www.lightandmatter.com/genrel},
479 eprint = {http://www.lightandmatter.com/genrel/genrel.pdf},
480 source = {git://lightandmatter.com/physics},
481 license = CC-BY-SA-3.0-US,