Jonathan Cruz | Visual Studies Workshop (SUNY The College at Brockport) (original) (raw)

Papers by Jonathan Cruz

Proceedings of the 56th Annual Design Automation Conference 2019

Electronic hardware trust is an emerging concern for all stakeholders in the semiconductor indust... more Electronic hardware trust is an emerging concern for all stakeholders in the semiconductor industry. Trust issues in electronic hardware span all stages of its life cycle-from creation of intellectual property (IP) blocks to manufacturing, test and deployment of hardware components and all abstraction levels-from chips to printed circuit boards (PCBs) to systems. The trust issues originate from a horizontal business model that promotes reliance of thirdparty untrusted facilities, tools, and IPs in the hardware life cycle. Today, designers are tasked with verifying the integrity of thirdparty IPs before incorporating them into system-on-chip (SoC) designs. Existing trust metric frameworks have limited applicability since they are not comprehensive. They capture only a subset of vulnerabilities such as potential vulnerabilities introduced through design mistakes and CAD tools, or quantify features in a design that target a particular Trojan model. Therefore, current practice uses ad-hoc security analysis of IP cores. In this paper, we propose a vector-based comprehensive coverage metric that quantifies the overall trust of an IP considering both vulnerabilities and direct malicious modifications. We use a variable weighted sum of a design's functional coverage, structural coverage, and asset coverage to assess an IP's integrity. Designers can also effectively use our trust metric to compare the relative trustworthiness of functionally equivalent third-party IPs. To demonstrate the applicability and usefulness of the proposed metric, we utilize our trust metric on Trojan-free and Trojan-inserted variants of an IP. Our results demonstrate that we are able to successfully distinguish between trusted and untrusted IPs.

2018 Design, Automation & Test in Europe Conference & Exhibition (DATE)

2018 IEEE International Test Conference (ITC)

2018 31st International Conference on VLSI Design and 2018 17th International Conference on Embedded Systems (VLSID)

2018 Asian Hardware Oriented Security and Trust Symposium (AsianHOST)

Obfuscation is a technique for protecting hardware intellectual property (IP) blocks against reve... more Obfuscation is a technique for protecting hardware intellectual property (IP) blocks against reverse engineering, piracy, and malicious modifications. Current obfuscation efforts mainly focus on functional locking of a design to prevent black-box usage. They do not directly address hiding design intent through structural transformations, which is an important objective of obfuscation. We note that current obfuscation techniques incorporate only: (1) local, and (2) predictable changes in circuit topology. In this paper, we present SAIL, a structural attack on obfuscation using machine learning (ML) models that exposes a critical vulnerability of these methods. Through this attack, we demonstrate that the gate-level structure of an obfuscated design can be retrieved in most parts through a systematic set of steps. The proposed attack is applicable to all forms of logic obfuscation, and significantly more powerful than existing attacks, e.g., SAT-based attacks, since it does not require the availability of golden functional responses (e.g. an unlocked IC). Evaluation on benchmark circuits show that we can recover an average of around 84% (up to 95%) transformations introduced by obfuscation. We also show that this attack is scalable, flexible, and versatile.

Poster Presentations - Proffered Abstracts

Science

Neutralizing antibodies have become an important tool in treating infectious diseases. Recently, ... more Neutralizing antibodies have become an important tool in treating infectious diseases. Recently, two separate approaches yielded successful antibody treatments for Ebola – one from genetically-humanized mice, and the other from a human survivor. Here, we describe parallel efforts using both humanized mice and convalescent patients to generate antibodies against the SARS-CoV-2 spike protein, yielding a large collection of fully-human antibodies that were characterized for binding, neutralization and three dimensional structure. Based on these criteria, we selected pairs of highly-potent individual antibodies that simultaneously bind the receptor-binding domain of the spike protein, providing ideal partners for a therapeutic antibody cocktail that aims to decrease the potential for virus escape mutants that might arise in response to selective pressure from a single antibody treatment.

