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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>Proteins: What are they?</h2>
  50                                                 <p>
  51                                                         <video width="640" height="480"
  52                                                                                  preload="auto" loop="" controls=""> <!--autoplay=""-->
  53                                                                 <source src="media/build/1TIT-atoms.mp4"
  54                                                                                                 type='video/mp4; codecs="avc1.42E01E, mp4a.40.2"' />
  55                                                         </video>
  56                                                         <!-- generated with PyMol from
  57                                                                          http://www.rcsb.org/pdb/explore.do?structureId=1TIT -->
  58                                                 </p>
  59                                         </section>
  60                                         <section>
  61                                                 <h2>Proteins: Where are they?</h2>
  62                                                 <p>
  63                                                         <img src="media/build/takamori-fig4b-fw-fh.png" />
  64                                                 </p>
  65                                                 <p style="text-align: center;">
  66                                                         <small>
  67                                                                 <a href="http://dx.doi.org/10.1016/j.cell.2006.10.030">
  68                                                                         Takamori, Holt, Stenius, et al., 2006
  69                                                                 </a>
  70                                                         </small>
  71                                                 </p>
  72                                         </section>
  73                                         <section>
  74                                                 <h2>Proteins: Titin</h2>
  75                                                 <p>
  76                                                         <img src="media/build/skeletal-muscle-fw-fh.png" />
  77                                                 </p>
  78                                                 <p style="text-align: center;">
  79                                                         <small>
  80                                                                 Adapted from
  81                                                                 <a href="http://en.wikipedia.org/wiki/File:Skeletal_muscle.jpg">
  82                                                                         Wikipedia
  83                                                                 </a>
  84                                                         </small>
  85                                                 </p>
  86                                         </section>
  87                                         <section>
  88                                                 <h2>Proteins: Titin's I27</h2>
  89                                                 <p>
  90                                                         <img src="media/build/titin-fw-fh.png" />
  91                                                 </p>
  92                                                 <p style="text-align: center;">
  93                                                         <small>
  94                                                                 <a href="http://www.ks.uiuc.edu/Research/telethonin/">
  95                                                                         U. Illinois Biophysics Group
  96                                                                 </a>
  97                                                         </small>
  98                                                 </p>
  99                                         </section>
 100                                         <section>
 101                                                 <h2>Proteins: I27</h2>
 102                                                 <p>
 103                                                         <img src="media/build/1TIT-fw-fh.png" />
 104                                                 </p>
 105                                                 <p style="text-align: center;">
 106                                                         <small>
 107                                                                 <a href="http://www.rcsb.org/pdb/explore.do?structureId=1TIT">
 108                                                                         PDB structure 1TIT
 109                                                                 </a>
 110                                                         </small>
 111                                                 </p>
 112                                         </section>
 113                                         <section>
 114                                                 <h2>Proteins: What's the problem?</h2>
 115                                                 <table class="center">
 116                                                         <tr>
 117                                                                 <td style="vertical-align: middle;">
 118                                                                         <pre style="display: table; width: auto;">
 119 MHHHHHHSSLIEV
 120 EKPLYGVEVFVGE
 121 TAHFEIELSEPDV
 122 HGQWKLKGQPLTA
 123 SPDCEIIEDGKKH
 124 ILILHNCQLGMTG
 125 EVSFQAANAKSAA
 126 NLKVKEL</pre>
 127                                                                 </td>
 128                                                                 <td style="vertical-align: middle;"><p>  →  </p></td>
 129                                                                 <td style="vertical-align: middle;">
 130                                                                         <img src="media/build/1TIT-tw-th.png" />
 131                                                                 </td>
 132                                                         </tr>
 133                                                         <tr>
 134                                                                 <td colspan="3">
 135                                                                         <p>
 136                                                                                 <img src="media/build/pirchi-fig1-fw-hh.png" />
 137                                                                         </p>
 138                                                                         <p style="text-align: center;">
 139                                                                                 <small>
 140                                                                                         <a href="http://dx.doi.org/10.1038/ncomms1504">
 141                                                                                                 Pirchi, Ziv, Riven, et al., 2011
 142                                                                                         </a>
 143                                                                                 </small>
 144                                                                         </p>
 145                                                                 </td>
 146                                                         </tr>
 147                                                 </table>
 148                                         </section>
 149                                 </section>
 150                                 <section>
 151                                         <section>
 152                                                 <h2>Atomic force microscopy</h2>
 153                                                 <p>
 154                                                         <img src="media/build/afm-3d-fw-fh.png" />
 155                                                 </p>
 156                                         </section>
 157                                         <section>
 158                                                 <h2>AFM: Cantilever geometry</h2>
