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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="stylesheet" href="style.css">
<link rel="stylesheet" href="hero.css">
<link rel="stylesheet" href="labnews.css">
<link rel="stylesheet" href="about.css">
<link rel="stylesheet" href="bios.css">
<link rel="stylesheet" href="contact.css">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">
<link rel="stylesheet" href="navbar.css">
<meta name="description"
content="Laboratory website for the Thiede Lab at Cornell University. We develop new algorithms that combine machine learning, molecular simulation, and chemical physics, to unpack fundamental protein biochemistry and help develop new therapeutics.">
<meta robots="index, follow">
<title>The Thiede Lab</title>
</head>
<body>
<!-- Navbar -->
<!-- <section id="nav-bar">
<div class="nav-bar container">
</div>
</section> -->
<!-- <ul class="topnav">
<li><a href="#hero" data-after="Home">Home</a></li>
<li><a href="#labnews" data-after="labnews">labnews</a></li>
</ul> -->
<!--
<ul class="topnav">
<li><a href="#hero">Home</a></li>
<li><a href="#aboutsection">About</a></li>
<li><a href="#labnews">News</a></li>
<li><a href="#biosection">People</a></li>
<li class="right"><a href="#contact">Contact</a></li>
<a href="javascript:void(0);" class="icon" onclick="myFunction()">
<i class="fa fa-bars"></i>
</a>
</ul>
-->
<div class="topnav" id="myTopnav">
<a href="#" class="active">Home</a>
<a href="#aboutsection">About</a>
<a href="#labnews">News</a>
<a href="#biosection">People</a>
<a href="#contact">Contact</a>
<a href="javascript:void(0);" class="icon" onclick="myFunction()">
<i class="fa fa-bars"></i>
</a>
</div>
<script>
function myFunction() {
var x = document.getElementById("myTopnav");
if (x.className === "topnav") {
x.className += " responsive";
} else {
x.className = "topnav";
}
}
</script>
<!-- Hero Section-->
<section id="hero">
<div class="hero container">
<!-- <div class="hero title"> -->
<div>
<!-- <h1 style="margin-top: 6rem;">The</h1> -->
<h1>The Thiede Lab</h1>
<h1><span>@</span> Cornell</h1>
<!-- <h1>The</h1>
<h1>Thiede</h1>
<h1>Lab</h1> -->
<!-- <h2> Coming soon..</h2>
<a href="https://ehthiede.github.io/" type="button" class="cta">
Erik's Personal Webpage
</a> -->
</div>
</div>
</section>
<!-- End Hero Section -->
<!-- About Us Section -->
<section id="aboutsection">
<div class="aboutsection container">
<div class="aboutsection-main">
<div class="value-statement">
<h1 class="section-title">
<span>A</span>bout the <span>L</span>ab
</h1>
<p>
We are a computational chemistry group at Cornell University.
Our focus is computational analytical chemistry:
designing and understanding how algorithms give quantitative predictions in chemistry.
Currently, our research centers on three areas:
<!-- Proteins are fundamental to the molecular machinery of life: they are nature's freight trains, -->
<!-- construction cranes, and chemical factories. -->
<!-- But the basic principles of this machinery are poorly understood. -->
<!-- By developing new algorithms that combine -->
<!-- machine learning, molecular simulation, and chemical physics, -->
<!-- we seek to unpack fundamental protein biochemistry -->
<!-- and help develop new therapeutics. -->
</p>
<!-- <h3 class="section-subtitle"> Research Focus -->
<!-- </h3> -->
<ul>
<li class="value-list-item">
<span class="value-highlight">Recovering Protein Heterogeneity from Cryo-EM.</span>
Proteins are fundamental to the molecular machinery of life.
Many proteins are highly conformationally heterogeneous, switching between structures to achieve their goals.
We attempt to build algorithms that can recover these changes in structure from cryogenic electron microscopy experiments.
</li>
<li class="value-list-item">
<span class="value-highlight">Heterogeneity in In-Situ EM</span>
Recently, in-situ electron microscope techniques have enabled materials to be imaged while they are undergoing meaningful chemical reaction.
Moreover, combining in-situ experiments with advanced electron microscopy techniques such as 4D-STEM or EELS provide rich data about how material composition changes over time.
However, the resulting data is often very noisy. We develop new algorithms for analyzing in-situ EM experiments that can function with noisy data, giving reliable insights in the face of statistical uncertainty.
</li>
<li class="value-list-item">
<span class="value-highlight">Manipulating Protein Language Models</span>
Protein language models apply the same technology that powers natural language models such as ChatGPT, Claude, and DeepSeek to the sequence of amino acids that make up a protein. We are exploring the capabilities of these models for zero-shot and few-shot prediction of protein properties. In addition, we are attempting to close the loop between protein language model and experimental peptide design, allowing for rapid and efficient iterations on peptide drug candidates.
</li>
</ul>
</div>
<div class="value-statement">
<h2 class="section-subtitle">
<!-- <span>L</span>ab <span>V</span>alues -->
Lab Values
</h2>
<ul>
<!-- <li><a class="active" href="#hero">Home</a></li> -->
<li class="value-list-item">
<span class="value-highlight">We are curious.</span>
Science is about learning, not knowing. We are always looking for new ways of thinking,
and are comfortable showing that we don't understand everything.
