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   7                 <title>Open source single molecule force spectroscopy</title>
   8
   9                 <meta name="description" content="Controlling and analyzing SMFS with varying salt concentrations">
  10                 <meta name="author" content="Trevor King">
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  39
  40                                 <section>
  41                                         <h2>Open source<br/> single molecule<br/> force spectroscopy</h2>
  42                                         <h3>Protein unfolding in varying salt concentrations</h3>
  43                                         <p style="text-align: center;">
  44                                                 <small>Trevor King</small>
  45                                         </p>
  46                                 </section>
  47                                 <section>
  48                                         <section>
  49                                                 <h2>Open source SMFS</h2>
  50                                                 <ol>
  51                                                         <li><a href="#/1" class="active">Proteins</a></li>
  52                                                         <li><a href="#/2">Atomic force microscopy</a></li>
  53                                                         <li><a href="#/3">Single molecule force spectroscopy</a></li>
  54                                                         <li><a href="#/4">Experiment control</a></li>
  55                                                         <li><a href="#/5">Cantilever calibration</a></li>
  56                                                         <li><a href="#/6">
  57                                                                         Modeling: Monte Carlo unfolding simulations</a></li>
  58                                                         <li><a href="#/7">
  59                                                                         Application: Unfolding in salty buffers</a></li>
  60                                                         <li><a href="#/8">Conclusions and future work</a></li>
  61                                                 </ol>
  62                                         </section>
  63                                         <section>
  64                                                 <h2>Proteins: What are they?</h2>
  65                                                 <p>
  66                                                         <video width="640" height="480"
  67                                                                                  preload="auto" loop="" controls=""> <!--autoplay=""-->
  68                                                                 <source src="media/build/1TIT-atoms.mp4"
  69                                                                                                 type='video/mp4; codecs="avc1.42E01E, mp4a.40.2"' />
  70                                                         </video>
  71                                                         <!-- generated with PyMol from
  72                                                                          http://www.rcsb.org/pdb/explore.do?structureId=1TIT -->
  73                                                 </p>
  74                                         </section>
  75                                         <section>
  76                                                 <h2>Proteins: Where are they?</h2>
  77                                                 <p>
  78                                                         <img src="media/build/takamori-fig4b-fw-fh.png" />
  79                                                 </p>
  80                                                 <p style="text-align: center;">
  81                                                         <small>
  82                                                                 <a href="http://dx.doi.org/10.1016/j.cell.2006.10.030">
  83                                                                         Takamori, Holt, Stenius, et al., 2006
  84                                                                 </a>
  85                                                         </small>
  86                                                 </p>
  87                                         </section>
  88                                         <section>
  89                                                 <h2>Proteins: Titin</h2>
  90                                                 <p>
  91                                                         <img src="media/build/skeletal-muscle-fw-fh.png" />
  92                                                 </p>
  93                                                 <p style="text-align: center;">
  94                                                         <small>
  95                                                                 Adapted from
  96                                                                 <a href="http://en.wikipedia.org/wiki/File:Skeletal_muscle.jpg">
  97                                                                         Wikipedia
  98                                                                 </a>
  99                                                         </small>
 100                                                 </p>
 101                                         </section>
 102                                         <section>
 103                                                 <h2>Proteins: Titin's I27</h2>
 104                                                 <p>
 105                                                         <img src="media/build/titin-fw-fh.png" />
 106                                                 </p>
 107                                                 <p style="text-align: center;">
 108                                                         <small>
 109                                                                 <a href="http://www.ks.uiuc.edu/Research/telethonin/">
 110                                                                         U. Illinois Biophysics Group
 111                                                                 </a>
 112                                                         </small>
 113                                                 </p>
 114                                         </section>
 115                                         <section>
 116                                                 <h2>Proteins: I27</h2>
 117                                                 <p>
 118                                                         <img src="media/build/1TIT-fw-fh.png" />
 119                                                 </p>
 120                                                 <p style="text-align: center;">
 121                                                         <small>
 122                                                                 <a href="http://www.rcsb.org/pdb/explore.do?structureId=1TIT">
 123                                                                         PDB structure 1TIT
 124                                                                 </a>
 125                                                         </small>
 126                                                 </p>
 127                                         </section>
 128                                         <section>
 129                                                 <h2>Proteins: What's the problem?</h2>
 130                                                 <table class="center">
 131                                                         <tr>
 132                                                                 <td style="vertical-align: middle;">
 133                                                                         <pre style="display: table; width: auto;">
 134 MHHHHHHSSLIEV
 135 EKPLYGVEVFVGE
 136 TAHFEIELSEPDV
 137 HGQWKLKGQPLTA
 138 SPDCEIIEDGKKH
 139 ILILHNCQLGMTG
 140 EVSFQAANAKSAA
 141 NLKVKEL</pre>
 142                                                                 </td>
 143                                                                 <td style="vertical-align: middle;"><p>  →  </p></td>
 144                                                                 <td style="vertical-align: middle;">
 145                                                                         <img src="media/build/1TIT-tw-th.png" />
 146                                                                 </td>
 147                                                         </tr>
 148                                                         <tr>
 149                                                                 <td colspan="3">
 150                                                                         <p>
 151                                                                                 <img src="media/build/pirchi-fig1-fw-hh.png" />
 152                                                                         </p>
 153                                                                         <p style="text-align: center;">
 154                                                                                 <small>
 155                                                                                         <a href="http://dx.doi.org/10.1038/ncomms1504">
 156                                                                                                 Pirchi, Ziv, Riven, et al., 2011
 157                                                                                         </a>
 158                                                                                 </small>
 159                                                                         </p>
 160                                                                 </td>
 161                                                         </tr>
 162                                                 </table>
 163                                         </section>
 164                                 </section>
 165                                 <section>
 166                                         <section>
 167                                                 <h2>Open source SMFS</h2>
 168                                                 <ol>
 169                                                         <li><a href="#/1">Proteins</a></li>
 170                                                         <li><a href="#/2" class="active">Atomic force microscopy</a></li>
