<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="3.10.0">Jekyll</generator><link href="https://shiling42.github.io/feed.xml" rel="self" type="application/atom+xml" /><link href="https://shiling42.github.io/" rel="alternate" type="text/html" /><updated>2026-03-05T09:40:08-08:00</updated><id>https://shiling42.github.io/feed.xml</id><title type="html">Shiling Liang </title><subtitle>ELBE Postdoctoral Fellow @ CSBD</subtitle><author><name>Shiling  Liang 梁师翎</name><email>shiling@pks.mpg.de</email></author><entry><title type="html">Coding with GPT-4: Simulating Emergent Phenomena in Complex Systems</title><link href="https://shiling42.github.io/posts/2023/03/GPT-simulator" rel="alternate" type="text/html" title="Coding with GPT-4: Simulating Emergent Phenomena in Complex Systems" /><published>2023-03-21T00:00:00-07:00</published><updated>2023-03-21T00:00:00-07:00</updated><id>https://shiling42.github.io/posts/2023/03/GPT-simulator</id><content type="html" xml:base="https://shiling42.github.io/posts/2023/03/GPT-simulator"><![CDATA[<blockquote>
  <p>This article was generated by GPT-4 under guidance.</p>
</blockquote>

<h2 id="introduction">Introduction</h2>

<p>Today we bring you a unique online interactive physics system simulation project, which uses HTML and JavaScript code generated by GPT-4 to implement a series of visual simulations that allow us to better understand physics, complex systems, and emergent phenomena.</p>

<p>In this project, we will show you some exciting simulations, including the XY model, the Vicsek bird flocking model, phase separation, and particle repulsion. These simulations all use code generated by GPT-4, allowing us to explore the physical world intuitively and understand various physical processes and emergent phenomena.</p>

<p>In addition, with the help of GPT-4, the natural language processing tool, programming becomes simpler, allowing more people to participate in project development. Even people without interface development experience can quickly develop such projects by commanding GPT-4 in ordinary language.</p>

<p>In this project, we will guide you through how to use GPT-4 technology to generate code for interactive physics system simulations, allowing you to experience the charm of physics and complex systems. Let’s start this exploration journey together!</p>

<h2 id="vicsek-model-of-flocking"><a href="https://shilingliang.com/web-simulator-by-GPT4/interactive_vicsek.html">Vicsek Model of Flocking</a></h2>

<p>Today, we are excited to introduce a cutting-edge, online interactive physics system simulation project that leverages the power of GPT-4-generated HTML and JavaScript code to create a suite of visually engaging simulations, aimed at enhancing our understanding of physics, complex systems, and emergent phenomena.</p>

<p>In this project, we showcase captivating simulations such as the XY model, the Vicsek bird flocking model, phase separation, and particle repulsion. Each of these simulations is powered by code generated by GPT-4, enabling us to explore the physical world in an intuitive manner and gain insights into various physical processes and emergent phenomena.</p>

<p>Furthermore, GPT-4’s natural language processing capabilities simplify the programming process, making it more accessible for a wider audience to contribute to the project’s development. Individuals without prior experience in interface development can swiftly create projects by providing GPT-4 with plain-language instructions.</p>

<p>Throughout this project, we will walk you through the process of utilizing GPT-4 technology to generate code for interactive physics system simulations, offering you the opportunity to delve into the fascinating world of physics and complex systems. Let’s embark on this thrilling journey of exploration together!</p>
<iframe src="https://shilingliang.com/web-simulator-by-GPT4/interactive_vicsek.html" width="780" height="500" allowfullscreen=""></iframe>

<h2 id="xy-model"><a href="https://shilingliang.com/web-simulator-by-GPT4/XY_model.html">XY Model</a></h2>

<p>The XY model originates from condensed matter physics and mainly studies a particle system on a two-dimensional plane. These particles can be imagined as compasses, distributed on the plane, and each particle has a direction. The core of this model lies in the interaction between particles: each particle tends to maintain the same direction as neighboring particles. This interaction forms an interesting balance, where particles strive to maintain consistency while responding to the influence of other particles.</p>