</li>
<li class="value-list-item">
<span class="value-highlight">We are open.</span>
Science is a team sport. To help out
teammates, we take pains to share
our science freely amongst the scientific community and with the world.
</li>
<li>
<span class="value-highlight">We are caring.</span> Doing good science requires delving deep
into the unknown: an
experience both exciting, and terrifying. On our journey, we celebrate each other's
achievements and support each other through setbacks.
</li>
<li>
<span class="value-highlight">We are inclusive.</span> We actively strive to make science a
place where everyone
thrives, no matter their background and identity. We resist oppression of any kind,
including but not limited to sexism, classism, racism, homophobia, transphobia, ableism and
xenophobia. Everyone is welcome and celebrated here.
</li>
</ul>
</div>
</div>
</div>
</section>
<!-- End About Us Section -->
<!-- labnews Section -->
<section id="labnews">
<div class="labnews container">
<div class="labnews-main">
<h1 class="section-title">
<span>L</span>ab <span>N</span>ews
</h1>
<div class="labnews-item">
<!-- <div class="icon">
<img src="https://img.icons8.com/ios-glyphs/60/null/protein.png" />
</div> -->
<h2 class="labnews-item-header">
Mar 19, 2025
</h2>
<p>
After a long hiatus, we have finally updated our website! Welcome to the many new faces and
exciting collaborations.
</p>
</div>
<div class="labnews-item">
<!-- <div class="icon">
<img src="https://img.icons8.com/ios-glyphs/60/null/protein.png" />
</div> -->
<h2 class="labnews-item-header">
Feb 18, 2024
</h2>
<p>
We have an job opportunity for a postdoctoral researcher.
<!-- A detailed job description can be found <a href="docs/postdoctoral_job_posting.pdf">here.</a> -->
<br />
<b>Update: This position has been filled, and Kwanghwi Je will be joining us in the summer.</b>
</p>
</div>
<div class="labnews-item">
<!-- <div class="icon">
<img src="https://img.icons8.com/ios-glyphs/60/null/protein.png" />
</div> -->
<h2 class="labnews-item-header">
Feb. 03, 2023
</h2>
<p>
Joshua and Diego have joined the lab as our first graduate students!
</p>
</div>
</div>
</div>
</section>
<!-- End labnews Section -->
<!-- Bios Section -->
<section id="biosection">
<div class="biosection container">
<h1 class="section-title">
<span>P</span>eople
</h1>
<div class="bios">
<div class="singlebio">
<div class="headshotdiv">
<img src="img/erik_thiede.jpg" alt="Erik Thiede" class="headshots">
</div>
<h3>Erik Henning Thiede</h3>
<!-- <h4>Principal Investigator</h4> -->
<p> Erik is a Professor of Chemistry at Cornell University.
He received his PhD from the University of Chicago working with Profs. Aaron Dinner and
Jonathan Weare. He then did a postdoc at the Flatiron Institute CCM,
working with Prof. Risi Kondor, Dr. Pilar Cossio, and Dr. Sonya Hanson.
</p>
<p style="margin-top: 6px; text-align: center;">
<a href="https://ehthiede.github.io">Personal Webpage</a>.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/jake_moomaw.jpg" alt="Jake Moomaw" class="headshots">
</div>
<h3>Jake Moomaw</h3>
<p>
Jake is a moonshot enthusiast who has worn many hats: algorithms researcher, amateur chemist,
software engineer, roboticist, vulnerability researcher and electronics hobbyist.
He is currently in the lab as a joint undergraduate researcher and part-time software developer.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/jeffrey_Xiang.jpeg" alt="Jeffrey Xiang" class="headshots">
</div>
<h3>Jeffrey Xiang</h3>
<p>
Jeffrey is a research associate working on combining cryo-EM with molecular dynamics.
</p>
<p style="margin-top: 6px; text-align: center;">
<a href="https://www.linkedin.com/in/jeffrey-xiang/">linkedin</a>.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/josh_rhodes.jpeg" alt="joshua rhodes" class="headshots">
</div>
<h3>Joshua Rhodes</h3>
<p>
Joshua is a graduate student in the Cornell Chemistry Department. His work
focuses on the intersection of statistics with electron microscopy, with a focus on
developing new hypothesis testing approaches.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/diego_w_eagle.jpg" alt="Diego Sanchez Espinoza" class="headshots">
</div>
<h3>Diego Sanchez Espinoza</h3>
<p>
Diego is a graduate student in the Cornell Center for Applied Math, jointly advised by Prof.
Yunan Yang. His work focuses on applying Wasserstein flows to the analysis of cryo-EM data.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/happy-robot-head.png" alt="Kawamura" class="headshots">
</div>
<h3>Kawamura</h3>
<p>
Kawamura is a graduate student in the Cornell Biophysics program.
She works on expanding the limits of cryo-EM to work on protein disordered regions.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/wenzhe_chen.JPG" alt="Wenzhe Chen" class="headshots">
</div>
<h3>Wenzhe Chen</h3>
<p>
Wenzhe Chen is a graduate student joint with Hening Lin at the University of Chicago.