 171                                                         <li><a href="#/3">Single molecule force spectroscopy</a></li>
 172                                                         <li><a href="#/4">Experiment control</a></li>
 173                                                         <li><a href="#/5">Cantilever calibration</a></li>
 174                                                         <li><a href="#/6">
 175                                                                         Modeling: Monte Carlo unfolding simulations</a></li>
 176                                                         <li><a href="#/7">
 177                                                                         Application: Unfolding in salty buffers</a></li>
 178                                                         <li><a href="#/8">Conclusions and future work</a></li>
 179                                                 </ol>
 180                                         </section>
 181                                         <section>
 182                                                 <h2>Atomic force microscopy</h2>
 183                                                 <p>
 184                                                         <img src="media/build/afm-3d-fw-fh.png" />
 185                                                 </p>
 186                                         </section>
 187                                         <section>
 188                                                 <h2>AFM: Cantilever geometry</h2>
 189                                                 <p>
 190                                                         <!-- need height to stretch low-resolution pictures -->
 191                                                         <img src="media/build/cantilever.jpg" height="272" />
 192                                                         <img src="media/build/tip.jpg" height="272" />
 193                                                 </p>
 194                                                 <p style="text-align: center;">
 195                                                         <small>
 196                                                                 <a href="http://probe.olympus-global.com/en/product/omcl_tr800psa_w/">
 197                                                                         Olympus TR800PSA
 198                                                                 </a>, images from
 199                                                                 <a href="http://www.asylumresearch.com/Probe/TR400PSA,Olympus">
 200                                                                         Asylum Research
 201                                                                 </a><br/>
 202                                                                 We use the thinner
 203                                                                 <a href="http://probe.olympus-global.com/en/product/omcl_tr400psa_hw/">
 204                                                                          TR400PSA
 205                                                                 </a>
 206                                                         </small>
 207                                                 </p>
 208                                         </section>
 209                                         <section>
 210                                                 <h2>AFM: Laser deflection</h2>
 211                                                 <p>
 212                                                         <video width="640" height="480"
 213                                                                                  preload="auto" loop="" controls=""> <!--autoplay=""-->
 214                                                                 <source src="media/build/contact-afm.ogv"
 215                                                                                                 type='video/ogg; codecs="theora,vorbis"' />
 216                                                         </video>
 217                                                 </p>
 218                                                 <p style="text-align: center;">
 219                                                         <small>
 220                                                                 <a href="http://www.freesbi.ch/fr/illustration/animations">
 221                                                                         Charles Roduit
 222                                                                 </a>
 223                                                         </small>
 224                                                 </p>
 225                                         </section>
 226                                         <section>
 227                                                 <h2>AFM: Piezo positioning</h2>
 228                                                 <p>
 229                                                         <img src="media/build/afm-fw-fh.png" />
 230                                                 </p>
 231                                         </section>
 232                                         <section>
 233                                                 <h2>The piezoelectric effect</h2>
 234                                                 <p>
 235                                                         <object data="media/perovskite.svg" type="image/svg+xml"
 236                                                                         width="640" height="350"></object>
 237                                                 </p>
 238                                                 <p style="text-align: center;">
 239                                                         <small>
 240                                                                 Lead zirconium titanate (PZT) from
 241                                                                 <a href="http://en.wikipedia.org/wiki/File:Perovskite.svg">
 242                                                                         Wikipedia
 243                                                                 </a>
 244                                                         </small>
 245                                                 </p>
 246                                         </section>
 247                                         <section>
 248                                                 <h2>AFM: Tubular piezos</h2>
 249                                                 <p>
 250                                                         <img src="media/build/piezo-fw-fh.png" />
 251                                                 </p>
 252                                         </section>
 253                                 </section>
 254                                 <section>
 255                                         <section>
 256                                                 <h2>Open source SMFS</h2>
 257                                                 <ol>
 258                                                         <li><a href="#/1">Proteins</a></li>
 259                                                         <li><a href="#/2">Atomic force microscopy</a></li>
 260                                                         <li><a href="#/3" class="active">
 261                                                                         Single molecule force spectroscopy</a></li>
 262                                                         <li><a href="#/4">Experiment control</a></li>
 263                                                         <li><a href="#/5">Cantilever calibration</a></li>
 264                                                         <li><a href="#/6">
 265                                                                         Modeling: Monte Carlo unfolding simulations</a></li>
 266                                                         <li><a href="#/7">
 267                                                                         Application: Unfolding in salty buffers</a></li>
 268                                                         <li><a href="#/8">Conclusions and future work</a></li>
 269                                                 </ol>
 270                                         </section>
 271                                         <section>
 272                                                 <h2>Single molecule force spectroscopy</h2>
 273                                                 <p>
 274                                                         <img src="media/build/unfolding-fw-fh.png" />
 275                                                 </p>
 276                                         </section>
 277                                         <section>
 278                                                 <h2>SMFS: Sawtooth curve</h2>
 279                                                 <p>
 280                                                         <img src="media/build/expt-sawtooth-fw-fh.png" width="640" />
 281                                                 </p>
 282                                         </section>
 283                                         <section>
 284                                                 <h2>SMFS: What's going on?</h2>
 285                                                 <p>
 286                                                         <img src="media/build/carrion-vazquez-fig2-fw-fh.png" />
 287                                                 </p>
 288                                                 <p>
 289                                                         <small>
 290                                                                 <a href="http://dx.doi.org/10.1016/S0079-6107(00)00017-1">
 291                                                                         Carrion-Vazquez, et al., 2000;
 292                                                                         adapted from Baljon and Robbins, 1996
 293                                                                 </a>
 294                                                         </small>
 295                                                 </p>
 296                                         </section>
 297                                         <section>
 298                                                 <h2>SMFS: Unfolding one domain</h2>
 299                                                 <p>
 300                                                         <img src="media/build/lu-fig1-fw-fh.png" />
 301                                                 </p>