<p>In the XY model, we can observe a fascinating emergent phenomenon: when the interaction between particles reaches a certain degree, the entire system will spontaneously form an ordered state, and the particles will point in roughly the same direction. This ordered state reflects the self-organizing behavior inside the system and is a typical phenomenon in complex systems.</p>

<p>The XY model also contains a very interesting and important physical phenomenon - the Berezinskii–Kosterlitz–Thouless (BKT) phase transition. The discovery of the KT phase transition brought revolutionary breakthroughs to the theory of phase transitions, and even led to the Nobel Prize in Physics being awarded to physicists Kosterlitz and Thouless in 2016.</p>

<p>Unlike the first- and second-order phase transitions we are familiar with, such as water turning into ice or water vapor, the KT phase transition is a topological phase transition. This means that it does not involve a sudden change in the density, magnetism, or other physical properties of matter, but rather involves a change in the internal topological structure of the system. In the XY model, this topological structure is manifested as vortices and antivortices, which can be understood as local rotational structures with different rotation directions.</p>

<p>When the temperature is low, vortices and antivortices form a stable paired state, and their mutual attraction makes the system present an ordered state. However, when the temperature rises to a critical point, vortices and antivortices begin to dissociate, and the degree of order in the system gradually decreases. This is the process described by the KT phase transition.</p>

<p>Through the XY model in the online interactive physics system simulation project, we can intuitively observe the process of the KT phase transition and understand how this unique topological phase transition occurs in complex systems. This is undoubtedly an attractive learning path for science enthusiasts who want to deepen their understanding of phase transitions, topological structures, and emergent phenomena.</p>

<centre>
<iframe src="https://shilingliang.com/web-simulator-by-GPT4/XY_model.html" width="780" height="650" allowfullscreen=""></iframe>
</centre>

<h2 id="phase-separation"><a href="https://shilingliang.com/web-simulator-by-GPT4/phase_separation.html">Phase Separation</a></h2>

<p>Phase separation is a widely existing phenomenon in nature, which refers to the spontaneous separation of different types of components into regions of a single component in a mixed system under certain conditions. This process is involved in many chemical, physical, and biological systems, such as oil-water mixtures, cooling and separation of alloys, and distribution of lipid molecules on cell membranes.</p>

<p>The concept closely related to phase separation is pattern formation, which describes the self-organizing phenomenon of spatial structure under certain conditions. This phenomenon is often accompanied by the appearance of local structure and order. In the process of phase separation, we can observe a series of complex pattern formation phenomena, such as bubble-like structures, stripe-like structures, etc. These patterns can be understood as stable structures formed by the system in the process of trying to reduce energy.</p>

<p>In the online interactive physics system simulation project, the phase separation model uses a simplified two-dimensional particle system to simulate the phase separation phenomenon. Although this model is simplified, it can intuitively demonstrate the basic mechanisms of phase separation, such as like attraction, unlike repulsion, and random motion between particles.</p>

<iframe src="https://shilingliang.com/web-simulator-by-GPT4/phase_separation.html#container" width="780" height="550"></iframe>

<h2 id="physics-visualization-platform"><a href="https://shilingliang.com/web-simulator-by-GPT4">Physics Visualization Platform</a></h2>

<p>In this ChatGPT-assisted project website, we strive to present an engaging and educational online physics visualization platform. Through this platform, users can personally interact with a variety of physical phenomena and complex systems, gaining a more intuitive and vivid understanding of the principles underlying these phenomena.</p>

<p>Our project website features multiple physics simulation examples generated by GPT-4, such as the Vicsek model, the XY model, and the phase separation model. These models are designed to help users comprehend the operational principles and emergent phenomena of complex systems. Additionally, the website offers a series of mouse-interactive models, enabling users to experience the allure of physical phenomena through real-time interaction.</p>

<h2 id="coding-with-gpt-4">Coding with GPT-4</h2>

<p>To conclude this article, let’s discuss how this project was brought to life through ChatGPT. In implementing the phase separation project, I didn’t specify any particular model. Instead, I provided the following requirements:</p>

<ul>
  <li>Implement a visual phase separation model using HTML.</li>
  <li>Add repulsion to the model to prevent particle aggregation.</li>
  <li>Handle boundary conditions.</li>
  <li>Introduce temperature as a parameter.</li>
  <li>Add sliders to control all parameters.</li>
</ul>

