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Abstract Primordial black holes (PBHs), theorized to have originated in the early Universe, are speculated to be a viable form of dark matter. If they exist, they should be detectable through photometric and astrometric signals resulting from gravitational microlensing of stars in the Milky Way. Population Synthesis for Compact-object Lensing Events, orPopSyCLE, is a simulation code that enables users to simulate microlensing surveys, and is the first of its kind to include both photometric and astrometric microlensing effects, which are important for potential PBH detection and characterization. To estimate the number of observable PBH microlensing events, we modifyPopSyCLEto include a dark matter halo consisting of PBHs. We detail our PBH population model, and demonstrate ourPopSyCLE+ PBH results through simulations of the Optical Gravitational Lensing Experiment-IV (OGLE-IV) and Nancy Grace Roman Space Telescope (Roman) microlensing surveys. We provide a proof-of-concept analysis for adding PBHs intoPopSyCLE, and thus include many simplifying assumptions, such asf_DM, the fraction of dark matter composed of PBHs, and ${\overline{m}}_{\mathrm{PBH}}$, mean PBH mass. Assuming ${\overline{m}}_{\mathrm{PBH}}=30$M_⊙, we find ∼3.6f_DMtimes as many PBH microlensing events than stellar evolved black hole events, a PBH average peak Einstein crossing time of ∼91.5 days, estimate on order of 10²f_DMPBH events within the 8 yr OGLE-IV results, and estimate Roman to detect ∼1000f_DMPBH microlensing events throughout its planned microlensing survey. 

Abstract Computational protein design is advancing rapidly. Here we describe efficient routes starting from validated parallel and antiparallel peptide assemblies to design two families of α-helical barrel proteins with central channels that bind small molecules. Computational designs are seeded by the sequences and structures of defined de novo oligomeric barrel-forming peptides, and adjacent helices are connected by loop building. For targets with antiparallel helices, short loops are sufficient. However, targets with parallel helices require longer connectors; namely, an outer layer of helix–turn–helix–turn–helix motifs that are packed onto the barrels. Throughout these computational pipelines, residues that define open states of the barrels are maintained. This minimizes sequence sampling, accelerating the design process. For each of six targets, just two to six synthetic genes are made for expression inEscherichia coli. On average, 70% of these genes express to give soluble monomeric proteins that are fully characterized, including high-resolution structures for most targets that match the design models with high accuracy. 

Abstract Primordial black holes (PBHs) could explain some fraction of dark matter and shed light on many areas of early-Universe physics. Despite over half a century of research interest, a PBH population has so far eluded detection. The most competitive constraints on the fraction of dark matter comprised of PBHs (f_DM) in the (10⁻⁹–10)M_⊙mass ranges come from photometric microlensing and boundf_DM≲ 10⁻²–10⁻¹. With the advent of the Roman Space Telescope with its submilliarcsecond astrometric capabilities and its planned Galactic Bulge Time Domain Survey (GBTDS), detecting astrometric microlensing signatures will become routine. Compared with photometric microlensing, astrometric microlensing signals are sensitive to different lens masses–distance configurations and contain different information, making it a complimentary lensing probe. At submilliarcsecond astrometric precision, astrometric microlensing signals are typically detectable at larger lens–source separations than photometric signals, suggesting a microlensing detection channel of pure astrometric events. We use a Galactic simulation to predict the number of detectable microlensing events during the GBTDS via this pure astrometric microlensing channel. Assuming an absolute astrometric precision floor for bright stars of 0.1 mas for the GBTDS, we find that the number of detectable events peaks at ≈10³f_DMfor a population of 1M_⊙PBHs and tapers to ≈10f_DMand ≈100f_DMat 10⁻⁴M_⊙and 10³M_⊙, respectively. Accounting for the distinguishability of PBHs from stellar lenses, we conclude the GBTDS will be sensitive to a PBH population atf_DMdown to ≈10⁻¹–10⁻³for (10⁻¹–10²)M_⊙likely yielding novel PBH constraints. 

Ab initioquantum mechanical models can characterize and predict intermolecular binding, but only recently have models including more than a few hundred atoms gained traction. Here, we simulate the electronic structure for approximately 13 000 atoms to predict and characterize binding of SARS-CoV-2 spike variants to the human ACE2 (hACE2) receptor using the quantum mechanics complexity reduction (QM-CR) approach. We compare four spike variants in our analysis: Wuhan, Omicron, and two Omicron-based variants. To assess binding, we mechanistically characterize the energetic contribution of each amino acid involved, and predict the effect of select single amino acid mutations. We validate our computational predictions experimentally by comparing the efficacy of spike variants binding to cells expressing hACE2. At the time we performed our simulations (December 2021), the mutation A484K which our model predicted to be highly beneficial to ACE2 binding had not been identified in epidemiological surveys; only recently (August 2023) has it appeared in variant BA.2.86. We argue that our computational model, QM-CR, can identify mutations critical for intermolecular interactions and inform the engineering of high-specificity interactors. 