 302                                                 <p>
 303                                                         <small>
 304                                                                 <a href="http://dx.doi.org/10.1016/S0006-3495(00)76273-4">
 305                                                                         Lu and Schulten, 2000
 306                                                                 </a>
 307                                                         </small>
 308                                                 </p>
 309                                         </section>
 310                                 </section>
 311                                 <section>
 312                                         <section>
 313                                                 <h2>Open source SMFS</h2>
 314                                                 <ol>
 315                                                         <li><a href="#/1">Proteins</a></li>
 316                                                         <li><a href="#/2">Atomic force microscopy</a></li>
 317                                                         <li><a href="#/3">Single molecule force spectroscopy</a></li>
 318                                                         <li><a href="#/4" class="active">Experiment control</a></li>
 319                                                         <li><a href="#/5">Cantilever calibration</a></li>
 320                                                         <li><a href="#/6">
 321                                                                         Modeling: Monte Carlo unfolding simulations</a></li>
 322                                                         <li><a href="#/7">
 323                                                                         Application: Unfolding in salty buffers</a></li>
 324                                                         <li><a href="#/8">Conclusions and future work</a></li>
 325                                                 </ol>
 326                                         </section>
 327                                         <section>
 328                                                 <h2>Experiment control</h2>
 329                                                 <p>
 330                                                         <img src="media/build/apparatus-fw-fh.png" />
 331                                                 </p>
 332                                         </section>
 333                                         <section>
 334                                                 <h2>Control: Quick-and-dirty</h2>
 335                                                 <p>
 336                                                         <img src="media/build/labview-fw-fh.png" />
 337                                                 </p>
 338                                         </section>
 339                                         <section>
 340                                                 <h2>Control: My modular stack</h2>
 341                                                 <p>
 342                                                         <img src="media/build/pyafm-fw-fh.png" />
 343                                                 </p>
 344                                         </section>
 345                                         <section>
 346                                                 <h2>Open source: Existing layers</h2>
 347                                                 <table class="center">
 348                                                         <tr>
 349                                                                 <td><img src="media/logo/tux.png" height="150" /></td>
 350                                                                 <td><object data="media/logo/gnu.svg" type="image/svg+xml"
 351                                                                                                                 height="150"></object></td>
 352                                                                 <td><object data="media/logo/gentoo.svg" type="image/svg+xml"
 353                                                                                                                 height="150"></object></td>
 354                                                                 <td><object data="media/logo/python.svg" type="image/svg+xml"
 355                                                                                                                 height="150"></object></td>
 356                                                                 <td><object data="media/logo/scipy.svg" type="image/svg+xml"
 357                                                                                                                 height="150"></object></td>
 358                                                         </tr>
 359                                                         <tr>
 360                                                                 <td><a href="https://www.kernel.org/">Linux</a></td>
 361                                                                 <td>
 362                                                                         <a href="http://www.gnu.org/">
 363                                                                                 <abbr title="GNU's Not Unix!">GNU</abbr>
 364                                                                         </a>
 365                                                                 </td>
 366                                                                 <td><a href="http://www.gentoo.org/">Gentoo</a></td>
 367                                                                 <td><a href="http://www.python.org/">Python</a></td>
 368                                                                 <td><a href="http://www.scipy.org/">SciPy</a></td>
 369                                                         </tr>
 370                                                         <tr>
 371                                                                 <td>
 372                                                                         <small>
 373                                                                                 <a href="http://www.comedi.org/">
 374                                                                                         <abbr title="Control and Measurement Device Interface">Comedi<abbr>
 375                                                                                 </a>
 376                                                                         </small>
 377                                                                 </td>
 378                                                                 <td>
 379                                                                         <small>
 380                                                                                 <a href="http://matplotlib.org/">matplotlib</a>
 381                                                                         </small>
 382                                                                 </td>
 383                                                                 <td>
 384                                                                         <small>
 385                                                                                 <a href="https://github.com/bashwork/pymodbus">pymodbus</a>
 386                                                                         </small>
 387                                                                 </td>
 388                                                                 <td>
 389                                                                         <small>
 390                                                                                 <a href="http://www.cython.org/">Cython</a>
 391                                                                         </small>
 392                                                                 </td>
 393                                                                 <td>
 394                                                                         <small>
 395                                                                                 <a href="https://www.numpy.org/">NumPy</a>
 396                                                                         </small>
 397                                                                 </td>
 398                                                         </tr>
 399                                                         <tr>
 400                                                                 <td>
 401                                                                         <small>
 402                                                                                 <a href="http://www.h5py.org/">h5py</a>
 403                                                                         </small>
 404                                                                 </td>
 405                                                                 <td><small>…</small></td>
 406                                                         </tr>
 407                                                 </table>
 408                                         </section>
 409                                         <section>
 410                                                 <h2>Open source: Teamwork</h2>
 411                                                 <p>
 412                                                         <img src="media/build/ants-fw-fh.png" />
 413                                                 </p>
 414                                                 <p style="text-align: center;">
 415                                                         <small>
 416                                                                 <a href="http://dx.doi.org/10.1073/pnas.1016658108">
 417                                                                         Mlot, Tovey, and Hu, 2011
 418                                                                 </a>
 419                                                         </small>
 420                                                 </p>
 421                                         </section>
 422                                         <section>
 423                                                 <h2>Control: Example code</h2>
 424                                                 <pre><code data-trim="">
 425 class Unfolder (object):
 426     …
 427     def run(self):
 428         """Approach-bind-unfold-save[-plot] cycle.