He works on finetuning and repurposing structure prediction tools to better match experimental
data.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/Kwanghwi_Je.jpeg" alt="Kwanghwi Je" class="headshots">
</div>
<h3>Kwanghwi Je</h3>
<p>
Kwanghwi Je is a postdoctoral researcher. He earned
his doctorate from the University of Michigan.
His expertise lies in using molecular simulation techniques to investigate biomolecular dynamics
and phase behavior of colloidal nanoparticles. Beyond the lab, he enjoys running and exploring
new places.
</p>
</div>
<!-- <div class="singlebio"> -->
<!-- <div class="headshotdiv"> -->
<!-- <img src="img/hailey_foster.jpg" alt="Hailey Foster" class="headshots"> -->
<!-- </div> -->
<!-- <h3>Hailey Foster</h3> -->
<!-- <p> -->
<!-- Hailey is a sophomore at Cornell University interested in chemistry. -->
<!-- She currently works with molecular dynamics techniques and is interested in investigating both -->
<!-- the computational and experimental aspects of chemistry. -->
<!-- </p> -->
<!-- </div> -->
<div class="singlebio">
<div class="headshotdiv">
<img src="img/happy-robot-head.png" alt="Yafet Nagesh" class="headshots">
</div>
<h3>Yafet Nagesh</h3>
<p>
Yafet is a sophomore at Cornell University.
He is working on developing algorithms to analyze cryo-EM images of nanoparticles.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/Emily_Almgren.JPG" alt="Emily Almgren" class="headshots">
</div>
<h3>Emily Almgren</h3>
<p>
Emily is a graduate student in Cornell's Center for Applied Math.
She is working jointly with Prof. Anil Damle on developing faster algorithms for
analyzing large EM datasets.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/josh_almonte.JPG" alt="Joshua Almonte" class="headshots">
</div>
<h3>Joshua Almonte</h3>
<p>
Joshua is a graduate student in Cornell's Chemical Engineering program.
Working together with Profs. Chris Alabi and Alexander Terenin, he is
exploring more efficient algorithms for designing peptides.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/happy-robot-head.png" alt="Triet Minh Vu" class="headshots">
</div>
<h3> Triet Minh Vu</h3>
<p>
Triet is a graduate student in the Cornell Chemistry Department working
jointly with our group and Yao Yang's group. Triet is developing new
representation learning algorithms for analyzing operando EM movies.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/happy-robot-head.png" alt="Zora Zhang" class="headshots">
</div>
<h3> Zora Zhang</h3>
<p>
Zora is a graduate student in the Cornell Chemistry Department working
jointly with our group and Yao Yang's group. Her research combines operando
electron microscopy with computational analysis and machine learning.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/Andrew_Ahn.JPG" alt="Andrew Ahn" class="headshots">
</div>
<h3>Andrew Ahn</h3>
<p>
Andrew is a sophomore at Cornell University. He is studying prompt engineering for protein language models.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/happy-robot-head.png" alt="Guanzhong (Alain) Wang" class="headshots">
</div>
<h3>Guanzhong (Alain) Wang</h3>
<p>
Alain is a Junior at Cornell.
He is investigating how different probabilistic metrics affect
the ensemble of structures we recover from cryo-EM experiments.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/ellis_kennedy.jpeg" alt="Ellis Rae Kennedy" class="headshots">
</div>
<h3>Ellis Rae Kennedy</h3>
<p>
Ellis Rae Kennedy is a Schmidt AI Fellow working on new algorithms for advanced 4D-STEM data.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/happy-robot-head.png" alt="Andrii Nykyforchyn" class="headshots">
</div>
<h3>Andrii Nykyforchyn</h3>
<p>
Andrii is an undergraduate researcher working on hypothesis testing strategies for analyzing cryo-EM data.
</p>
</div>
<div class="singlebio">
<div class="headshotdiv">
<img src="img/happy-robot-head.png" alt="Tianxing (Eddie) Xu" class="headshots">
</div>
<h3>Tianxing (Eddie) Xu</h3>
<p>
Tianxing is a masters student working on applying and developing new methods for analyzing heterogeneous cryo-EM data.
</p>
</div>
</div>
<h2>Alumni</h2>
<!-- <p> -->
<!-- <b>Jeffrey Xiang</b> Accepted to the -->
<!-- </p> -->
<p>
<b>Hailey Foster</b> Undergraduate Researcher in the Craine Lab.
</p>
<!-- <h1 class="section-title"> -->
<!-- <span>A</span>lumni -->
<!-- </h1> -->
</div>
</section>
<!-- End Bios Section -->
<!-- Contact Section -->
<section id="contact">
<div class="contact container">
<div class="contact-main">
<h1 class="section-title">
<span>C</span>ontact
</h1>
<div class="contact-info">
<p>
Correspondence can be addressed to
<a href="mailto:eht45@cornell.edu">eht45[at]cornell.edu</a>.
</p>
</div>
</div>
</div>
</section>
<!-- End Contact Section -->
</body>