<p>Based on these requirements, ChatGPT generated the corresponding HTML and JavaScript code, creating an interactive physics simulation project (there were five or six conversations from the initial command to the generation of a functional model that could display phenomena, followed by more detailed discussions with ChatGPT to refine the page’s appearance). Throughout this process, GPT-4 exhibited an incredible ability to understand my project’s core objectives based on my requirements and generate the appropriate code to fulfill them. It is worth noting, however, that there is a limit to the length of code output by ChatGPT. If the output is interrupted, you can copy and paste the end of the output code and ask GPT to continue writing, ensuring a seamless code-writing process.</p>

<p>Although I’m not well-versed in JavaScript syntax details, I was able to understand how specific calculations were implemented in the physics portion by examining the code (as a pseudo-code reader), which allowed me to verify its accuracy. Overall, correctness checks still require some coding experience, but developers don’t need to know every syntax detail.</p>

<p>For the interface layer, the logic is visually apparent, so it can also be checked. If errors are detected, feedback can be given directly, and GPT-4 possesses a robust self-checking capability.</p>

<p>In collaboration with ChatGPT, we have successfully developed a fun and practical online interactive physics system simulation project. This project not only enables us to grasp complex physical phenomena intuitively but also showcases GPT-4’s enormous potential in code generation and project implementation. Furthermore, GPT-4’s powerful features have saved significant time and effort during the development process, making it possible for physicists and novices alike to swiftly create high-quality visualization and interactive projects.</p>

<p>In conclusion, while GPT-4 cannot currently replace all human work, it can significantly streamline the development process and empower beginners to accomplish tasks that were previously unattainable. In the future, we eagerly anticipate deeper collaboration with artificial intelligence technologies like GPT-4 to explore more innovative applications and solutions.</p>]]></content><author><name>Shiling  Liang 梁师翎</name><email>shiling@pks.mpg.de</email></author><category term="ChatGPT" /><category term="GPT-4" /><category term="Complex system" /><category term="Flocking" /><category term="Phase separation" /><category term="XY model" /><summary type="html"><![CDATA[This article was generated by GPT-4 under guidance.]]></summary></entry><entry><title type="html">Thermophroesis as an emergent phenomenon: the role of internal states</title><link href="https://shiling42.github.io/posts/2023/01/emergent-thermophoresis" rel="alternate" type="text/html" title="Thermophroesis as an emergent phenomenon: the role of internal states" /><published>2023-01-02T00:00:00-08:00</published><updated>2023-01-02T00:00:00-08:00</updated><id>https://shiling42.github.io/posts/2023/01/Thermophoresis</id><content type="html" xml:base="https://shiling42.github.io/posts/2023/01/emergent-thermophoresis"><![CDATA[<blockquote>
  <ul>
    <li>In our recent paper, we showed that thermophoresis can be an emergent phenomenon from chemical reaction systems. This blog is a <strong>lay summary</strong> of our work.</li>
  </ul>
</blockquote>

<h2 id="what-is-thermophoresis">What is thermophoresis?</h2>

<p><strong>After establishing a temperature gradient in a solution system, we may observe the accumulation of solute particles on the cold or warm side</strong>. This phenomenon is known as thermophoresis. Its exact microscopic origin is still under debate. In our work<sup id="fnref:1" role="doc-noteref"><a href="#fn:1" class="footnote" rel="footnote">1</a></sup>, we propose a simple and intuitive mechanism to explain this phenomenon, which relies on the correlation of the energy-diffusion properties of the different states of the particles. It is based on a simple idea: <strong>particles stay longer where diffusion is slower, and temperature can modulate the transport property of particles.</strong></p>

<table>
  <thead>
    <tr>
      <th style="text-align: center"><img src="/files/thermophoresis/热泳.png" alt="" /></th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <td style="text-align: center">The phenomenon of inhomogeneous concentration gradients driven by a temperature gradient.</td>
    </tr>
  </tbody>
</table>

<h2 id="from-einsteins-diffusion-relation-to-thermophoresis">From Einstein’s diffusion relation to thermophoresis</h2>

<p>For the understanding of thermophoresis we can go back to the basic Einstein relation of diffusion:</p>

\[D= \frac{T}{\gamma}\propto T R^{-1}\]

<p>The diffusion coefficient is proportional to the temperature divided by the damping constant, and the larger the particle the greater the damping (damping is proportional to particle size), which leads to an inverse relationship between diffusion coefficient and particle size as shown above.</p>

<p>Why do we mention the diffusion coefficient? Because the thermophoretic mechanism we propose here is rooted in nonhomogeneous diffusion and is simply based on a simple concept:</p>

<blockquote>
  <p><strong>Particles tend to stay in the slow diffusion region for a longer time</strong></p>
</blockquote>

<p>This is quite intuitive idea. The diffusion process is essentially the random walk of microscopic particles, and where the random walk is slow, the particles will wander around for a longer time.</p>

<p>Then the emergence of thermophoresis is natural: the diffusion coefficient depends on temperature. Therefore, let’s look at the first term of Einstein’s relation, $\boxed{T}R^{-1}$. Isn’t it exactly the temperature? To put it more bluntly, this term tells us that <em>particles diffuse faster in hot places and slower in cold places.</em></p>

<p>The temperature term in Einstein’s relation gives us a direct Soret coefficient:</p>

\[S_T^0=\frac{1}{T}\]

<p>However, there are two issues with this simple result.</p>

<ol>
  <li>
    <p>This coefficient is always positive, which means that it can only indicate the tendency of accumulation in the cold region, namely the thermophoretic phenomenon. In contrast, it is observed experimentally that solute particles can move to the hot region.</p>
  </li>
  <li>
    <p>This Soret coefficient is two orders of magnitude smaller than the experimentally measured values.</p>
  </li>
</ol>

<p>So we need to extract additional information from the Einstein relation. If we look at the Einstein relation again, $D\propto T R^{-1}$, there is a term related to the size of the particle, so can we derive thermophoresis from this term? The answer is yes, and this is the focus of our paper: chemical thermophoresis.</p>

<h2 id="chemical-thermophoresis">Chemical thermophoresis</h2>

<p>To understand the thermophoresis from thermoresponsive particle size,  we can start with a simple and intuitive example which is the foldable polymer</p>

<table>
  <thead>
    <tr>
      <th style="text-align: center"><img src="/files/thermophoresis/聚合物反应.png" alt="" /></th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <td style="text-align: center">Folded and unfolded states of a polymer.</td>
    </tr>
  </tbody>
</table>

<p>A polymer can be in both folded and unfolded states. These two states have different free energies, taking into account the interactions between the various parts of the long chain and the interaction with the solvent molecules. Also, it is straightforward that <strong>the unfolded state of the polymer has a larger size</strong>. The Einstein relation tells us that particles of larger size encounter greater damping and diffuse more slowly. So, if temperature regulates the switching between these two states, we immediately have an <strong>average size</strong> that depends on temperature and thus a temperature-dependent effective diffusion coefficient.</p>

<p>And this temperature regulation is obvious, especially if we consider that the switching between unfolding and folding is reached fast enough in comparison to diffusion, the probability of being in each state is determined by the local temperature (local equilibrium approximation).</p>

\[p_i=\frac{1}{Z}e^{-G_i/k_BT(x)}\]

<p>From the above Boltzmann distribution, which is the most fundamental law in thermodynamics, we can see that the probability of being in each state depends on the free energy of the state and the temperature of the local environment. Then, if we calculate the average, the effective diffusion coefficient is</p>

\[\langle D\rangle = p_u D_u +p_fD_f\]

<p>which directly depends on the occupations in the two states, and the occupations are determined by the local temperature. Therefore, we have an <strong>effective diffusion coefficient that depends on the temperature.</strong></p>

<p>To gain a better understanding, let’s consider the following limit: in the cold region, the particle is almost completely in the folded state, while in the hot region it is almost completely unfolded. The unfolded state in the hot region diffuses more slowly and thus leads to a <strong>negative Soret coefficient</strong>, which means that such a polymer can show <strong>thermophilic</strong> behavior.</p>

<table>
  <thead>
    <tr>
      <th style="text-align: center"><img src="/files/thermophoresis/聚合物热泳.png" alt="" /></th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <td style="text-align: center">Polymer can show thermophilic behavior.</td>
    </tr>
  </tbody>
</table>