 429         """
 430         ret = {}
 431         ret['timestamp'] = _email_utils.formatdate(localtime=True)
 432         ret['temperature'] = self.afm.get_temperature()
 433         ret['approach'] = self._approach()
 434         self._bind()
 435         ret['unfold'] = self._unfold()
 436         self._save(**ret)
 437         if _package_config['matplotlib']:
 438             self._plot(**ret)
 439         return ret
 440                                                 </code></pre>
 441                                         </section>
 442                                         <section>
 443                                                 <h2>Archival: HDF5 and h5config</h2>
 444                                                 <!-- h5dump -H 2013-03-04T12-43-38.h5 |
 445                                                                  grep 'GROUP\|DATASET' | sed 's/ {.*//' -->
 446                                                 <pre>
 447 GROUP <span style="color: blue">&quot;/&quot;</span>
 448    GROUP <span style="color: blue">&quot;approach&quot;</span>
 449       …
 450    GROUP <span style="color: blue">&quot;config&quot;</span>
 451       GROUP <span style="color: blue">&quot;afm&quot;</span>
 452          …
 453       GROUP <span style="color: blue">&quot;approach&quot;</span>
 454          …
 455       DATASET <span style="color: blue">&quot;bind time&quot;</span>
 456       …
 457       GROUP <span style="color: blue">&quot;unfold&quot;</span>
 458          …
 459          DATASET <span style="color: blue">&quot;velocity&quot;</span>
 460    GROUP <span style="color: blue">&quot;environment&quot;</span>
 461       DATASET <span style="color: blue">&quot;temperature&quot;</span>
 462       DATASET <span style="color: blue">&quot;timestamp&quot;</span>
 463       …
 464    GROUP <span style="color: blue">&quot;unfold&quot;</span>
 465       DATASET <span style="color: blue">&quot;deflection&quot;</span>
 466       DATASET <span style="color: blue">&quot;frequency&quot;</span>
 467       DATASET <span style="color: blue">&quot;z&quot;</span></pre>
 468                                         </section>
 469                                         <section>
 470                                                 <h2>Archival: Version control</h2>
 471                                                 <pre>
 472 <span style="color: red">commit 32bfbf98d79c73eba50b77d0917df100e0e33bcf</span>
 473 Author: W. Trevor King &lt;wking@tremily.us&gt;
 474 Date:   Fri Jan 18 22:54:49 2013 -0500
 475
 476     afm: Optionally return stepper_approach data with `record_data`
 477
 478     Sometimes these approach curves are pretty funky, so I'll start
 479     recording them by default in calibcant-calibrate.py.
 480
 481 <span style="font-weight: bold">diff --git a/pyafm/afm.py b/pyafm/afm.py
 482 index 60741c6..e76b118 100644
 483 --- a/pyafm/afm.py
 484 +++ b/pyafm/afm.py</span>
 485 <span style="color: blue">@@ -460,10 +460,11 @@</span> class AFM (object):
 486          _LOG.warn(e)
 487          raise e
 488
 489 <span style="color: red">-    def stepper_approach(self, target_deflection):</span>
 490 <span style="color: green">+    def stepper_approach(self, target_deflection, record_data=None):</span>
 491 …</pre>
 492                                         </section>
 493                                 </section>
 494                                 <section>
 495                                         <section>
 496                                                 <h2>Open source SMFS</h2>
 497                                                 <ol>
 498                                                         <li><a href="#/1">Proteins</a></li>
 499                                                         <li><a href="#/2">Atomic force microscopy</a></li>
 500                                                         <li><a href="#/3">Single molecule force spectroscopy</a></li>
 501                                                         <li><a href="#/4">Experiment control</a></li>
 502                                                         <li><a href="#/5" class="active">Cantilever calibration</a></li>
 503                                                         <li><a href="#/6">
 504                                                                         Modeling: Monte Carlo unfolding simulations</a></li>
 505                                                         <li><a href="#/7">
 506                                                                         Application: Unfolding in salty buffers</a></li>
 507                                                         <li><a href="#/8">Conclusions and future work</a></li>
 508                                                 </ol>
 509                                         </section>
 510                                         <section>
 511                                                 <h2>Cantilever calibration</h2>
 512                                                 <p>
 513                                                         <img src="media/build/unfolding-fw-fh.png" />
 514                                                 </p>
 515                                         </section>
 516                                         <section>
 517                                                 <h2>Calibration: Geometry</h2>
 518                                                 <p>
 519                                                         <!-- need height to stretch low-resolution pictures -->
 520                                                         <img src="media/build/cantilever.jpg" height="272" />
 521                                                         <img src="media/build/tip.jpg" height="272" />
 522                                                 </p>
 523                                                 <p style="text-align: center;">
 524                                                         <small>
 525                                                                 <a href="http://probe.olympus-global.com/en/product/omcl_tr800psa_w/">
 526                                                                         Olympus TR800PSA
 527                                                                 </a>, images from
 528                                                                 <a href="http://www.asylumresearch.com/Probe/TR400PSA,Olympus">
 529                                                                         Asylum Research
 530                                                                 </a><br/>
 531                                                                 We use the thinner
 532                                                                 <a href="http://probe.olympus-global.com/en/product/omcl_tr400psa_hw/">
 533                                                                          TR400PSA
 534                                                                 </a>
 535                                                         </small>
 536                                                 </p>
 537                                         </section>
 538                                         <section>
 539                                                 <h2>Calibration: Equipartition</h2>
 540                                                 <table class="center">
 541                                                         <tr>
 542                                                                 <td style="vertical-align: middle;">
 543                                                                         <img src="media/build/calibcant-flow-hw-fh.png" />
 544                                                                 </td>
 545                                                                 <td>
 546                                                                         <p>
 547                                                                                 The average spring energy is
 548                                                                         </p>
 549
 550 \[
 551   \frac{1}{2} \kappa \left\langle x_c^2 \right\rangle = \frac{1}{2}k_B T \;,
 552 \]
 553
 554                                                                         <p>
 555                                                                                 where $k_B$ is Boltzmann's constant and $T$ is the
 556                                                                                 temperature.
