UMBC Faculty Collection

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Optimized Preparation of Segmentally Labeled RNAs for NMR Structure Determination
(Elsevier, 2025-03-05) Grossman, Brian D.; Beyene, Bethel G.; Tekle, Bersabel; Sakowicz, William; Ji, Xinjie; Camacho, Joshua Miguele; Vaishnav, Nandini; Ahmed, Amina; Bhandari, Naman; Desai, Kush; Hardy, Josiah; Hollman, Nele M.; Marchant, Jan; Summers, Michael F.
RNA structures are significantly underrepresented in public repositories (∼ 100-fold compared to proteins) despite their importance for mechanistic understanding and for development of structure prediction/validation tools. A substantial portion of deposited RNA structures have been determined by NMR (∼30%), but most comprise fewer than 60 nucleotides due to complications associated with NMR signal overlap. A promising approach for applying NMR to larger RNAs involves use of a mutated DNA polymerase (TGK) that can extend “primer” RNA strands generated independently by synthetic or enzymatic methods [Haslecker et al., Nature Commun. 2023]. In attempts to employ this technology, we uncovered sequence- and enzyme-dependent complications for most constructs examined that prohibited preparation of homogeneous samples. By using TGK extension efficiency and NMR as guides, we identified non-templated run-on by wild-type T7-RNA polymerase (RNAPWT) as the primary source of product heterogeneity. Use of 2′-O-methylated DNA templates did not prevent RNAPWT run-on for most constructs examined. However, primer RNAs with appropriate 3′ end homogeneity were obtained in high yield using a recently described T7 RNAP mutant designed for improved immunogenic behavior. Minor spectral heterogeneity sometimes observed for 3′ residues, caused by partial premature TGK termination, could be moved to sites downstream of the RNA region of interest by employing extended template DNAs that encode additional non-interacting 3′ nucleotides. We additionally present an approach for large-scale synthesis of homogeneous template DNA required for TGK extension. With these modifications, segmentally labeled RNAs appropriate for high resolution structural studies are now routinely obtainable.
Observable-based reformulation of time-delay interferometry
(2025-02-16) Yamamoto, Kohei; Reinhardt, Jan Niklas; Hartwig, Olaf
Spaceborne gravitational-wave observatories utilize a post-processing technique known as time-delay interferometry (TDI) to reduce the otherwise overwhelming laser frequency noise by around eight orders of magnitude. While, in its traditional form, TDI considers the spacecraft as point masses, recent studies have enhanced this simplified scenario by incorporating more realistic metrology chain models, which include onboard optical, electronic, and digital delays. These studies have updated the TDI algorithm to include onboard delays obtained from pre-launch and in-flight calibrations. Conversely, the processing scheme presented in this article naturally treats onboard delays as part of the TDI combinations: instead of having separate calibration stages, it directly expresses all delays appearing in the algorithm in terms of onboard measurements, especially pseudo-random-noise ranging (PRNR) measurements. The only onboard delays that need to be corrected in our processing scheme are PRNR delays in the digital domain, which are determined by commandable digital-signal-processing parameters; hence, they can be easily managed in post-processing. Furthermore, our processing scheme does not require a prior interspacecraft clock synchronization, and it automatically corrects for potential relative drifts between the clocks driving local phase measurement systems. The proposed observable-based processing scheme significantly strengthens the bond between TDI and the real metrology system.
No-go theorem for environment-assisted invariance in non-unitary dynamics
(2025-03-13) Sone, Akira; Touil, Akram; Maeda, Kenji; Cappellaro, Paola; Deffner, Sebastian
We elucidate the requirements for quantum operations that achieve environment-assisted invariance (envariance), a symmetry of entanglement. While envariance has traditionally been studied within the framework of local unitary operations, we extend the analysis to consider non-unitary local operations. First, we investigate the conditions imposed on operators acting on pure bipartite entanglement to attain envariance. We show that the local operations must take a direct-sum form in their Kraus operator representations, establishing decoherence-free subspaces. Furthermore, we prove that the unitary operation on the system's subspace uniquely determines the corresponding unitary operator on the environment's subspace. As an immediate consequence, we demonstrate that environment-assisted shortcuts to adiabaticity cannot be achieved through non-unitary operations. In addition, we identify the requirements that local operations must satisfy to ensure that the eternal black hole states remain static in AdS/CFT.
