Redesign homepage with hero splash layout and research callouts

_config.yml

@@ -14,9 +14,9 @@
 # You can create any custom variable you would like, and they will be accessible
 # in the templates via {{ site.myvariable }}.
 
-title: The Diffuse Project
+title: The DiffUSE Project
 email: diffuse@astera.org
-description: The Diffuse Project
+description: The DiffUSE Project
 twitter_username: username
 github_username: diff-use
 minimal_mistakes_skin: default

_data/navigation.yml

@@ -1,13 +1,12 @@
 main:
+  - title: "About"
+    url: /about/
   - title: "Research"
     url: /research/
   - title: "Members"
     url: /members/
   - title: "Posts"
     url: /posts/
-  - title: "Tags"
-    url: /tags/
   - title: "Logbook"
     url: "http://diffuse.science/logbook"
-  - title: "About"
-    url: /about/
+

_includes/head/custom.html

@@ -9,3 +9,4 @@
   src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js">
 </script>
 
+<link rel="icon" type="image/png" href="/assets/images/favicon.png">

_pages/about.md

@@ -1,12 +1,46 @@
 ---
 permalink: /about/
-title: "About The Diffuse Project"
+title: "About The DiffUSE Project"
+toc: true
+toc_label: "On This Page"
+toc_icon: "list"
+toc_sticky: true
 ---
-**An ambitious push to make protein motion routine**<br>
-Structural biology is ready for its next leap. The Diffuse Project sets out to turn the faint “diffuse” background in X-ray diffraction images into everyday maps of how proteins breathe and bend—information that static crystal structures and even AlphaFold predictions leave behind.
 
-**Why now?**<br>
+
+
+### An ambitious push to make protein motion routine
+
+Structural biology is ready for its next leap. The DiffUSE Project sets out to turn the faint “diffuse” background in X-ray diffraction images into everyday maps of how proteins breathe and bend—information that static crystal structures and even AlphaFold predictions leave behind.
+
+We believe that changing the way protein motion is understood will require not just new methods but also new ways we work together as scientists. Namely, we are experimenting with how we coordinate efforts across the team and also how we share our scientific process and results. Read more about the philosophy behind the project [here](https://seemay.substack.com/p/from-systems-operators-to-systems).
+
+### Why now?
 Static structures have plateaued. AlphaFold and traditional crystallography capture only a single snapshot; the diffuse signal around Bragg peaks holds the hidden information needed to model motion. With room-temperature collection methods improving and GPUs putting heavy computation within reach, the field finally has the tools to make that signal mainstream.
 
+![diffuse scattering pattern](/assets/images/main.jpg){:style="max-height:300px; display: block; margin-left: auto; margin-right: auto;"}
+
+#### A distributed team
+
+We are developing infrastructure alongside science. We are a distributed team experimenting with tightly interconnected workflows.
+
+We’re testing a new ways to fund several parts of the pipeline at once, enabling team members to closely design and coordinate different dimensions. We believe in a more holistic approach to rethinking what changes are possible and scalable.
+
+
+#### Novel publishing practices
+
+We strive for scientific rigor while ensuring our tools are broadly useful, as widespread adoption across the structural biology community will amplify our impact in both basic and translational science. To achieve this, we commit to opening our processes and [sharing our methods as early as possible](https://diffuse.science/posts/).
+
+##### How we are sharing our science
+
+- [The DiffUSE Project Logbook](http://diffuse.science/logbook): Catalog X-ray datasets, collect notes from synchrotron data collection, share reports from data processing, and post preliminary analysis without filters.
+
+- [The DiffUSE Data Management App](https://app.diffuse.science): Under active development, this site will function to document experiment processing with markdown, images, tables, and rich     metadata fields for comprehensive research tracking across datasets and beamlines.
+
+- [Posts from our Scientists](https://diffuse.science/posts/):  Read direct dispatches from our distributed DiffUSE team.
+
+
+Specifically, we are experimenting with novel [publishing practices](https://zenodo.org/records/15548989) outside of traditional journals, in accordance with Astera’s publication policy. 
+
 
-*Resources generously provided by Astera Institute and Voltage Park.* 
+Check back with us [here](https://diffuse.science/posts/) for updates on all of our various experiments!

_pages/research.md

@@ -1,12 +1,41 @@
 ---
 permalink: /research/
 title: "Research"
+toc: true
+toc_label: "On This Page"
+toc_icon: "list"
+toc_sticky: true
 ---
+---
+
+## Unlocking Protein Dynamics
+Structural biology has long been a key enabler for drug discovery and for understanding protein function. As a field, structural biology has come a long way towards our understanding of static protein structures. But, proteins are dynamic and their functions are critically linked to fluctuations in state and motion. Our ability to measure these protein motions experimentally has been limited. 
+
+![diffuse scattering signals](/assets/images/diffuse_signals.png){:style="max-height:300px; display: block; margin-left: auto; margin-right: auto;"}
+
+To unlock the next frontier of advancements, we need new method advancements, more experimental data, and better ways to model and encode the dynamics of proteins.
+
+The DiffUSE Project is dedicated to advancing our understanding of protein motion through the use of diffuse scattering: a largely overlooked signal measured by X-ray crystallography that could unlock our ability to measure protein dynamics. Concurrently, the DiffUSE Project aims to build the infrastructure for learning and representing the rich information from this data.
+
+The DiffUSE Project was co-developed with funders and scientists. The team includes both dedicated staff and institutional researchers to enable fast-paced infrastructure-building and specialized basic research. 
+
+## How we are sharing our science
+
+- [The DiffUSE Project Logbook](http://diffuse.science/logbook): Catalog X-ray datasets, collect notes from synchrotron data collection, share reports from data processing, and post preliminary analysis without filters.
+
+- [The DiffUSE Data Management App](https://app.diffuse.science): Under active development, this site will function to document experiment processing with markdown, images, tables, and rich     metadata fields for comprehensive research tracking across datasets and beamlines.
+
+- [Posts from our Scientists](https://diffuse.science/posts/):  Read direct dispatches from our distributed DiffUSE team.
+
+
+![MD simulated diffuse scattering](/assets/images/20250805_Mac1_diffuse_crop.png){:style="max-height:300px; display: block; margin-left: auto; margin-right: auto;"}
+
+## The DiffUSE Project is working to
 