 557                                                                         </p>
 558                                                                 </td>
 559                                                         </tr>
 560                                                 </table>
 561                                         </section>
 562                                         <section>
 563                                                 <h2>Calibration: Vibration</h2>
 564                                                 <p>
 565                                                         <img src="media/build/vibration-fw-fh.png" width="620" />
 566                                                 </p>
 567                                         </section>
 568                                         <section>
 569                                                 <h2>Calibration: Photodiode calibration</h2>
 570                                                 <p>
 571                                                         <img src="media/build/bump-fw-fh.png" />
 572                                                 </p>
 573                                         </section>
 574                                         <section>
 575                                                 <h2>Calibration: Results</h2>
 576
 577 \[
 578 \begin{aligned}
 579   T &= 298.15 \pm 0.03 \; \text{K}  &
 580   \sigma_p &= 35.7 \pm 0.9 \; \text{mV/nm} \\
 581   \left\langle V_p^2 \right\rangle &= 97 \pm 1 \; \text{mV}^2  &
 582   \sqrt{\left\langle x_c^2 \right\rangle}
 583     &= \sqrt{\frac{\left\langle V_p^2 \right\rangle}{\sigma_p^2}}
 584     = 0.28 \; \text{nm} \\
 585   \kappa = \frac{k_B T \sigma_p^2}{\left\langle V_p^2 \right\rangle}
 586     &= 54 \pm 3 \; \text{pN/nm}
 587 \end{aligned}
 588 \]
 589
 590                                         </section>
 591                                         <section>
 592                                                 <h2>Calibration: Stability</h2>
 593                                                 <table class="center">
 594                                                         <thead>
 595                                                                 <tr>
 596                                                                         <th>Quant.</th>
 597                                                                         <th>Units</th>
 598                                                                         <th> </th>
 599                                                                         <!-- 2013-03-03T16-37-12 -->
 600                                                                         <th colspan="2" style="text-align: center">Day 1</th>
 601                                                                         <th> </th>
 602                                                                         <!-- 2013-03-04T12-21-54 -->
 603                                                                         <th colspan="2" style="text-align: center">Day 2</th>
 604                                                                 </tr>
 605                                                         </thead>
 606                                                         <tbody>
 607                                                                 <tr>
 608                                                                         <td>$T$</td>
 609                                                                         <td>K</td>
 610                                                                         <td></td>
 611                                                                         <td>296.30</td>
 612                                                                         <td>±0.02</td>
 613                                                                         <td></td>
 614                                                                         <td>294.27</td>
 615                                                                         <td>±0.02</td>
 616                                                                 </tr>
 617                                                                 <tr>
 618                                                                         <td>$\sigma_p$</td>
 619                                                                         <td>mV/nm</td>
 620                                                                         <td></td>
 621                                                                         <td>&#x2007;46.2</td>
 622                                                                         <td>±0.8</td>
 623                                                                         <td></td>
 624                                                                         <td>&#x2007;41.3</td>
 625                                                                         <td>±0.2</td>
 626                                                                 </tr>
 627                                                                 <tr>
 628                                                                         <td>$\left\langle V_p^2 \right\rangle$</td>
 629                                                                         <td>mV$^2$</td>
 630                                                                         <td></td>
 631                                                                         <td>108</td>
 632                                                                         <td>±1</td>
 633                                                                         <td></td>
 634                                                                         <td>105</td>
 635                                                                         <td>±2</td>
 636                                                                 </tr>
 637                                                                 <tr>
 638                                                                         <td>$\kappa$</td>
 639                                                                         <td>pN/nm</td>
 640                                                                         <td></td>
 641                                                                         <td>&#x2007;67</td>
 642                                                                         <td>±2</td>
 643                                                                         <td></td>
 644                                                                         <td>&#x2007;66</td>
 645                                                                         <td>±2</td>
 646                                                                 </tr>
 647                                                         </tbody>
 648                                                 </table>
 649                                         </section>
 650                                         <section>
 651                                                 <h2>Calibration: Inconsistency</h2>
 652                                                 <table class="center">
 653                                                         <tr>
 654                                                                 <td style="vertical-align: middle;">
 655                                                                         <img src="media/build/florin-fig2-hw-fh.png" />
 656                                                                 </td>
 657                                                                 <td style="vertical-align: middle;">
 658                                                                         <img src="media/build/vibration-hw-fh.png" />
 659                                                                 </td>
 660                                                         </tr>
 661                                                 </table>
 662                                                 <p style="text-align: center;">
 663                                                         <small>
 664                                                                 <a href="http://dx.doi.org/10.1016/0896-6273(88)90139-0">
 665                                                                         Florin, Rief, Lehmann, et al., 1995
 666                                                                 </a>
 667                                                         </small>
 668                                                 </p>
 669                                         </section>
 670                                 </section>
 671                                 <section>
 672                                         <section>
 673                                                 <h2>Open source SMFS</h2>
 674                                                 <ol>
 675                                                         <li><a href="#/1">Proteins</a></li>
 676                                                         <li><a href="#/2">Atomic force microscopy</a></li>
 677                                                         <li><a href="#/3">Single molecule force spectroscopy</a></li>
 678                                                         <li><a href="#/4">Experiment control</a></li>
 679                                                         <li><a href="#/5">Cantilever calibration</a></li>
 680                                                         <li><a href="#/6" class="active">
 681                                                                         Modeling: Monte Carlo unfolding simulations</a></li>
