This tutorial demonstrates how PhD students and academic researchers can leverage multiple MCP servers to create a comprehensive research workflow. By integrating arXiv, Perplexity Web Search, Memory Bank, Notion, and Sequential Thinking servers, researchers can streamline literature reviews, track emerging trends, organize findings, and tackle complex theoretical problems systematically. Key Benefits: - Automated literature discovery and summarization from arXiv - Real-world application tracking through web search - Persistent knowledge storage across research sessions - Structured note organization in Notion - Systematic problem-solving for complex theoretical challenges
You are an advanced AI research assistant specializing in academic research workflows, with expertise in quantum computing and theoretical physics. You have integrated access to multiple knowledge sources and organizational tools through MCP servers. Your capabilities include: - Literature Discovery & Analysis - Real-World Application Tracking - Knowledge Management - Research Organization - Complex Problem Solving When assisting with research, always: - Prioritize peer-reviewed and credible sources - Maintain academic integrity and proper citations - Create clear connections between theoretical and practical aspects - Build upon previous findings stored in memory - Structure information for long-term research use
1. arXiv MCP Server 2. Perplexity Web Search Server 3. Memory Bank Server 4. Notion MCP Server 5. Sequential Thinking Server
API Keys and Accounts
MCP Server Installation
# Install all required MCP servers
npm install -g @arxiv/mcp-server
npm install -g @perplexity/mcp-server
npm install -g @memory-bank/mcp-server
npm install -g @notion/mcp-server
npm install -g @sequential-thinking/mcp-server
Add the following to your Claude MCP configuration:
{
"servers": {
"arxiv": {
"command": "npx",
"args": ["@arxiv/mcp-server"],
"env": {}
},
"perplexity": {
"command": "npx",
"args": ["@perplexity/mcp-server"],
"env": {
"PERPLEXITY_API_KEY": "your_perplexity_api_key"
}
},
"memory-bank": {
"command": "npx",
"args": ["@memory-bank/mcp-server"],
"env": {
"MEMORY_BANK_PATH": "/path/to/your/research/memory"
}
},
"notion": {
"command": "npx",
"args": ["@notion/mcp-server"],
"env": {
"NOTION_API_KEY": "your_notion_api_key",
"NOTION_DATABASE_ID": "your_research_database_id"
}
},
"sequential-thinking": {
"command": "npx",
"args": ["@sequential-thinking/mcp-server"],
"env": {}
}
}
}
"Please verify that all MCP servers are connected: arXiv, Perplexity, Memory Bank, Notion, and Sequential Thinking."
"Search arXiv for papers on 'topological quantum error correction' published in the last 6 months.
Summarize the top 5 most relevant papers."
"Find papers on arXiv that:
- Focus on surface codes in quantum computing
- Published by authors from MIT, IBM, or Google
- Have more than 10 citations
- Published between 2023-2024"
"Search for papers by [Author Name] on quantum error correction, then find any industry
applications mentioned in tech news using Perplexity."
"Create a Notion database for my quantum error correction literature review with columns:
- Paper Title
- Authors
- Key Contributions
- Methodology
- Limitations
- Relevance to My Research
- Citation Count"
"For each paper found on topological quantum computing:
1. Extract key information
2. Add entry to Notion database
3. Store important insights in Memory Bank
4. Tag connections between papers"
"Store these key insights in Memory Bank:
- Main breakthrough from [Paper Title]
- Connection to my previous research on [Topic]
- Potential applications identified
- Open questions for future investigation"
"Using my stored memories, create a concept map in Notion showing:
- Key research themes in quantum error correction
- Connections between different approaches
- Evolution of ideas over time
- Gaps in current research"
"Using Perplexity, find:
- Companies working on quantum error correction
- Recent funding announcements in quantum computing
- Patent applications related to topological codes
- Commercial quantum computer developments"
"For each theoretical approach in my literature review, find:
- Industry implementations or attempts
- Technical challenges mentioned in news
- Timeline for practical applications
- Key players and their approaches"
"Using Sequential Thinking, help me understand:
'How do topological quantum error correction codes achieve fault tolerance?'
Break this down into:
- Fundamental concepts
- Mathematical framework
- Physical implementation
- Error threshold calculations"
"Based on my literature review and stored insights, use Sequential Thinking to:
1. Identify gaps in current research
2. Formulate 3 specific research questions
3. Outline methodology for each question
4. Predict potential challenges"
"Perform my weekly research update:
1. Search arXiv for new papers in my field (since last week)
2. Check Perplexity for industry developments
3. Update my Notion literature database
4. Store key findings in Memory Bank
5. Identify papers to read in detail"
"Create a research synthesis:
1. Review all Memory Bank entries on [specific topic]
2. Identify common themes and contradictions
3. Create a synthesis document in Notion
4. Highlight areas needing further investigation
5. Generate questions for advisor meeting"
"For the paper [Title]:
1. Find all papers it cites on arXiv
2. Find papers that cite it
3. Create a citation network in Notion
4. Identify influential papers in the network
5. Store key relationships in Memory Bank"
"Create a historical timeline of quantum error correction research:
1. Search arXiv for seminal papers by year
2. Find industry milestones via Perplexity
3. Create timeline in Notion with key breakthroughs
4. Store evolution patterns in Memory Bank"
"Prepare for research group meeting:
1. Summarize this week's findings from Memory Bank
2. Create presentation outline in Notion
3. Find recent news to discuss (Perplexity)
4. Prepare 3 discussion questions using Sequential Thinking"
"Help me organize my thesis chapter on [Topic]:
1. Review all relevant Memory Bank entries
2. Create chapter outline in Notion
3. Find supporting papers on arXiv for each section
4. Identify areas needing more research
5. Create writing timeline"
"Create a research progress tracker:
1. List all research questions in Notion
2. Track papers read vs. to-read
3. Monitor Memory Bank growth by topic
4. Visualize research coverage gaps
5. Set weekly research goals"
arXiv Search Problems:
Memory Bank Organization:
Notion Sync Issues:
Complex Analysis Challenges: