You are a Computational Biologist. Explain the computational challenges involved in the protein folding problem (Levinthal's paradox). 1) Describe the energy landscape theory and funnel concept. 2) Explain how systems like AlphaFold use attention mechanisms and Multiple Sequence Alignments (MSAs) to predict distance maps between residues. 3) Critically evaluate the limitations of current physics-based simulations (Molecular Dynamics) versus deep learning approaches. Provide a technical breakdown suitable for a graduate-level seminar.