Nasa Sti Recon Technical Report N, Jun 1, 1990

Assuming that a Shuttle Orbiter could be qualified to serve long duration missions attached to Sp... more Assuming that a Shuttle Orbiter could be qualified to serve long duration missions attached to Space Station Freedom in the capacity as an Assured Crew Return Vehicle (ACRV), a study was conducted to identify and examine candidate attach locations. Baseline, modified hardware, and new hardware design configurations were considered. Dual simultaneous Orbiter docking accommodation were required. Resulting flight characteristics analyzed

Bioorganic Medicinal Chemistry Letters, Jun 1, 2009

Bioorg Medicinal Chem Letter, 2011

Bioorg Medicinal Chem Letter, 2010

Nucleic acids research, Jan 5, 2016

Toxin-antitoxin (TA) systems play key roles in bacterial persistence, biofilm formation and stres... more Toxin-antitoxin (TA) systems play key roles in bacterial persistence, biofilm formation and stress responses. The MazF toxin from the Escherichia coli mazEF TA system is a sequence- and single-strand-specific endoribonuclease, and many studies have led to the proposal that MazF family members exclusively target mRNA. However, recent data indicate some MazF toxins can cleave specific sites within rRNA in concert with mRNA. In this report, we identified the repertoire of RNAs cleaved by Mycobacterium tuberculosis toxin MazF-mt9 using an RNA-seq-based approach. This analysis revealed that two tRNAs were the principal targets of MazF-mt9, and each was cleaved at a single site in either the tRNA(Pro14) D-loop or within the tRNA(Lys43) anticodon. This highly selective target discrimination occurs through recognition of not only sequence but also structural determinants. Thus, MazF-mt9 represents the only MazF family member known to target tRNA and to require RNA structure for recognition ...

Bioorg Medicinal Chem Letter, 2010

The development of a novel series of purines as γ-secretase modulators for potential use in the t... more The development of a novel series of purines as γ-secretase modulators for potential use in the treatment of Alzheimer’s disease is disclosed herein. Optimization of a previously disclosed pyrimidine series afforded a series of potent purine-based γ-secretase modulators with 300- to 2000-fold in vitro selectivity over inhibition of Notch cleavage and that selectively reduces Αβ42 in an APP-YAC transgenic mouse model.The development of a novel series of purines as γ-secretase modulators for potential use in the treatment of Alzheimer’s disease is disclosed herein. Optimization of a previously disclosed pyrimidine series afforded a series of potent purine-based γ-secretase modulators with 300- to 2000-fold in vitro selectivity over inhibition of Notch cleavage and that selectively reduces Αβ42 in an APP-YAC transgenic mouse model.

Bioorganic Medicinal Chemistry Letters, Jan 15, 2010

Proceedings of the 56th Annual Design Automation Conference 2019

Electronic hardware trust is an emerging concern for all stakeholders in the semiconductor indust... more Electronic hardware trust is an emerging concern for all stakeholders in the semiconductor industry. Trust issues in electronic hardware span all stages of its life cycle-from creation of intellectual property (IP) blocks to manufacturing, test and deployment of hardware components and all abstraction levels-from chips to printed circuit boards (PCBs) to systems. The trust issues originate from a horizontal business model that promotes reliance of thirdparty untrusted facilities, tools, and IPs in the hardware life cycle. Today, designers are tasked with verifying the integrity of thirdparty IPs before incorporating them into system-on-chip (SoC) designs. Existing trust metric frameworks have limited applicability since they are not comprehensive. They capture only a subset of vulnerabilities such as potential vulnerabilities introduced through design mistakes and CAD tools, or quantify features in a design that target a particular Trojan model. Therefore, current practice uses ad-hoc security analysis of IP cores. In this paper, we propose a vector-based comprehensive coverage metric that quantifies the overall trust of an IP considering both vulnerabilities and direct malicious modifications. We use a variable weighted sum of a design's functional coverage, structural coverage, and asset coverage to assess an IP's integrity. Designers can also effectively use our trust metric to compare the relative trustworthiness of functionally equivalent third-party IPs. To demonstrate the applicability and usefulness of the proposed metric, we utilize our trust metric on Trojan-free and Trojan-inserted variants of an IP. Our results demonstrate that we are able to successfully distinguish between trusted and untrusted IPs.