<p>Of course, in the limit case shown above, the always positive term, $S_T^0=1/T$, is not included. Overall, the thermophoresis of the particle depends on $D\propto \boxed{T}\boxed{R^{-1}}$ these two individual contributions. In the case of the example polymer, these two terms are positive and negative, respectively, which leads to the fact that the particle can switch from <strong>thermophobic</strong> to <strong>thermophilic</strong> as the temperature changes, i.e. the sign of the Soret coefficient changes. This positive and negative thermophoresis of polymers has been widely observed in experiments<sup id="fnref:2" role="doc-noteref"><a href="#fn:2" class="footnote" rel="footnote">2</a></sup>.</p>

<table>
  <thead>
    <tr>
      <th style="text-align: center"><img src="/files/thermophoresis/热泳_符号变化.png" alt="" /></th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <td style="text-align: center">The thermotropic and thermophilic behaviors of polymer be changed depending on the temperature.</td>
    </tr>
  </tbody>
</table>

<p>Here $S_T^0=1/T$ is the contribution of the direct temperature-dependent term. While $S_T^\mathrm{chem}$ is what we call chemical thermophoresis, which originates from the thermoresponsive particle size.</p>

<p>For a more general case, we can consider that the particles have many internal states, which have different energies and diffusion coefficients. This energy-diffusion correlation leads to chemical thermophoresis. We can derive a very simple expression for the chemical Soret coefficient as</p>

\[S_T^\mathrm{chem}=\frac{\mathrm{Cov}_\mathrm{eq}(E,D)}{\langle D\rangle k_BT^2}\]

<p>Here, the Soret coefficient is directly related to the covariance between the energies and the diffusion coefficients. If the energy and diffusion coefficients of the different states are positively correlated, we get a positive Soret coefficient, i.e. thermophobic, and vice versa, a more interesting thermophilic behavior.</p>

<table>
  <thead>
    <tr>
      <th style="text-align: center"><img src="\../files/thermophoresis/正负热泳.png" alt="" /></th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <td style="text-align: center">Positive or negative chemical thermophoresis depends on the energy-diffusion correlation.</td>
    </tr>
  </tbody>
</table>

<h2 id="complex-chemical-reactions">Complex chemical reactions</h2>

<p>The chemical reactions covered in the previous section are the basic isomerization reactions, that is, no chemical complexes are formed. However, conceptually, it is straightforward to extend the chemical thermophoresis to more complex chemical reactions. For example, the following polymerization reaction</p>

<table>
  <thead>
    <tr>
      <th style="text-align: center"><img src="/files/thermophoresis/聚合反应.png" alt="" /></th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <td style="text-align: center">Dimerization reaction can also exhibit thermophoresis.</td>
    </tr>
  </tbody>
</table>

<p>Two monomers can form a dimer. Although the Soret coefficient derived from the previous isomerization cannot be directly applied, we can still use the energy-diffusion coefficient correlation to understand this thermophoretic phenomenon. Here, the energy and diffusion coefficients of the monomer and dimer are different, and as long as they are not the same, the system can respond to the temperature gradient and exhibit thermophoresis (inhomogeneous distribution) of the total concentration.</p>

<h2 id="discussion">Discussion</h2>

<p>Our theory gives a microscopic mechanism for the emergence of thermophoresis, which can be decomposed into several terms: the contribution of the temperature term of the Einstein relation itself, and the chemical thermophoresis as a consequence of energy-diffusion correlation. The actual thermophoretic phenomenon might be influenced by other mechanisms, such as those originating from the direct interaction of the particles with the solvent molecules<sup id="fnref:3" role="doc-noteref"><a href="#fn:3" class="footnote" rel="footnote">3</a></sup><sup id="fnref:4" role="doc-noteref"><a href="#fn:4" class="footnote" rel="footnote">4</a></sup>. Therefore, the emergent chemical thermophoresis we discuss here may be the dominant term, but it may also be a small higher-order quantity that can be neglected. From our understanding, <strong>it is highly likely to observe chemical thermophoresis as the dominant mechanism when the structure of the particle is very sensitive to temperature change.</strong> For example, in PNIPAM systems, the folding and unfolding of the polymer exhibit phase transition with temperature, and “giant thermophoresis” can be measured at this phase transition point<sup id="fnref:5" role="doc-noteref"><a href="#fn:5" class="footnote" rel="footnote">5</a></sup><sup id="fnref:6" role="doc-noteref"><a href="#fn:6" class="footnote" rel="footnote">6</a></sup><sup id="fnref:7" role="doc-noteref"><a href="#fn:7" class="footnote" rel="footnote">7</a></sup>. We expect that some experiments will be inspired to explore this direction.</p>

