The document discusses using field programmable gate arrays (FPGAs) to efficiently simulate protein folding through Monte Carlo simulations. FPGAs offer high programmability and efficiency compared to CPUs and GPUs for this compute-intensive biological application. FPGAs are identified as the best candidate platform due to their flexibility, performance, and lower power consumption and cost compared to application-specific integrated circuits.

2. Application
Protein folding
• Identify tertiary structure of protein.
• Based on Monte Carlo simulation.
COMPUTE INTENSIVE
• Pure software implementation is
inefficient.
• Need to find another solution.
2
PH: mpg.de

3. CPU
3
Platforms Overview
Platform
Performance
Power
Consumption
Cost
Flexibility
Design
ASIC GPU FPGA

4. 4
Platforms Overview

5. 5
FPGA
Best candidate in such context:
•High programmability
•Good efficiency

6. FPGAs are the smartest move!
Biopharmaceutical players have to focus on:
• cost;
• quality;
• scale.
FPGA & Biopharmaceutical
Speed, process innovation, and adaptation capabilities are
essential.

7. 7
Thanks for your attention
Lorenzo Di Tucci
Giulia Guidi
lorenzo.ditucci@mail.polimi.it
giulia.guidi@mail.polimi.it
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