 {% assign interests = site.research | sort: "index" %}
 
 {% for interest in interests %}
-## {{ interest.name }}
+### {{ interest.name }}
 
 {% assign parity = interest.index | modulo:2 %}
 {% if parity == 0 %}

index.md

@@ -1,45 +1,44 @@
 ---
-layout: home
+layout: splash
 author: diffuse
-author_profile: true
----
-
-![diffUSE Project logo](/assets/images/diffuse_logo_banner.jpg){:style="max-height:300px; display: block; margin-left: auto; margin-right: auto;"}
-
-## Unlocking Protein Dynamics
-Structural biology has long been a key enabler for drug discovery and for understanding protein function. As a field, structural biology has come a long way towards our understanding of static protein structures. But, proteins are dynamic and their functions are critically linked to fluctuations in state and motion. Our ability to measure these protein motions experimentally has been limited. 
-
-To unlock the next frontier of advancements, we need new method advancements, more experimental data, and better ways to model and encode the dynamics of proteins.
-
-![diffuse scattering signals](/assets/images/diffuse_signals.png){:style="max-height:300px; display: block; margin-left: auto; margin-right: auto;"}
-
-The Diffuse Project is dedicated to advancing our understanding of protein motion through the use of diffuse scattering: a largely overlooked signal measured by X-ray crystallography that could unlock our ability to measure protein dynamics. Concurrently, the Diffuse Project aims to build the infrastructure for learning and representing the rich information from this data.
-
-The Diffuse Project was co-developed with funders and scientists. The team includes both dedicated staff and institutional researchers to enable fast-paced infrastructure-building and specialized basic research. 
-
-![MD simulated diffuse scattering](/assets/images/20250805_Mac1_diffuse_crop.png){:style="max-height:300px; display: block; margin-left: auto; margin-right: auto;"}
-
-## Reimagining how we approach science
-We believe that changing the way protein motion is understood will require not just new methods but also new ways we work together as scientists. Namely, we are experimenting with how we coordinate efforts across the team and also how we share our scientific process and results. Read more about the philosophy behind the project [here](https://seemay.substack.com/p/from-systems-operators-to-systems).
+author_profile: false
+header:
+  overlay_image: assets/images/20250805_Mac1_diffuse_crop.png
+  overlay_filter: 0.4
+excerpt: "Advancing our understanding of protein motion"
+
+feature_row_science:
+  - image_path: assets/images/morph2.gif
+    alt: "diffuse scattering signals"
+    title: "Unlocking Protein Dynamics"
+    excerpt: >
+      Proteins are dynamic and their functions are critically linked to fluctuations in state and motion. The DiffUSE Project is dedicated to advancing our understanding of protein motion through diffuse scattering, a largely overlooked signal in X-ray crystallography that could unlock our ability to measure protein dynamics.
+    url: /research/
+    btn_label: "Our Research"
+    btn_class: "btn--primary"
+
+feature_row_philosophy:
+  - image_path: assets/images/diffuse_group_2026_01.jpg
+    alt: "DiffUSE kick-off meeting"
+    title: "Reimagining How We Approach Science"
+    excerpt: >
+      We believe that changing the way protein motion is understood will require not just new methods but also new ways we work together as scientists. We are experimenting with how we coordinate efforts and share our scientific process and results.
+    url: /about/
+    btn_label: "About the Project"
+    btn_class: "btn--primary"
 
-![diffuse scattering pattern](/assets/images/main.jpg){:style="max-height:300px; display: block; margin-left: auto; margin-right: auto;"}
-
-#### Coordination
-
-We’re working on a greenfield problem in a multi-dimensional methods system. Each part of our workflow depends on the others, so co-iterating across the full cycle significantly expands what you can try. 
-
-Therefore, we’re testing a new way to fund several parts of the pipeline at once, enabling team members to closely design and coordinate different dimensions. We believe in a more holistic approach to rethinking what changes are possible and scalable.
-
-
-
-#### Publishing
-
-We strive for scientific rigor while ensuring our tools are broadly useful, as widespread adoption across the structural biology community will amplify our impact in both basic and translational science. To achieve this, we commit to opening our processes and [sharing our methods as early as possible](https://diffuse.science/posts/).
+---
+{% include feature_row id="feature_row_science" type="left" %}
 
+{% include feature_row id="feature_row_philosophy" type="right" %}
 
-Specifically, we are experimenting with novel [publishing practices](https://zenodo.org/records/15548989) outside of traditional journals, in accordance with Astera’s publication policy. 
+<h2 style="text-align: center;"><a href="/posts/" style="text-decoration: none; color: inherit;">Latest Posts from our Scientists</a></h2>
 
+<div class="grid__wrapper">
+  {% for post in site.posts limit:3 %}
+    {% include archive-single.html type="list" %}
+  {% endfor %}
+</div>
 
-Check back with us [here](https://diffuse.science/posts/) for updates on all of our various experiments!
+![diffUSE Project logo](/assets/images/diffuse_logo_banner.jpg){:style="max-height:300px; display: block; margin-left: auto; margin-right: auto;"}
 
-![diffUSE kick-off meeting group photo](/assets/images/diffuse_meeting_202507.jpg)