<p><a href="/files/thermophoresis/emergent_thermophoresis.pdf">Download the PDF</a></p>

<h2 id="references">References</h2>

<div class="footnotes" role="doc-endnotes">
  <ol>
    <li id="fn:1" role="doc-endnote">
      <p>Liang S, Busiello D M and De Los Rios P, 2022. Emergent thermophoretic behavior in chemical reaction systems. New Journal of Physics <a href="http://doi.org/10.1088/1367-2630/aca556"><strong>24</strong> 123006</a> <a href="#fnref:1" class="reversefootnote" role="doc-backlink">&#8617;</a></p>
    </li>
    <li id="fn:2" role="doc-endnote">
      <p>Wang Z, Kriegs H and Wiegand S 2012 Thermal diffusion of nucleotides J. Phys. Chem. B <a href="https://doi.org/10.1021/jp3032644">116 7463–9</a> <a href="#fnref:2" class="reversefootnote" role="doc-backlink">&#8617;</a></p>
    </li>
    <li id="fn:3" role="doc-endnote">
      <p>Burelbach Jerome, Frenkel D, Pagonabarraga I and Eiser E 2018 A unified description of colloidal thermophoresis Eur. Phys. J. E <a href="https://doi.org/10.1140/epje/i2018-11610-3"><strong>41</strong> 1–12</a> <a href="#fnref:3" class="reversefootnote" role="doc-backlink">&#8617;</a></p>
    </li>
    <li id="fn:4" role="doc-endnote">
      <p>Piazza R 2008 Thermophoresis: moving particles with thermal gradients Soft Matter <a href="https://doi.org/10.1039/B805888C"><strong>4</strong> 1740–4</a> <a href="#fnref:4" class="reversefootnote" role="doc-backlink">&#8617;</a></p>
    </li>
    <li id="fn:5" role="doc-endnote">
      <p>Kita R and Wiegand S 2005 Soret coefficient of poly (n-isopropylacrylamide)/water in the vicinity of coil- globule transition temperature Macromolecules <a href="https://doi.org/10.1021/ma050526+"><strong>38</strong> 4554–6</a> <a href="#fnref:5" class="reversefootnote" role="doc-backlink">&#8617;</a></p>
    </li>
    <li id="fn:6" role="doc-endnote">
      <p>Wongsuwarn S, Vigolo D, Cerbino R, Howe A M, Vailati A, Piazza R and Cicuta P 2012 Giant thermophoresis of poly(n-isopropylacrylamide) microgel particles Soft Matter <a href="https://doi.org/10.1039/C2SM25061F"><strong>8</strong> 5857–63</a> <a href="#fnref:6" class="reversefootnote" role="doc-backlink">&#8617;</a></p>
    </li>
    <li id="fn:7" role="doc-endnote">
      <p>Königer A, Plack N, Köhler W, Siebenbürger M and Ballauff M 2013 Thermophoresis of thermoresponsive polystyrene–poly (n-isopropylacrylamide) core–shell particles Soft Matter <a href="https://doi.org/10.1039/C2SM27417E"><strong>9</strong> 1418–21</a> <a href="#fnref:7" class="reversefootnote" role="doc-backlink">&#8617;</a></p>
    </li>
  </ol>
</div>]]></content><author><name>Shiling  Liang 梁师翎</name><email>shiling@pks.mpg.de</email></author><category term="thermophoresis" /><category term="chemical reaction systems" /><category term="Einstein relation" /><summary type="html"><![CDATA[In our recent paper, we showed that thermophoresis can be an emergent phenomenon from chemical reaction systems. This blog is a lay summary of our work.]]></summary></entry></feed>