diff --git a/src/utils/agent_controller.py b/src/utils/agent_controller.py
index c644c3e..f229aa4 100644
--- a/src/utils/agent_controller.py
+++ b/src/utils/agent_controller.py
@@ -12,6 +12,7 @@ from dotenv import load_dotenv
 from src.analysis.llm_analyzer import LLMAnalyzer
 from src.storage.paper_store import PaperStore
 from src.storage.vector_store import VectorStore
+from src.data_acquisition.pdf_downloader import PDFDownloader
 
 logger = logging.getLogger(__name__)
 
@@ -24,6 +25,7 @@ class AgentController:
         self.llm_analyzer = None
         self.paper_store = None
         self.vector_store = None
+        self.pdf_downloader = None
         self.papers_dir = Path("papers")
         
     async def __aenter__(self):
@@ -57,6 +59,7 @@ class AgentController:
             self.llm_analyzer = LLMAnalyzer(api_key=deepseek_key, provider='deepseek')
             self.paper_store = PaperStore()
             self.vector_store = VectorStore()
+            self.pdf_downloader = PDFDownloader()
             
             # Initialize database
             await self.paper_store.initialize()
@@ -86,6 +89,15 @@ class AgentController:
             if paper_data.get('abstract'):
                 paper_text += f"Abstract: {paper_data['abstract']}\n\n"
                 
+            # Download PDF if URL is available
+            if paper_data.get('pdf_url'):
+                try:
+                    pdf_path = await self.pdf_downloader.download_pdf(paper_data['pdf_url'], paper_data['entry_id'].split('/')[-1])
+                    if pdf_path:
+                        logger.info(f"Successfully downloaded PDF to {pdf_path}")
+                except Exception as e:
+                    logger.error(f"Error downloading PDF: {e}")
+                
             # Analyze paper using LLM
             analysis = await self.llm_analyzer.analyze_paper(paper_text)
             
@@ -107,14 +119,6 @@ class AgentController:
                     await self._repair_orphaned_paper(paper_id, paper_data)
                     return {}
                 
-                # Clean paper_id to use as filename
-                safe_id = paper_id.replace('.', '_')
-                
-                # Save paper content to file
-                paper_path = self.papers_dir / f"{safe_id}.json"
-                with open(paper_path, 'w', encoding='utf-8') as f:
-                    json.dump(paper_data, f, indent=2, ensure_ascii=False)
-                
                 # Store metadata in PostgreSQL
                 metadata = {
                     'id': paper_id,
@@ -140,9 +144,9 @@ class AgentController:
                     {'paper_id': paper_id, 'type': 'technical_concepts'}
                 ]
                 chunk_ids = [
-                    f"{safe_id}_text",
-                    f"{safe_id}_summary",
-                    f"{safe_id}_concepts"
+                    f"{paper_id}_text",
+                    f"{paper_id}_summary",
+                    f"{paper_id}_concepts"
                 ]
                 self.vector_store.add_chunks(chunks, chunk_metadata, chunk_ids)
                 
@@ -180,13 +184,6 @@ class AgentController:
             for paper_id in paper_ids:
                 paper = await self.paper_store.get_paper(paper_id)
                 if paper:
-                    # Load full paper data if needed
-                    safe_id = paper_id.replace('.', '_')
-                    paper_path = self.papers_dir / f"{safe_id}.json"
-                    if paper_path.exists():
-                        with open(paper_path, 'r', encoding='utf-8') as f:
-                            full_paper = json.load(f)
-                            paper['full_data'] = full_paper
                     papers.append(paper)
                     
             return papers
@@ -207,6 +204,8 @@ class AgentController:
                 await self.paper_store.close()
             if self.vector_store:
                 await self.vector_store.close()
+            if self.pdf_downloader:
+                await self.pdf_downloader.close()
                 
             self.initialized = False
             logger.info("Agent controller closed successfully")