 159                                                 <p>
 160                                                         <!-- need height to stretch low-resolution pictures -->
 161                                                         <img src="media/build/cantilever.jpg" height="272" />
 162                                                         <img src="media/build/tip.jpg" height="272" />
 163                                                 </p>
 164                                                 <p style="text-align: center;">
 165                                                         <small>
 166                                                                 <a href="http://probe.olympus-global.com/en/product/omcl_tr800psa_w/">
 167                                                                         Olympus TR800PSA
 168                                                                 </a>, images from
 169                                                                 <a href="http://www.asylumresearch.com/Probe/TR400PSA,Olympus">
 170                                                                         Asylum Research
 171                                                                 </a><br/>
 172                                                                 We use the thinner
 173                                                                 <a href="http://probe.olympus-global.com/en/product/omcl_tr400psa_hw/">
 174                                                                          TR400PSA
 175                                                                 </a>
 176                                                         </small>
 177                                                 </p>
 178                                         </section>
 179                                         <section>
 180                                                 <h2>AFM: Laser deflection</h2>
 181                                                 <p>
 182                                                         <video width="640" height="480"
 183                                                                                  preload="auto" loop="" controls=""> <!--autoplay=""-->
 184                                                                 <source src="media/build/contact-afm.ogv"
 185                                                                                                 type='video/ogg; codecs="theora,vorbis"' />
 186                                                         </video>
 187                                                 </p>
 188                                                 <p style="text-align: center;">
 189                                                         <small>
 190                                                                 <a href="http://www.freesbi.ch/fr/illustration/animations">
 191                                                                         Charles Roduit
 192                                                                 </a>
 193                                                         </small>
 194                                                 </p>
 195                                         </section>
 196                                         <section>
 197                                                 <h2>AFM: Piezo positioning</h2>
 198                                                 <p>
 199                                                         <img src="media/build/afm-fw-fh.png" />
 200                                                 </p>
 201                                         </section>
 202                                         <section>
 203                                                 <h2>The piezoelectric effect</h2>
 204                                                 <p>
 205                                                         <object data="media/perovskite.svg" type="image/svg+xml"
 206                                                                         width="640" height="350"></object>
 207                                                 </p>
 208                                                 <p style="text-align: center;">
 209                                                         <small>
 210                                                                 <a href="http://en.wikipedia.org/wiki/File:Perovskite.svg">
 211                                                                         Wikipedia
 212                                                                 </a>
 213                                                         </small>
 214                                                 </p>
 215                                         </section>
 216                                         <section>
 217                                                 <h2>AFM: Tubular piezos</h2>
 218                                                 <p>
 219                                                         <img src="media/build/piezo-fw-fh.png" />
 220                                                 </p>
 221                                         </section>
 222                                 </section>
 223                                 <section>
 224                                         <section>
 225                                                 <h2>Single molecule force spectroscopy</h2>
 226                                                 <p>
 227                                                         <img src="media/build/unfolding-fw-fh.png" />
 228                                                 </p>
 229                                         </section>
 230                                         <section>
 231                                                 <h2>SMFS: Sawtooth curve</h2>
 232                                                 <p>
 233                                                         <img src="media/build/expt-sawtooth-fw-fh.png" width="640" />
 234                                                 </p>
 235                                         </section>
 236                                         <section>
 237                                                 <h2>SMFS: What's going on?</h2>
 238                                                 <p>
 239                                                         <img src="media/build/carrion-vazquez-fig2-fw-fh.png" />
 240                                                 </p>
 241                                                 <p>
 242                                                         <small>
 243                                                                 <a href="http://dx.doi.org/10.1016/S0079-6107(00)00017-1">
 244                                                                         Carrion-Vazquez, et al., 2000;
 245                                                                         adapted from Baljon and Robbins, 1996
 246                                                                 </a>
 247                                                         </small>
 248                                                 </p>
 249                                         </section>
 250                                         <section>
 251                                                 <h2>SMFS: Unfolding one domain</h2>
 252                                                 <p>
 253                                                         <img src="media/build/lu-fig1-fw-fh.png" />
 254                                                 </p>
 255                                                 <p>
 256                                                         <small>
 257                                                                 <a href="http://dx.doi.org/10.1016/S0006-3495(00)76273-4">
 258                                                                         Lu and Schulten, 2000
 259                                                                 </a>
 260                                                         </small>
 261                                                 </p>
 262                                         </section>
 263                                 </section>
 264                                 <section>
 265                                         <section>
 266                                                 <h2>Experiment control</h2>