NASA Innovative Advanced Concepts Phase I Final Report -- A Lunar Long-Baseline UV/Optical Imaging Interferometer: Artemis-enabled Stellar Imager (AeSI)
(2025-03-03) Carpenter, Kenneth G.; Boyajian, Tabetha; Buzasi, Derek; Clark, Jim; Creech-Eakman, Michelle; Dean, Bruce; Elliott, Ashley; Foster, Julianne; Gong, Qian; Karovska, Margarita; Kim, David; Hulberg, Jon; Leisawitz, David; Maher, Mike; Morse, Jon; Mozurkewich, Dave; Peacock, Sarah; Petro, Noah; Rau, Gioia; Scowen, Paul; Seals, Len; Smith, Walter; Smuda, Max; Sitarski, Breann; Taylor, Buddy; van Belle, Gerard; Wilkinson, Erik
This report presents the findings of a NIAC Phase I feasibility study for the Artemis-enabled Stellar Imager (AeSI), a proposed high-resolution, UV/Optical interferometer designed for deployment on the lunar surface. Its primary science goal is to image the surfaces and interiors of stars with unprecedented detail, revealing new details about their magnetic processes and dynamic evolution and enabling the creation of a truly predictive solar/stellar dynamo model. This capability will transform our understanding of stellar physics and has broad applicability across astrophysics, from resolving the cores of Active Galactic Nuclei (AGN) to studying supernovae, planetary nebulae, and the late stages of stellar evolution. By leveraging the stable vacuum environment of the Moon and the infrastructure being established for the Artemis Program, AeSI presents a compelling case for a lunar-based interferometer. In this study, the AeSI Team, working with the NASA Goddard Space Flight Center's Integrated Design Center (IDC), has firmly established the feasibility of building and operating a reconfigurable, dispersed aperture telescope (i.e., an interferometer) on the lunar surface. The collaboration produced a credible Baseline design featuring 15 primary mirrors arranged in an elliptical array with a 1 km major axis, with the potential to expand to 30 mirrors and larger array sizes through staged deployments. Additionally, this study identified numerous opportunities for optimization and the necessary trade studies to refine the design further. These will be pursued in follow-up investigations, such as a NIAC Phase II study, to advance the concept toward implementation.
Nano-Newton electrostatic force actuators for femto-Newton-sensitive measurements: System performance test in the LISA Pathfinder mission
(APS, 2024-05-22) LISA Pathfinder Collaboration; Armano, M.; Audley, H.; Baird, J.; Bassan, M.; Binetruy, P.; Born, M.; Bortoluzzi, D.; Castelli, Eleonora; Cavalleri, A.; Cesarini, A.; Chiavegato, V.; Cruise, A. M.; Dal Bosco, D.; Danzmann, K.; De Deus Silva, M.; De Rosa, R.; Di Fiore, L.; Diepholz, I.; Dixon, G.; Dolesi, R.; Ferraioli, L.; Ferroni, V.; Fitzsimons, E. D.; Freschi, M.; Gesa, L.; Giardini, D.; Gibert, F.; Giusteri, R.; Grado, A.; Grimani, C.; Grzymisch, J.; Harrison, I.; Hartig, M. S.; Heinzel, G.; Hewitson, M.; Hollington, D.; Hoyland, D.; Hueller, M.; Inchauspé, H.; Jennrich, O.; Jetzer, P.; Johlander, B.; Karnesis, N.; Kaune, B.; Korsakova, N.; Killow, C. J.; Liu, L.; Lobo, J. A.; López-Zaragoza, J. P.; Maarschalkerweerd, R.; Mance, D.; Martín, V.; Martin-Polo, L.; Martin-Porqueras, F.; Martino, J.; McNamara, P. W.; Mendes, J.; Mendes, L.; Meshksar, N.; Moerschell, J.; Nofrarias, M.; Paczkowski, S.; Perreur-Lloyd, M.; Petiteau, A.; Plagnol, E.; Praplan, C.; Ramos-Castro, J.; Reiche, J.; Rivas, F.; Robertson, D. I.; Russano, G.; Sala, L.; Sarra, P.; Schule-Walewski, S. L.; Slutsky, J.; Sopuerta, C. F.; Stanga, R.; Sumner, T.; ten Pierick, J.; Texier, D.; Thorpe, J. I.; Vetrugno, D.; Vitale, S.; Wanner, G.; Ward, H.; Wass, P. J.; Weber, W. J.; Wissel, L.; Wittchen, A.; Zanoni, C.; Zweifel, P.
