Update and rename 2024_08_aquapointer to 2024_09_aquapointer

src/content/blog/2024_09_aquapointer

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+---
+title: "Aquapointer, a software package for quantum biology applications" 
+author: Misty Wahl
+day: 8
+month: 9
+year: 2024
+tags: 
+  - Q4Bio
+  - Open source software
+---
+
+[Aquapointer](https://github.com/unitaryfund/aquapointer) is an open source software package developed by the Unitary Fund team with consortium partners [Pasqal](https://www.pasqal.com/) and [Qubit Pharmaceuticals](https://www.qubit-pharmaceuticals.com/) and funding from [Wellcome Leap](https://wellcomeleap.org/).
+The library is designed to be a computational tool used in pharmaceutical development, specifically for studying the placement of water molecules in protein cavities.
+
+Proteins are complex molecules with cavities that can be occupied by water molecules, particularlly in living tissue.
+The presence of water molecules influences the binding of small molecules called ligands to specific protein sites, a problem of interest in drug discovery.
+Protein solvation effects can be studied either by modeling the interactions experimentally, which is generally a costly and relatively inefficient process, or by using numerical models.
+Classical numerical methods, such as Monte Carlo or molecular dynamics, can give some insight but the computational complexity of these methods are too large for certain hard cases. 
+An alternative approach is to find first the density distribution of water molecules, through methods such as the [3D Reference Interactive Site Model (3D-RISM)](). 
+By looking at 2D slices of the 3D-RISM density function, we can define a discrete optimization problem (per slice) whose solutions correspond to positions of water molecules.
+
+Aquapointer generates 2D slices of an input 3D-RISM density function, maps the slices to a QUBO problem, translates the QUBO to an analog pulse sequence or a digital circuit, and then calls the backend API and processes the results.
+The analog workflow in Aquapointer uses [Pulser](https://github.com/pasqal-io/Pulser) for intermediate representations (IR) of the pulse sequences and for interfacing to supported backends, e.g. QuTip
+The digital workflow uses Qiskit for IR and simulated backends.
+
+![image demonstating the analog workflow in Aquapointer](/images/aquapointer_analogflow.png)
+
+Since we first introduced Aquapointer, we have upgraded it to include 3D-RISM density processing, in the form of the `slicing` and `densitycanvas` modules.
+The `slicing` module takes a 3D-RISM density file and transforms it into 2D slices along user-specified planes. 
+The `densitycanvas` module contains classes and functions for transforming the 2D slices or generating them from a probability distribution and mapping the density distributions into a QUBO formulation.
+
+![image demonstating the slicing workflow in Aquapointer](/images/aquapointer_slicing.png)
+
+We are in process of upgrading our [docs](https://aquapointer.readthedocs.io/en/latest/), so stay tuned for an annoucement on our [Discord](https://discord.com/invite/JqVGmpkP96), [X](https://twitter.com/unitaryfund), and [LinkedIn](https://www.linkedin.com/company/unitary-fund/).