2018 Design, Automation & Test in Europe Conference & Exhibition (DATE)

2018 IEEE International Test Conference (ITC)

2018 31st International Conference on VLSI Design and 2018 17th International Conference on Embedded Systems (VLSID)

2018 Asian Hardware Oriented Security and Trust Symposium (AsianHOST)

Obfuscation is a technique for protecting hardware intellectual property (IP) blocks against reve... more Obfuscation is a technique for protecting hardware intellectual property (IP) blocks against reverse engineering, piracy, and malicious modifications. Current obfuscation efforts mainly focus on functional locking of a design to prevent black-box usage. They do not directly address hiding design intent through structural transformations, which is an important objective of obfuscation. We note that current obfuscation techniques incorporate only: (1) local, and (2) predictable changes in circuit topology. In this paper, we present SAIL, a structural attack on obfuscation using machine learning (ML) models that exposes a critical vulnerability of these methods. Through this attack, we demonstrate that the gate-level structure of an obfuscated design can be retrieved in most parts through a systematic set of steps. The proposed attack is applicable to all forms of logic obfuscation, and significantly more powerful than existing attacks, e.g., SAT-based attacks, since it does not require the availability of golden functional responses (e.g. an unlocked IC). Evaluation on benchmark circuits show that we can recover an average of around 84% (up to 95%) transformations introduced by obfuscation. We also show that this attack is scalable, flexible, and versatile.

Poster Presentations - Proffered Abstracts

Science

Neutralizing antibodies have become an important tool in treating infectious diseases. Recently, ... more Neutralizing antibodies have become an important tool in treating infectious diseases. Recently, two separate approaches yielded successful antibody treatments for Ebola – one from genetically-humanized mice, and the other from a human survivor. Here, we describe parallel efforts using both humanized mice and convalescent patients to generate antibodies against the SARS-CoV-2 spike protein, yielding a large collection of fully-human antibodies that were characterized for binding, neutralization and three dimensional structure. Based on these criteria, we selected pairs of highly-potent individual antibodies that simultaneously bind the receptor-binding domain of the spike protein, providing ideal partners for a therapeutic antibody cocktail that aims to decrease the potential for virus escape mutants that might arise in response to selective pressure from a single antibody treatment.

Nasa Sti Recon Technical Report N, Jun 1, 1990

Assuming that a Shuttle Orbiter could be qualified to serve long duration missions attached to Sp... more Assuming that a Shuttle Orbiter could be qualified to serve long duration missions attached to Space Station Freedom in the capacity as an Assured Crew Return Vehicle (ACRV), a study was conducted to identify and examine candidate attach locations. Baseline, modified hardware, and new hardware design configurations were considered. Dual simultaneous Orbiter docking accommodation were required. Resulting flight characteristics analyzed

Bioorganic Medicinal Chemistry Letters, Jun 1, 2009

Bioorg Medicinal Chem Letter, 2011

Bioorg Medicinal Chem Letter, 2010

Nucleic acids research, Jan 5, 2016

Toxin-antitoxin (TA) systems play key roles in bacterial persistence, biofilm formation and stres... more Toxin-antitoxin (TA) systems play key roles in bacterial persistence, biofilm formation and stress responses. The MazF toxin from the Escherichia coli mazEF TA system is a sequence- and single-strand-specific endoribonuclease, and many studies have led to the proposal that MazF family members exclusively target mRNA. However, recent data indicate some MazF toxins can cleave specific sites within rRNA in concert with mRNA. In this report, we identified the repertoire of RNAs cleaved by Mycobacterium tuberculosis toxin MazF-mt9 using an RNA-seq-based approach. This analysis revealed that two tRNAs were the principal targets of MazF-mt9, and each was cleaved at a single site in either the tRNA(Pro14) D-loop or within the tRNA(Lys43) anticodon. This highly selective target discrimination occurs through recognition of not only sequence but also structural determinants. Thus, MazF-mt9 represents the only MazF family member known to target tRNA and to require RNA structure for recognition ...

Bioorg Medicinal Chem Letter, 2010

The development of a novel series of purines as γ-secretase modulators for potential use in the t... more The development of a novel series of purines as γ-secretase modulators for potential use in the treatment of Alzheimer’s disease is disclosed herein. Optimization of a previously disclosed pyrimidine series afforded a series of potent purine-based γ-secretase modulators with 300- to 2000-fold in vitro selectivity over inhibition of Notch cleavage and that selectively reduces Αβ42 in an APP-YAC transgenic mouse model.The development of a novel series of purines as γ-secretase modulators for potential use in the treatment of Alzheimer’s disease is disclosed herein. Optimization of a previously disclosed pyrimidine series afforded a series of potent purine-based γ-secretase modulators with 300- to 2000-fold in vitro selectivity over inhibition of Notch cleavage and that selectively reduces Αβ42 in an APP-YAC transgenic mouse model.

Bioorganic Medicinal Chemistry Letters, Jan 15, 2010