 267                                                 <p>
 268                                                         <img src="media/build/apparatus-fw-fh.png" />
 269                                                 </p>
 270                                         </section>
 271                                         <section>
 272                                                 <h2>Control: Quick-and-dirty</h2>
 273                                                 <p>
 274                                                         <img src="media/build/labview-fw-fh.png" />
 275                                                 </p>
 276                                         </section>
 277                                         <section>
 278                                                 <h2>Control: Modular stack</h2>
 279                                                 <p>
 280                                                         <img src="media/build/pyafm-fw-fh.png" />
 281                                                 </p>
 282                                         </section>
 283                                         <section>
 284                                                 <h2>Open source: Existing layers</h2>
 285                                                 <table class="center">
 286                                                         <tr>
 287                                                                 <td><img src="media/logo/tux.png" height="150" /></td>
 288                                                                 <td><object data="media/logo/gnu.svg" type="image/svg+xml"
 289                                                                                                                 height="150"></object></td>
 290                                                                 <td><object data="media/logo/gentoo.svg" type="image/svg+xml"
 291                                                                                                                 height="150"></object></td>
 292                                                                 <td><object data="media/logo/python.svg" type="image/svg+xml"
 293                                                                                                                 height="150"></object></td>
 294                                                                 <td><object data="media/logo/scipy.svg" type="image/svg+xml"
 295                                                                                                                 height="150"></object></td>
 296                                                         </tr>
 297                                                         <tr>
 298                                                                 <td><a href="https://www.kernel.org/">Linux</a></td>
 299                                                                 <td>
 300                                                                         <a href="http://www.gnu.org/">
 301                                                                                 <abbr title="GNU's Not Unix!">GNU</abbr>
 302                                                                         </a>
 303                                                                 </td>
 304                                                                 <td><a href="http://www.gentoo.org/">Gentoo</a></td>
 305                                                                 <td><a href="http://www.python.org/">Python</a></td>
 306                                                                 <td><a href="http://www.scipy.org/">SciPy</a></td>
 307                                                         </tr>
 308                                                         <tr>
 309                                                                 <td>
 310                                                                         <small>
 311                                                                                 <a href="http://www.comedi.org/">
 312                                                                                         <abbr title="Control and Measurement Device Interface">Comedi<abbr>
 313                                                                                 </a>
 314                                                                         </small>
 315                                                                 </td>
 316                                                                 <td>
 317                                                                         <small>
 318                                                                                 <a href="http://matplotlib.org/">matplotlib</a>
 319                                                                         </small>
 320                                                                 </td>
 321                                                                 <td>
 322                                                                         <small>
 323                                                                                 <a href="https://github.com/bashwork/pymodbus">pymodbus</a>
 324                                                                         </small>
 325                                                                 </td>
 326                                                                 <td>
 327                                                                         <small>
 328                                                                                 <a href="http://www.cython.org/">Cython</a>
 329                                                                         </small>
 330                                                                 </td>
 331                                                                 <td>
 332                                                                         <small>
 333                                                                                 <a href="https://www.numpy.org/">NumPy</a>
 334                                                                         </small>
 335                                                                 </td>
 336                                                         </tr>
 337                                                         <tr>
 338                                                                 <td>
 339                                                                         <small>
 340                                                                                 <a href="http://www.h5py.org/">h5py</a>
 341                                                                         </small>
 342                                                                 </td>
 343                                                                 <td><small>…</small></td>
 344                                                         </tr>
 345                                                 </table>
 346                                         </section>
 347                                         <section>
 348                                                 <h2>Open source: Teamwork</h2>
 349                                                 <p>
 350                                                         <img src="media/build/ants-fw-fh.png" />
 351                                                 </p>
 352                                                 <p style="text-align: center;">
 353                                                         <small>
 354                                                                 <a href="http://dx.doi.org/10.1073/pnas.1016658108">
 355                                                                         Mlot, Tovey, and Hu, 2011
 356                                                                 </a>
 357                                                         </small>
 358                                                 </p>
 359                                         </section>
 360                                         <section>
 361                                                 <h2>Control: Example code</h2>
 362                                                 <pre><code data-trim="">
 363 class Unfolder (object):
 364     …
 365     def run(self):
 366         """Approach-bind-unfold-save[-plot] cycle.