 682                                                         <li><a href="#/7">
 683                                                                         Application: Unfolding in salty buffers</a></li>
 684                                                         <li><a href="#/8">Conclusions and future work</a></li>
 685                                                 </ol>
 686                                         </section>
 687                                         <section>
 688                                                 <h2>Monte Carlo unfolding simulations</h2>
 689                                                 <table class="center">
 690                                                         <tr>
 691                                                                 <td rowspan="2" style="vertical-align: middle;">
 692                                                                         <img src="media/build/unfolding-hw-fh.png" />
 693                                                                 </td>
 694                                                                 <td style="vertical-align: top;">
 695                                                                         <img src="media/build/expt-sawtooth-hw-hh.png" />
 696                                                                 </td>
 697                                                         </tr>
 698                                                         <tr>
 699                                                                 <td><img src="media/build/pbs-hist-hw-hh.png" /></td>
 700                                                         </tr>
 701                                                 </table>
 702                                         </section>
 703                                         <section>
 704                                                 <h2>Hooke: Experimental histograms</h2>
 705                                                 <p>
 706                                                         <img src="media/build/expt-sawtooth-hw-hh.png"
 707                                                                          style="vertical-align: middle;" />
 708                                                         <img src="media/build/pbs-hist-hw-hh.png"
 709                                                                          style="vertical-align: middle;" />
 710                                                 </p>
 711                                                 <p>
 712                                                         <a href="http://dx.doi.org/10.1093/bioinformatics/btp180">Sandal,
 713                                                                 Benedetti, et al., 2009</a>
 714                                                 </p>
 715                                         </section>
 716                                         <section>
 717                                                 <h2>Sawsim: State model</h2>
 718                                                 <p>
 719                                                         <img src="media/build/unfolding-hw-fh.png"
 720                                                                          style="vertical-align: middle;">
 721                                                         <img src="media/build/sawsim-states-hw-fh.png"
 722                                                                          style="vertical-align: middle;">
 723                                                 </p>
 724                                                 <p>
 725                                                         My simulation framework.
 726                                                 </p>
 727                                         </section>
 728                                         <section>
 729                                                 <h2>Sawsim: Simulation loop</h2>
 730                                                 <ol>
 731                                                         <li>Calculate piezo-induced gap $x_t(t)=v t$</li>
 732                                                         <li>
 733                                                                 Find tension model parameters for each state
 734                                                         </li>
 735                                                         <li>
 736                                                                 Distribute per-state stretching ($x_c$, $x_u$, …) to
 737                                                                 balance the tension
 738                                                         </li>
 739                                                         <li>
 740                                                                 Calculate the transition rates between states
 741                                                         </li>
 742                                                         <li>
 743                                                                 Roll the dice to determine if transitions take
 744                                                                 place as you step forward in time
 745                                                         </li>
 746                                                 </ol>
 747                                         </section>
 748                                         <section>
 749                                                 <h2>Sawsim: Monte Carlo</h2>
 750                                                 <p>
 751                                                         <img src="media/build/monte-carlo-fw-fh.png" />
 752                                                 </p>
 753                                         </section>
 754                                         <section>
 755                                                 <h2>Sawsim: Unfolding models</h2>
 756                                                 <table class="center">
 757                                                         <tr>
 758                                                                 <td style="text-align: center;">
 759                                                                         <img src="media/build/unfolding-hw-hh.png"
 760                                                                                          style="vertical-align: middle;">
 761                                                                 </td>
 762                                                                 <td>
 763                                                                         <img src="media/build/landscape-hw-hh.png"
 764                                                                                          style="vertical-align: middle;">
 765                                                                 </td>
 766                                                         </tr>
 767                                                         <tr>
 768                                                                 <td style="text-align: center;">
 769                                                                         <img src="media/build/sawsim-states-hw-hh.png"
 770                                                                                          style="vertical-align: middle;">
 771                                                                 </td>
 772                                                                 <td>
 773                                                                         <img src="media/build/landscape-bell-hw-hh.png"
 774                                                                                          style="vertical-align: middle;">
 775                                                                 </td>
 776                                                         </tr>
 777                                                 </table>
 778                                         </section>
 779                                         <section>
 780                                                 <h2>Sawsim: Kramers' model</h2>
 781
 782 \[
 783   \frac{1}{k_u}
 784     = \frac{1}{D}
 785       \int_{-\infty}^{\infty} \mathrm{d}\! x \;
 786         e^{\frac{U_F(x)}{k_B T}}
 787         \int_{-\infty}^{x} \mathrm{d}\! x' \;
 788           e^{\frac{-U_F(x')}{k_B T}}
 789 \]
 790
 791                                                 <p>
 792                                                         <img src="media/build/landscape-hw-hh.png"
 793                                                                          style="vertical-align: middle;">
 794                                                         <img src="media/build/kramers-integrand-hw-hh.png"
 795                                                                          style="vertical-align: middle;">
 796                                                 </p>
 797                                         </section>
 798                                         <section>
 799                                                 <h2>Sawsim: Tension models</h2>
 800                                                 <table class="center">
 801                                                         <tr>
 802                                                                 <td style="text-align: center;">
 803                                                                         <img src="media/build/unfolding-hw-hh.png"
 804                                                                                          style="vertical-align: middle;">
 805                                                                 </td>