Abstract From the formation mechanisms of stars and compact objects to nuclear physics, modern astronomy frequently leverages surveys to understand populations of objects to answer fundamental questions. The population of dark and isolated compact objects in the Galaxy contains critical information related to many of these topics, but is only practically accessible via gravitational microlensing. However, photometric microlensing observables are degenerate for different types of lenses, and one can seldom classify an event as involving either a compact object or stellar lens on its own. To address this difficulty, we apply a Bayesian framework that treats lens type probabilistically and jointly with a lens population model. This method allows lens population characteristics to be inferred despite intrinsic uncertainty in the lens class of any single event. We investigate this method’s effectiveness on a simulated ground-based photometric survey in the context of characterizing a hypothetical population of primordial black holes (PBHs) with an average mass of 30M_⊙. On simulated data, our method outperforms current black hole (BH) lens identification pipelines and characterizes different subpopulations of lenses while jointly constraining the PBH contribution to dark matter to ≈25%. Key to robust inference, our method can marginalize over population model uncertainty. We find the lower mass cutoff for stellar origin BHs, a key observable in understanding the BH mass gap, particularly difficult to infer in our simulations. This work lays the foundation for cutting-edge PBH abundance constraints to be extracted from current photometric microlensing surveys. 

Abstract We employ a recently developed complexity-reduction quantum mechanical (QM-CR) approach, based on complexity reduction of density functional theory calculations, to characterize the interactions of the SARS-CoV-2 spike receptor binding domain (RBD) with ACE2 host receptors and antibodies. QM-CR operates via ab initio identification of individual amino acid residue’s contributions to chemical binding and leads to the identification of the impact of point mutations. Here, we especially focus on the E484K mutation of the viral spike protein. We find that spike residue 484 hinders the spike's binding to the human ACE2 receptor (hACE2). In contrast, the same residue is beneficial in binding to the bat receptor Rhinolophus macrotis ACE2 (macACE2). In agreement with empirical evidence, QM-CR shows that the E484K mutation allows the spike to evade categories of neutralizing antibodies like C121 and C144. The simulation also shows how the Delta variant spike binds more strongly to hACE2 compared to the original Wuhan strain, and predicts that a E484K mutation can further improve its binding. Broad agreement between the QM-CR predictions and experimental evidence supports the notion that ab initio modeling has now reached the maturity required to handle large intermolecular interactions central to biological processes. 

Abstract We investigate laccase-mediated detoxification of aflatoxins, fungal carcinogenic food contaminants. Our experimental comparison between two aflatoxins with similar structures (AFB₁and AFG₂) shows significant differences in laccase-mediated detoxification. A multi-scale modeling approach (Docking, Molecular Dynamics, and Density Functional Theory) identifies the highly substrate-specific changes required to improve laccase detoxifying performance. We employ a large-scale density functional theory-based approach, involving more than 7000 atoms, to identify the amino acid residues that determine the affinity of laccase for aflatoxins. From this study we conclude: (1) AFB₁is more challenging to degrade, to the point of complete degradation stalling; (2) AFG₂is easier to degrade by laccase due to its lack of side products and favorable binding dynamics; and (3) ample opportunities to optimize laccase for aflatoxin degradation exist, especially via mutations leading to π–π stacking. This study identifies a way to optimize laccase for aflatoxin bioremediation and, more generally, contributes to the research efforts aimed at rational enzyme optimization. 

Abstract Modern surveys of gravitational microlensing events have progressed to detecting thousands per year, and surveys are capable of probing Galactic structure, stellar evolution, lens populations, black hole physics, and the nature of dark matter. One of the key avenues for doing this is the microlensing Einstein radius crossing time ( t E ) distribution. However, systematics in individual light curves as well as oversimplistic modeling can lead to biased results. To address this, we developed a model to simultaneously handle the microlensing parallax due to Earth's motion, systematic instrumental effects, and unlensed stellar variability with a Gaussian process model. We used light curves for nearly 10,000 OGLE-III and -IV Milky Way bulge microlensing events and fit each with our model. We also developed a forward model approach to infer the t E distribution by forward modeling from the data rather than using point estimates from individual events. We find that modeling the variability in the baseline removes a source of significant bias in individual events, and the previous analyses overestimated the number of t E > 100 day events due to their oversimplistic model ignoring parallax effects. We use our fits to identify the hundreds filling a regime in the microlensing parameter space that are 50% pure of black holes. Finally, we have released the largest-ever catalog of Markov Chain Monte Carlo parameter estimates for microlensing events. 

Abstract This Roadmap article provides a succinct, comprehensive overview of the state of electronic structure (ES) methods and software for molecular and materials simulations. Seventeen distinct sections collect insights by 51 leading scientists in the field. Each contribution addresses the status of a particular area, as well as current challenges and anticipated future advances, with a particular eye towards software related aspects and providing key references for further reading. Foundational sections cover density functional theory and its implementation in real-world simulation frameworks, Green’s function based many-body perturbation theory, wave-function based and stochastic ES approaches, relativistic effects and semiempirical ES theory approaches. Subsequent sections cover nuclear quantum effects, real-time propagation of the ES, challenges for computational spectroscopy simulations, and exploration of complex potential energy surfaces. The final sections summarize practical aspects, including computational workflows for complex simulation tasks, the impact of current and future high-performance computing architectures, software engineering practices, education and training to maintain and broaden the community, as well as the status of and needs for ES based modeling from the vantage point of industry environments. Overall, the field of ES software and method development continues to unlock immense opportunities for future scientific discovery, based on the growing ability of computations to reveal complex phenomena, processes and properties that are determined by the make-up of matter at the atomic scale, with high precision.