 367         """
 368         ret = {}
 369         ret['timestamp'] = _email_utils.formatdate(localtime=True)
 370         ret['temperature'] = self.afm.get_temperature()
 371         ret['approach'] = self._approach()
 372         self._bind()
 373         ret['unfold'] = self._unfold()
 374         self._save(**ret)
 375         if _package_config['matplotlib']:
 376             self._plot(**ret)
 377         return ret
 378                                                 </code></pre>
 379                                         </section>
 380                                         <section>
 381                                                 <h2>Archival: HDF5 and h5config</h2>
 382                                                 <!-- h5dump -H 2013-03-04T12-43-38.h5 |
 383                                                                  grep 'GROUP\|DATASET' | sed 's/ {.*//' -->
 384                                                 <pre>
 385 GROUP <span style="color: blue">&quot;/&quot;</span>
 386    GROUP <span style="color: blue">&quot;approach&quot;</span>
 387       …
 388    GROUP <span style="color: blue">&quot;config&quot;</span>
 389       GROUP <span style="color: blue">&quot;afm&quot;</span>
 390          …
 391       GROUP <span style="color: blue">&quot;approach&quot;</span>
 392          …
 393       DATASET <span style="color: blue">&quot;bind time&quot;</span>
 394       …
 395       GROUP <span style="color: blue">&quot;unfold&quot;</span>
 396          …
 397          DATASET <span style="color: blue">&quot;velocity&quot;</span>
 398    GROUP <span style="color: blue">&quot;environment&quot;</span>
 399       DATASET <span style="color: blue">&quot;temperature&quot;</span>
 400       DATASET <span style="color: blue">&quot;timestamp&quot;</span>
 401       …
 402    GROUP <span style="color: blue">&quot;unfold&quot;</span>
 403       DATASET <span style="color: blue">&quot;deflection&quot;</span>
 404       DATASET <span style="color: blue">&quot;frequency&quot;</span>
 405       DATASET <span style="color: blue">&quot;z&quot;</span></pre>
 406                                         </section>
 407                                         <section>
 408                                                 <h2>Archival: Version control</h2>
 409                                                 <pre>
 410 <span style="color: red">commit 32bfbf98d79c73eba50b77d0917df100e0e33bcf</span>
 411 Author: W. Trevor King &lt;wking@tremily.us&gt;
 412 Date:   Fri Jan 18 22:54:49 2013 -0500
 413
 414     afm: Optionally return stepper_approach data with `record_data`
 415
 416     Sometimes these approach curves are pretty funky, so I'll start
 417     recording them by default in calibcant-calibrate.py.