 806                                                                 <td rowspan="2" style="vertical-align: middle;">
 807                                                                         <img src="media/build/wlc-model-hw-fh.png">
 808                                                                 </td>
 809                                                                 <td rowspan="2" style="vertical-align: middle;">
 810                                                                         <img src="media/build/fjc-model-hw-fh.png">
 811                                                                 </td>
 812                                                         </tr>
 813                                                         <tr>
 814                                                                 <td style="text-align: center;">
 815                                                                         <img src="media/build/sawsim-states-hw-hh.png"
 816                                                                                          style="vertical-align: middle;">
 817                                                                 </td>
 818                                                         </tr>
 819                                                 </table>
 820                                         </section>
 821                                         <section>
 822                                                 <h2>Sawsim: Fitting models</h2>
 823                                                 <p>
 824                                                         <img src="media/build/fit-valley-fw-fh.png" />
 825                                                 </p>
 826                                         </section>
 827                                 </section>
 828                                 <section>
 829                                         <section>
 830                                                 <h2>Open source SMFS</h2>
 831                                                 <ol>
 832                                                         <li><a href="#/1">Proteins</a></li>
 833                                                         <li><a href="#/2">Atomic force microscopy</a></li>
 834                                                         <li><a href="#/3">Single molecule force spectroscopy</a></li>
 835                                                         <li><a href="#/4">Experiment control</a></li>
 836                                                         <li><a href="#/5">Cantilever calibration</a></li>
 837                                                         <li><a href="#/6">
 838                                                                         Modeling: Monte Carlo unfolding simulations</a></li>
 839                                                         <li><a href="#/7" class="active">
 840                                                                         Application: Unfolding in salty buffers</a></li>
 841                                                         <li><a href="#/8">Conclusions and future work</a></li>
 842                                                 </ol>
 843                                         </section>
 844                                         <section>
 845                                                 <h2>Unfolding in salty buffers</h2>
 846                                                 <p>
 847                                                         <img src="media/build/lu-fig1-fw-fh.png" />
 848                                                 </p>
 849                                                 <p style="text-align: center;">
 850                                                         <small>
 851                                                                 <a href="http://dx.doi.org/10.1016/S0006-3495(00)76273-4">
 852                                                                         Lu and Schulten, 2000
 853                                                                 </a>
 854                                                         </small>
 855                                                 </p>
 856                                         </section>
 857                                         <section>
 858                                                 <h2>Salt: Glutamic acid</h2>
 859                                                 <p>
 860                                                         <img src="media/build/1TIT-hbond-fw-fh.png" />
 861                                                 </p>
 862                                         </section>
 863                                         <section>
 864                                                 <h2>Salt: Reduced stability in CaCl₂</h2>
 865                                                 <p>
 866                                                         <img src="media/build/pbs-0.5M-CaCl2-hist-fw-fh.png" />
 867                                                 </p>
 868                                         </section>
 869                                         <section>
 870                                                 <h2>Salt: Sawsim fits</h2>
 871                                                 <p>
 872                                                         <img src="media/build/fit-valley-PBS-hw-hh.png" />
 873                                                         <img src="media/build/fit-valley-PBS-0.5M-CaCl2-hw-hh.png" />
 874                                                 </p>
 875                                                 <table class="center" style="width: 640px;">
 876                                                         <thead>
 877                                                                 <tr>
 878                                                                         <th>Buffer</th>
 879                                                                         <th>$\Delta x$ (Å)</th>
 880                                                                         <th>$k_{u0}$ (s$^{-1}$)</th>
 881                                                                 </tr>
 882                                                         </thead>
 883                                                         <tbody>
 884                                                                 <tr>
 885                                                                         <td>PBS</td>
 886                                                                         <td>1.32</td>
 887                                                                         <td>0.222</td>
 888                                                                 </tr>
 889                                                                 <tr>
 890                                                                         <td>PBS + 0.5 M CaCl₂</td>
 891                                                                         <td>1.23</td>
 892                                                                         <td>0.450</td>
 893                                                                 </tr>
 894                                                         </tbody>
 895                                                 </table>
 896                                                 <p><small>Ca²⁺ radius ∼1.1 Å, H-bond ∼2 Å.</small></p>
 897                                         </section>
 898                                 </section>
 899                                 <section>
 900                                         <section>
 901                                                 <h2>Open source SMFS</h2>
 902                                                 <ol>
 903                                                         <li><a href="#/1">Proteins</a></li>
 904                                                         <li><a href="#/2">Atomic force microscopy</a></li>
 905                                                         <li><a href="#/3">Single molecule force spectroscopy</a></li>
 906                                                         <li><a href="#/4">Experiment control</a></li>
 907                                                         <li><a href="#/5">Cantilever calibration</a></li>
 908                                                         <li><a href="#/6">
 909                                                                         Modeling: Monte Carlo unfolding simulations</a></li>
 910                                                         <li><a href="#/7">
 911                                                                         Application: Unfolding in salty buffers</a></li>
 912                                                         <li><a href="#/8" class="active">
 913                                                                         Conclusions and future work</a></li>
 914                                                 </ol>
 915                                         </section>
 916                                         <section>
 917                                                 <h2>Conclusions: Salt</h2>
 918                                                 <ul>
 919                                                         <li>
 920                                                                 Prelimiary results show the expected destabilizing
 921                                                                 effect of CaCl₂
 922                                                         </li>
 923                                                         <li>More contextual data!
