Quantum Simulation for High Energy Physics

It is for the first time that Quantum Simulation for High Energy Physics (HEP) is studied in the U.S. decadal particle-physics community planning, and in fact until recently, this was not considered a mainstream topic in the community. This fact speaks of a remarkable rate of growth of this subfield over the past few years, stimulated by the impressive advancements in Quantum Information Sciences (QIS) and associated technologies over the past decade, and the significant investment in this area by the government and private sectors in the U.S. and other countries. High-energy physicists have quickly identified problems of importance to our understanding of nature at the most fundamental level, from tiniest distances to cosmological extents, that are intractable with classical computers but may benefit from quantum advantage. They have initiated, and continue to carry out, a vigorous program in theory, algorithm, and hardware co-design for simulations of relevance to the HEP mission. This community whitepaper is an attempt to bring this exciting and yet challenging area of research to the spotlight, and to elaborate on what the promises, requirements, challenges, and potential solutions are over the next decade and beyond.Comment: This is a whitepaper prepared for the topical groups CompF6 (Quantum computing), TF05 (Lattice Gauge Theory), and TF10 (Quantum Information Science) within the Computational Frontier and Theory Frontier of the U.S. Community Study on the Future of Particle Physics (Snowmass 2021). 103 pages and 1 figur

Human Immunodeficiency Virus Envelope Protein Gp120 Induces Proliferation but Not Apoptosis in Osteoblasts at Physiologic Concentrations

Patients with HIV infection have decreased numbers of osteoblasts, decreased bone mineral density and increased risk of fracture compared to uninfected patients; however, the molecular mechanisms behind these associations remain unclear. We questioned whether Gp120, a component of the envelope protein of HIV capable of inducing apoptosis in many cell types, is able to induce cell death in bone-forming osteoblasts. We show that treatment of immortalized osteoblast-like cells and primary human osteoblasts with exogenous Gp120 in vitro at physiologic concentrations does not result in apoptosis. Instead, in the osteoblast-like U2OS cell line, cells expressing CXCR4, a receptor for Gp120, had increased proliferation when treated with Gp120 compared to control (P<0.05), which was inhibited by pretreatment with a CXCR4 inhibitor and a G-protein inhibitor. This suggests that Gp120 is not an inducer of apoptosis in human osteoblasts and likely does not directly contribute to osteoporosis in infected patients by this mechanism

Minimum Information about a Biosynthetic Gene cluster

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.Chemistry and Chemical Biolog

Agenda Control and Electoral Success in the U.S. House

Cartel theory is based on the premise that there is an essential link between party in government and party in elections. Specifically, that theory---and much subsequent legislative research---rests on the assumption that agenda control is the essential mechanism used to manage the party brand; what does and does not get on the legislative agenda determines some portion of the electoral reward or punishment shared by all majority party members. Yet, an essential implication of the theory has never been tested: does successful legislative agenda control improve the electoral fortunes of majority party members? This letter tests this implication. Searching over 160,000 model specifications, we fail to find robust support for the hypothesis that successful agenda control yields electoral benefits to majority members in the US House. While this surprising result may not be definitive---and falls far short of toppling Cartel theory---it raises important questions regarding the mechanisms incentivizing legislative agenda control

Using a Mock Trial to Teach Science and the Law

Over the course of 3 years, the Political Science and Biology Programs at a regional HBCU have built a curricular learning community centered on a mock trial competition, where a microbiology course was paired with an introductory legal studies course. Over the course of a semester, students enrolled in both courses studied a real appellate case that dealt with some aspect of forensic science (DNA evidence for example). The legal studies students were to act as prosecution and defense and the microbiology students played the role of expert witnesses and consultants. To be successful, students had to build an interdisciplinary team, outline their side’s case, and learn scientific and legal principles. This paper evaluates the impact of this experience on student learning using a mixed-methods approach. Students completed a self-reported knowledge survey and participated in a focus group debriefing session. Students report important gains in understanding the legal system and aspects of forensic science

Energetic Coupling between Ligand Binding and Dimerization in <i>Escherichia coli</i> Phosphoglycerate Mutase

Energetic coupling of two molecular events in a protein molecule is ubiquitous in biochemical reactions mediated by proteins, such as catalysis and signal transduction. Here, we investigate energetic coupling between ligand binding and folding of a dimer using a model system that shows three-state equilibrium unfolding of an exceptional quality. The homodimeric <i>Escherichia coli</i> cofactor-dependent phosphoglycerate mutase (dPGM) was found to be stabilized by ATP in a proteome-wide screen, although dPGM does not require or utilize ATP for enzymatic function. We investigated the effect of ATP on the thermodynamic stability of dPGM using equilibrium unfolding. We found that, in the absence of ATP, dPGM populates a partially unfolded, monomeric intermediate during equilibrium unfolding. However, addition of 1.0 mM ATP drastically reduces the population of the intermediate by selectively stabilizing the native dimer. Using a computational ligand docking method, we predicted ATP binds to the active site of the enzyme using the triphosphate group. By performing equilibrium unfolding and isothermal titration calorimetry with active-site variants of dPGM, we confirmed that active-site residues are involved in ATP binding. Our findings show that ATP promotes dimerization of the protein by binding to the active site, which is distal from the dimer interface. This cooperativity suggests an energetic coupling between the active site and the dimer interface. We also propose a structural link to explain how ligand binding to the active site is energetically coupled with dimerization