 418
 419 <span style="font-weight: bold">diff --git a/pyafm/afm.py b/pyafm/afm.py
 420 index 60741c6..e76b118 100644
 421 --- a/pyafm/afm.py
 422 +++ b/pyafm/afm.py</span>
 423 <span style="color: blue">@@ -460,10 +460,11 @@</span> class AFM (object):
 424          _LOG.warn(e)
 425          raise e
 426
 427 <span style="color: red">-    def stepper_approach(self, target_deflection):</span>
 428 <span style="color: green">+    def stepper_approach(self, target_deflection, record_data=None):</span>
 429 …</pre>
 430                                         </section>
 431                                 </section>
 432                                 <section>
 433                                         <section>
 434                                                 <h2>Cantilever calibration</h2>
 435                                                 <p>
 436                                                         <img src="media/build/unfolding-fw-fh.png" />
 437                                                 </p>
 438                                         </section>
 439                                         <section>
 440                                                 <h2>Calibration: Geometry</h2>
 441                                                 <p>
 442                                                         <!-- need height to stretch low-resolution pictures -->
 443                                                         <img src="media/build/cantilever.jpg" height="272" />
 444                                                         <img src="media/build/tip.jpg" height="272" />
 445                                                 </p>
 446                                                 <p style="text-align: center;">
 447                                                         <small>
 448                                                                 <a href="http://probe.olympus-global.com/en/product/omcl_tr800psa_w/">
 449                                                                         Olympus TR800PSA
 450                                                                 </a>, images from
 451                                                                 <a href="http://www.asylumresearch.com/Probe/TR400PSA,Olympus">
 452                                                                         Asylum Research
 453                                                                 </a><br/>
 454                                                                 We use the thinner
 455                                                                 <a href="http://probe.olympus-global.com/en/product/omcl_tr400psa_hw/">
 456                                                                          TR400PSA
 457                                                                 </a>
 458                                                         </small>
 459                                                 </p>
 460                                         </section>
 461                                         <section>
 462                                                 <h2>Calibration: Equipartition</h2>
 463                                                 <p>
 464                                                         For a damped harmonic oscillator
 465                                                 </p>
 466
 467 \[
 468   -\kappa x_c
 469   - \gamma \frac{\mathrm{d}\! x_c}{\mathrm{d}\! t}
 470   + F_\text{ext}(t)
 471     = m\frac{\mathrm{d}^2\! x}{\mathrm{d}\! t^2} \;,
 472 \]
 473
 474                                                 <p>
 475                                                         the energy in each degree of freedom is $\frac{1}{2}k_B
 476                                                         T$.
 477                                                 </p>
 478
 479 \[
 480   \frac{1}{2} \kappa \left\langle x_c^2 \right\rangle = \frac{1}{2}k_B T \;,
 481 \]
 482
 483                                                 <p>
 484                                                         where $k_B$ is Boltzmann's constant and $T$ is the
 485                                                         temperature.
 486                                                 </p>
 487                                         </section>
 488                                         <section>
 489                                                 <h2>Calibration: Vibration</h2>
 490                                                 <p>
 491                                                         <img src="media/build/vibration-fw-fh.png" width="620" />
 492                                                 </p>
 493                                         </section>
 494                                         <section>
 495                                                 <h2>Calibration: Photodiode calibration</h2>
 496                                                 <p>
 497                                                         <img src="media/build/bump-fw-fh.png" />
 498                                                 </p>
 499                                         </section>
 500                                         <section>
 501                                                 <h2>Calibration: Results</h2>
 502
 503 \[
 504 \begin{aligned}
 505   T &= 298.15 \pm 0.03 \; \text{K}  &
 506   \sigma_p &= 35.7 \pm 0.9 \; \text{mV/nm} \\
 507   \left\langle V_p^2 \right\rangle &= 97 \pm 1 \; \text{mV}^2  &
 508   \sqrt{\left\langle x_c^2 \right\rangle}
 509     &= \sqrt{\frac{\left\langle V_p^2 \right\rangle}{\sigma_p^2}}
 510     = 0.28 \; \text{nm} \\
 511   \kappa &= \frac{k_B T \sigma_p^2}{\left\langle V_p^2 \right\rangle}
 512     = 54 \pm 3 \; \text{pN/nm}
 513 \end{aligned}
 514 \]
 515
 516                                         </section>
 517                                         <section>
 518                                                 <h2>Calibration: Stability</h2>
 519                                                 <table class="center">
 520                                                         <thead>
 521                                                                 <tr>
 522                                                                         <th>Quant.</th>
 523                                                                         <th>Units</th>
 524                                                                         <th> </th>
 525                                                                         <!-- 2013-03-03T16-37-12 -->
 526                                                                         <th colspan="2" style="text-align: center">Day 1</th>
 527                                                                         <th> </th>
 528                                                                         <!-- 2013-03-04T12-21-54 -->
 529                                                                         <th colspan="2" style="text-align: center">Day 2</th>
 530                                                                 </tr>
 531                                                         </thead>
 532                                                         <tbody>
 533                                                                 <tr>
 534                                                                         <td>$T$</td>
 535                                                                         <td>K</td>
 536                                                                         <td></td>
 537                                                                         <td>296.30</td>
 538                                                                         <td>±0.02</td>
 539                                                                         <td></td>
 540                                                                         <td>294.27</td>
 541                                                                         <td>±0.02</td>
 542                                                                 </tr>
 543                                                                 <tr>
 544                                                                         <td>$\sigma_p$</td>