 924                                                                 <ul>
 925                                                                         <li>Pulling speeds</li>
 926                                                                         <li>Salt concentrations (physiological levels)</li>
 927                                                                         <li>Salt species</li>
 928                                                                 </ul>
 929                                                         </li>
 930                                                         <li>Mutated proteins?
 931                                                                 <ul>
 932                                                                         <li>Is glutamic acid special?</li>
 933                                                                 </ul>
 934                                                         </li>
 935                                                 </ul>
 936                                         </section>
 937                                         <section>
 938                                                 <h2>Conclusions: Hardware</h2>
 939                                                 <table class="center">
 940                                                         <tr>
 941                                                                 <td style="vertical-align: top;">
 942                                                                         <img src="media/build/afm-hw-hh.png" />
 943                                                                 </td>
 944                                                                 <td>
 945                                                                         <p>For automatic control, it would be nice to have…</p>
 946                                                                         <ul>
 947                                                                                 <li>Piezos with capacitive feedback ($10k an axis)</li>
 948                                                                                 <li>Independent 4-segment photodiode readout</li>
 949                                                                                 <li>Control over photodiode positioning</li>
 950                                                                                 <li>Control over laser alignment</li>
 951                                                                         </ul>
 952                                                                 </td>
 953                                                         </tr>
 954                                                 </table>
 955                                         </section>
 956                                         <section>
 957                                                 <h2>Conclusions: Software</h2>
 958                                                 <p>
 959                                                         <img src="media/build/pyafm-hw-hh.png" />
 960                                                 </p>
 961                                                 <p style="text-align: left;">
 962                                                         Everything works for me, and I expect it will work for
 963                                                         others… but no software (except
 964                                                         maybe <a href="http://en.wikipedia.org/wiki/TeX#Development">TeX</a>)
 965                                                         is without bugs.  Testers welcome!
 966                                                 </p>
 967                                         </section>
 968                                 </section>
 969                                 <section>
 970                                         <section>
 971                                                 <h1>The End</h1>
 972                                         </section>
 973                                         <section>
 974                                                 <h1>Thanks!</h1>
 975                                                 <table>
 976                                                         <tr>
 977                                                                 <td rowspan="2" style="vertical-align: top;">
 978                                                                         <ul>
 979                                                                                 <li>Guoliang Yang</li>
 980                                                                                 <li>Luis Cruz Cruz</li>
 981                                                                                 <li>Marisa Roman</li>
 982                                                                                 <li>Runcong Liu</li>
 983                                                                                 <li>Jian-Min Yuan</li>
 984                                                                                 <li>Jun Xi</li>
 985                                                                                 <li>Som Tyagi</li>
 986                                                                                 <li>Michel Vallières</li>
 987                                                                                 <li>Everyone else in Drexel physics!</li>
 988                                                                                 <li>
 989                                                                                         <a href="http://dx.doi.org/10.1093/bioinformatics/btp180">Sandal,
 990                                                                                                 Benedetti, et al.</a> for initial work on Hooke</li>
 991                                                                         </ul>
 992                                                                 </td>
 993                                                                 <td style="vertical-align: top;">
 994                                                                         <ul>
 995                                                                                 <li><a href="http://lab.hakim.se/reveal-js/">reveal.js</a></li>
 996                                                                                 <li><a href="http://sourceforge.net/projects/pymol/">PyMOL</a></li>
 997                                                                                 <li><a href="http://asymptote.sourceforge.net/">Asymptote</a></li>
 998                                                                                 <li>…</li>
 999                                                                         </ul>
1000                                                                 </td>
1001                                                         </tr>
1002                                                         <tr>
1003                                                                 <td style="vertical-align: top;">
1004                                                                         <ul>
1005                                                                                 <li>My family!</li>
1006                                                                         </ul>
1007                                                                 </td>
1008                                                         </tr>
1009                                                 </table>
1010                                         </section>
1011                                 </section>
1012                         </div>
1013                 </div>
1014                 <script src="lib/js/head.min.js"></script>
1015                 <script src="js/reveal.min.js"></script>
1016                 <script>
1017                         // Full list of configuration options available here:
1018                         // https://github.com/hakimel/reveal.js#configuration
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1023                                 center: true,
1024                                 theme: Reveal.getQueryHash().theme, // available themes are in /css/theme
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1026                                 // Optional libraries used to extend on reveal.js
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