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Design-level vulnerabilities are a major source of security risks in software. To improve trustworthiness of software design, this paper presents a formal threat-driven approach, which explores explicit behaviors of security threats as the mediator between security goals and applications of security features. Security threats are potential attacks, i.e., misuses and anomalies that violate the security goals of systems' intended functions. Security threats suggest what, where, and how security features for threat mitigation should be applied. To specify the intended functions, security threats, and threat mitigations of a security design as a whole, we exploit aspect-oriented Petri nets as a unified formalism. Intended functions and security threats are modeled by Petri nets, whereas threat mitigations are modeled by Petri net-based aspects due to the incremental and crosscutting nature of security features. The unified formalism facilitates verifying correctness of security threats against intended functions and verifying absence of security threats from integrated functions and threat mitigations. As a result, our approach can make software design provably secured from anticipated security threats and, thus, reduce significant design-level vulnerabilities. We demonstrate our approach through a systematic case study on the threat-driven modeling and verification of a real-world shopping cart application.