 545                                                                         <td>mV/nm</td>
 546                                                                         <td></td>
 547                                                                         <td>&#x2007;46.2</td>
 548                                                                         <td>±0.8</td>
 549                                                                         <td></td>
 550                                                                         <td>&#x2007;41.3</td>
 551                                                                         <td>±0.2</td>
 552                                                                 </tr>
 553                                                                 <tr>
 554                                                                         <td>$\left\langle V_p^2 \right\rangle$</td>
 555                                                                         <td>mV$^2$</td>
 556                                                                         <td></td>
 557                                                                         <td>108</td>
 558                                                                         <td>±1</td>
 559                                                                         <td></td>
 560                                                                         <td>105</td>
 561                                                                         <td>±2</td>
 562                                                                 </tr>
 563                                                                 <tr>
 564                                                                         <td>$\kappa$</td>
 565                                                                         <td>pN/nm</td>
 566                                                                         <td></td>
 567                                                                         <td>&#x2007;67</td>
 568                                                                         <td>±2</td>
 569                                                                         <td></td>
 570                                                                         <td>&#x2007;66</td>
 571                                                                         <td>±2</td>
 572                                                                 </tr>
 573                                                         </tbody>
 574                                                 </table>
 575                                         </section>
 576                                         <section>
 577                                                 <h2>Calibration: Inconsistency</h2>
 578                                                 <table class="center">
 579                                                         <tr>
 580                                                                 <td style="vertical-align: middle;">
 581                                                                         <img src="media/build/florin-fig2-hw-fh.png" />
 582                                                                 </td>
 583                                                                 <td style="vertical-align: middle;">
 584                                                                         <img src="media/build/vibration-hw-fh.png" />
 585                                                                 </td>
 586                                                         </tr>
 587                                                 </table>
 588                                                 <p style="text-align: center;">
 589                                                         <small>
 590                                                                 <a href="http://dx.doi.org/10.1016/0896-6273(88)90139-0">
 591                                                                         Florin, Rief, Lehmann, et al., 1995
 592                                                                 </a>
 593                                                         </small>
 594                                                 </p>
 595                                         </section>
 596                                 </section>
 597                                 <section>
 598                                         <section>
 599                                                 <h2>Monte Carlo unfolding simulations</h2>
 600                                                 <table class="center">
 601                                                         <tr>
 602                                                                 <td rowspan="2" style="vertical-align: middle;">
 603                                                                         <img src="media/build/unfolding-fw-fh.png" />
 604                                                                 </td>
 605                                                                 <td style="vertical-align: top;">
 606                                                                         <img src="media/build/expt-sawtooth-hw-hh.png" />
 607                                                                 </td>
 608                                                         </tr>
 609                                                         <tr>
 610                                                                 <td><img src="media/build/pbs-hist-hw-hh.png" /></td>
 611                                                         </tr>
 612                                                 </table>
 613                                         </section>
 614                                         <section>
 615                                                 <h2>Sawsim: State model</h2>
 616                                                 <p>
 617                                                         <img src="media/build/unfolding-hw-fh.png"
 618                                                                          style="vertical-align: middle;">
 619                                                         <img src="media/build/sawsim-states-hw-fh.png"
 620                                                                          style="vertical-align: middle;">
 621                                                 </p>
 622                                         </section>
 623                                         <section>
 624                                                 <h2>Sawsim: Simulation loop</h2>
 625                                                 <ol>
 626                                                         <li>Calculate piezo-induced gap $x_t(t)=v t$</li>
 627                                                         <li>
 628                                                                 Find tension model parameters for each state
 629                                                         </li>
 630                                                         <li>
 631                                                                 Distribute per-state stretching ($x_c$, $x_u$, …) to
 632                                                                 balance the tension
 633                                                         </li>
 634                                                         <li>
 635                                                                 Calculate the transition rates between states
 636                                                         </li>
 637                                                         <li>
 638                                                                 Roll the dice to determine if transitions take
 639                                                                 place as you step forward in time
 640                                                         </li>
 641                                                 </ol>
 642                                         </section>
 643                                         <section>
 644                                                 <h2>Sawsim: Monte Carlo</h2>
 645                                                 <p>
 646                                                         <img src="media/build/monte-carlo-fw-fh.png" />
 647                                                 </p>
 648                                         </section>
 649                                         <section>
 650                                                 <h2>Sawsim: Unfolding models</h2>
 651                                                 <table class="center">
 652                                                         <tr>
 653                                                                 <td style="text-align: center;">
 654                                                                         <img src="media/build/unfolding-hw-hh.png"
 655                                                                                          style="vertical-align: middle;">
 656                                                                 </td>
 657                                                                 <td>
 658                                                                         <img src="media/build/landscape-hw-hh.png"
 659                                                                                          style="vertical-align: middle;">
 660                                                                 </td>
 661                                                         </tr>
 662                                                         <tr>
 663                                                                 <td style="text-align: center;">
 664                                                                         <img src="media/build/sawsim-states-hw-hh.png"
 665                                                                                          style="vertical-align: middle;">
 666                                                                 </td>
 667                                                                 <td>
 668                                                                         <img src="media/build/landscape-bell-hw-hh.png"
 669                                                                                          style="vertical-align: middle;">
 670                                                                 </td>
 671                                                         </tr>
 672                                                 </table>
 673                                         </section>
 674                                         <section>
 675                                                 <h2>Sawsim: Kramers' model</h2>
 676
 677 \[
 678   \frac{1}{k_u}
 679     = \frac{1}{D}
 680       \int_{-\infty}^{\infty} \mathrm{d}\! x \;
 681         e^{\frac{U_F(x)}{k_B T}}
 682         \int_{-\infty}^{x} \mathrm{d}\! x' \;
 683           e^{\frac{-U_F(x')}{k_B T}}
 684 \]
 685
 686                                                 <p>
 687                                                         <img src="media/build/landscape-hw-hh.png"
 688                                                                          style="vertical-align: middle;">
 689                                                         <img src="media/build/kramers-integrand-hw-hh.png"
 690                                                                          style="vertical-align: middle;">
 691                                                 </p>
 692                                         </section>
 693                                         <section>
 694                                                 <h2>Sawsim: Tension models</h2>
 695                                                 <table class="center">
 696                                                         <tr>
 697                                                                 <td style="text-align: center;">
 698                                                                         <img src="media/build/unfolding-hw-hh.png"
 699                                                                                          style="vertical-align: middle;">
 700                                                                 </td>
 701                                                                 <td rowspan="2" style="vertical-align: middle;">
 702                                                                         <img src="media/build/wlc-model-hw-fh.png">
 703                                                                 </td>
 704                                                                 <td rowspan="2" style="vertical-align: middle;">
 705                                                                         <img src="media/build/fjc-model-hw-fh.png">
 706                                                                 </td>
 707                                                         </tr>
 708                                                         <tr>
 709                                                                 <td style="text-align: center;">
 710                                                                         <img src="media/build/sawsim-states-hw-hh.png"
 711                                                                                          style="vertical-align: middle;">
 712                                                                 </td>
 713                                                         </tr>
 714                                                 </table>
 715                                         </section>
 716                                         <section>
 717                                                 <h2>Sawsim: Fitting models</h2>
 718                                                 <p>
 719                                                         <img src="media/build/fit-valley-fw-fh.png" />
 720                                                 </p>
 721                                         </section>
 722                                 </section>
 723                                 <section>
 724                                         <section>
 725                                                 <h2>Sawsim: Salt</h2>
 726                                                 <p>
 727                                                         <img src="media/build/lu-fig1-fw-fh.png" />
 728                                                 </p>
 729                                                 <p style="text-align: center;">
 730                                                         <small>
 731                                                                 <a href="http://dx.doi.org/10.1016/S0006-3495(00)76273-4">
 732                                                                         Lu and Schulten, 2000
 733                                                                 </a>
 734                                                         </small>
 735                                                 </p>
 736                                         </section>
 737                                         <section>
 738                                                 <h2>Sawsim: Glutamic acid</h2>
 739                                                 <p>
 740                                                         <img src="media/build/1TIT-hbond-fw-fh.png" />
 741                                                 </p>
 742                                         </section>
 743                                 </section>
 744                                 <section>
 745                                         <h1>THE END</h1>
 746                                         <p style="text-align: center;">
 747                                         Written with <a href="http://lab.hakim.se/reveal-js/">reveal.js</a>
 748                                         </p>
 749                                 </section>
 750                         </div>
 751                 </div>
 752                 <script src="lib/js/head.min.js"></script>
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 761                                 center: true,
 762                                 theme: Reveal.getQueryHash().theme, // available themes are in /css/theme
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