Electrostatic force actuation is a key component of the system of geodesic reference test masses (TM) for the LISA orbiting gravitational wave observatory and in particular for performance at low frequencies, below 1 mHz, where the observatory sensitivity is limited by stray force noise. The system needs to apply forces of order 10?9 N while limiting fluctuations in the measurement band to levels approaching 10?15 N/Hz1/2. We present here the LISA actuation system design, based on audio-frequency voltage carrier signals, and results of its in-flight performance test with the LISA Pathfinder test mission. In LISA, TM force actuation is used to align the otherwise free-falling TM to the spacecraft-mounted optical metrology system, without any forcing along the critical gravitational wave-sensitive interferometry axes. In LISA Pathfinder, on the other hand, the actuation was used also to stabilize the TM along the critical ?? axis joining the two TM, with the commanded actuation force entering directly into the mission’s main differential acceleration science observable. The mission allowed demonstration of the full compatibility of the electrostatic actuation system with the LISA observatory requirements, including dedicated measurement campaigns to amplify, isolate, and quantify the two main force noise contributions from the actuation system, from actuator gain noise and from low frequency “in band” voltage fluctuations. These campaigns have shown actuation force noise to be a relevant, but not dominant, noise source in LISA Pathfinder and have allowed performance projections for the conditions expected in the LISA mission.
Multispectral Land Surface Reflectance Reconstruction Based on Non-Negative Matrix Factorization: Bridging Spectral Resolution Gaps for GRASP TROPOMI BRDF Product in Visible
(MDPI, 2025-03-17) Hou, Weizhen; Liu, Xiong; Wang, Jun; Chen, Cheng; Xu, Xiaoguang
In satellite remote sensing, mixed pixels commonly arise in medium- and low-resolution imagery, where surface reflectance is a combination of various land cover types. The widely adopted linear mixing model enables the decomposition of mixed pixels into constituent endmembers, effectively bridging spectral resolution gaps by retrieving the spectral properties of individual land cover types. This study introduces a method to enhance multispectral surface reflectance data by reconstructing additional spectral information, particularly in the visible spectral range, using the TROPOMI BRDF product generated by the Generalized Retrieval of Atmosphere and Surface Properties (GRASP) algorithm. Employing non-negative matrix factorization (NMF), the approach extracts spectral basis vectors from reference spectral libraries and reconstructs key spectral features using a limited number of wavelength bands. The comprehensive test results show that this method is particularly effective in supplementing surface reflectance information for specific wavelengths where gas absorption is strong or atmospheric correction errors are significant, demonstrating its applicability not only within the 400–800 nm range but also across the broader spectral range of 400–2400 nm. While not a substitute for hyperspectral observations, this approach provides a cost-effective means to address spectral resolution gaps in multispectral datasets, facilitating improved surface characterization and environmental monitoring. Future research will focus on refining spectral libraries, improving reconstruction accuracy, and expanding the spectral range to enhance the applicability and robustness of the method for diverse remote sensing applications.
Multi?Scale Spatial Effects Determine Nest Success in Small Urban Forest Patches
(Wiley, 2025-2-28) Ohad, Paris; Studds, Colin
Urban development and resulting habitat fragmentation affect species populations and inter-specific relationships. While urban ecology research often focuses on species distribution and abundance in habitat fragments, less is known about how urban environments affect reproductive success. Here, we show that factors driving songbird nest success in small urban forest patches vary with landscape-specific edge effects and Light Detection and Ranging (LiDAR) derived vegetation structure. Nest success declined within 30 meters of patch edge, but only in more developed urban landscapes. In addition, nest success increased along two fundamental axes of vegetation structure in urban fragments: overstory density and number of ground-to-canopy gaps. Hence, results indicate that forest fragmentation can generate sufficient variation in ecological conditions to create heterogeneity in edge effects and vegetation structure even across the limited urban development gradient. These findings expand to our understanding of fragmentation effects beyond the traditional rural-developed paradigm.
Multi-GNSS Airborne Radio Occultation Observations as a Complement to Dropsondes in Atmospheric River Reconnaissance
(AGU, 2021-11-22) Haase, J. S.; Murphy, Michael; Cao, B.; Ralph, F. M.; Zheng, M.; Delle Monache, L.
Variations in the water vapor that atmospheric rivers (ARs) carry toward North America within Pacific storms strongly modulates the spatiotemporal distribution of west-coast precipitation. The “AR Recon” program was established to improve forecasts of landfalling Pacific-coast ARs and their associated precipitation. Dropsondes are deployed from weather reconnaissance aircraft and pressure sensors have been added to drifting ocean buoys to fill a major gap in standard weather observations, while research is being conducted on the potential for airborne Global Navigation Satellite System (GNSS) radio occultation (ARO) to also contribute to forecast improvement. ARO further expands the spatial coverage of the data collected during AR Recon flights. This study provides the first description of these data, which provide water vapor and temperature information typically as far as 300 km to the side of the aircraft. The first refractivity profiles from European Galileo satellites are provided and their accuracy is evaluated using the dropsondes. It is shown that spatial variations in the refractivity anomaly (difference from the climatological background) are modulated by AR features, including the low-level jet and tropopause fold, illustrating the potential for RO measurements to represent key AR characteristics. It is demonstrated that assimilation of ARO refractivity profiles can influence the moisture used as initial conditions in a high-resolution model. While the dropsonde measurements provide precise, in situ wind, temperature and water vapor vertical profiles beneath the aircraft, and the buoys provide surface pressure, ARO provides complementary thermodynamic information aloft in broad areas not otherwise sampled at no additional expendable cost.
Matrix Factorization for Inferring Associations and Missing Links
(2025-03-06) Barron, Ryan; Eren, Maksim; Truong, Duc P.; Matuszek, Cynthia; Wendelberger, James; Dorn, Mary F.; Alexandrov, Boian
Missing link prediction is a method for network analysis, with applications in recommender systems, biology, social sciences, cybersecurity, information retrieval, and Artificial Intelligence (AI) reasoning in Knowledge Graphs. Missing link prediction identifies unseen but potentially existing connections in a network by analyzing the observed patterns and relationships. In proliferation detection, this supports efforts to identify and characterize attempts by state and non-state actors to acquire nuclear weapons or associated technology - a notoriously challenging but vital mission for global security. Dimensionality reduction techniques like Non-Negative Matrix Factorization (NMF) and Logistic Matrix Factorization (LMF) are effective but require selection of the matrix rank parameter, that is, of the number of hidden features, k, to avoid over/under-fitting. We introduce novel Weighted (WNMFk), Boolean (BNMFk), and Recommender (RNMFk) matrix factorization methods, along with ensemble variants incorporating logistic factorization, for link prediction. Our methods integrate automatic model determination for rank estimation by evaluating stability and accuracy using a modified bootstrap methodology and uncertainty quantification (UQ), assessing prediction reliability under random perturbations. We incorporate Otsu threshold selection and k-means clustering for Boolean matrix factorization, comparing them to coordinate descent-based Boolean thresholding. Our experiments highlight the impact of rank k selection, evaluate model performance under varying test-set sizes, and demonstrate the benefits of UQ for reliable predictions using abstention. We validate our methods on three synthetic datasets (Boolean and uniformly distributed) and benchmark them against LMF and symmetric LMF (symLMF) on five real-world protein-protein interaction networks, showcasing an improved prediction performance.
LLM-based Corroborating and Refuting Evidence Retrieval for Scientific Claim Verification
(2025-03-11) Wang, Siyuan; Foulds, James; Gani, Md Osman; Pan, Shimei
In this paper, we introduce CIBER (Claim Investigation Based on Evidence Retrieval), an extension of the Retrieval-Augmented Generation (RAG) framework designed to identify corroborating and refuting documents as evidence for scientific claim verification. CIBER addresses the inherent uncertainty in Large Language Models (LLMs) by evaluating response consistency across diverse interrogation probes. By focusing on the behavioral analysis of LLMs without requiring access to their internal information, CIBER is applicable to both white-box and black-box models. Furthermore, CIBER operates in an unsupervised manner, enabling easy generalization across various scientific domains. Comprehensive evaluations conducted using LLMs with varying levels of linguistic proficiency reveal CIBER's superior performance compared to conventional RAG approaches. These findings not only highlight the effectiveness of CIBER but also provide valuable insights for future advancements in LLM-based scientific claim verification.
Magnetic-Induced Force Noise in LISA Pathfinder Free-Falling Test Masses
(APS, 2025-02-18) Armano, M.; Audley, H.; Baird, J.; Binetruy, P.; Born, M.; Bortoluzzi, D.; Castelli, Eleonora; Cavalleri, A.; Cesarini, A.; Cruise, A. M.; Danzmann, K.; de Deus Silva, M.; Diepholz, I.; Dixon, G.; Dolesi, R.; Ferraioli, L.; Ferroni, V.; Fitzsimons, E. D.; Freschi, M.; Gesa, L.; Giardini, D.; Gibert, F.; Giusteri, R.; Grimani, C.; Grzymisch, J.; Harrison, I.; Hartig, M.-S.; Heinzel, G.; Hewitson, M.; Hollington, D.; Hoyland, D.; Hueller, M.; Inchauspé, H.; Jennrich, O.; Jetzer, P.; Karnesis, N.; Kaune, B.; Korsakova, N.; Killow, C. J.; Liu, L.; Lobo, J. A.; López-Zaragoza, J. P.; Maarschalkerweerd, R.; Mance, D.; Martín, V.; Martin-Polo, L.; Martin-Porqueras, F.; Martino, J.; McNamara, P. W.; Mendes, J.; Mendes, L.; Meshksar, N.; Nofrarias, M.; Paczkowski, S.; Perreur-Lloyd, M.; Petiteau, A.; Pivato, P.; Plagnol, E.; Ramos-Castro, J.; Reiche, J.; Rivas, F.; Robertson, D. I.; Russano, G.; Sala, L.; Serrano, D.; Slutsky, J.; Sopuerta, C. F.; Sumner, T.; Texier, D.; Thorpe, J. I.; Vetrugno, D.; Vitale, S.; Wanner, G.; Ward, H.; Wass, P. J.; Weber, W. J.; Wissel, L.; Wittchen, A.; Zweifel, P.
LISA Pathfinder was a mission designed to test key technologies required for gravitational wave detection in space. Magnetically driven forces play a key role in the instrument sensitivity in the low-frequency regime, which corresponds to the measurement band of interest for future space-borne gravitational wave observatories. Magnetically induced forces couple to the test mass motion, introducing a contribution to the relative acceleration noise between the free-falling test masses. In this Letter we present the first complete estimate of this term of the instrument performance model.
Key Governance Practices That Facilitate the Use of Remote Sensing Information for Wildfire Management: A Case Study in Spain
(MDPI, 2025-2-14) Prados, Ana; Allen, Mackenzie
We present results from a comprehensive analysis on the use of Earth Observations (EO) in Spain for wildfire risk management. Our findings are based on interviews with scientists, firefighters, forest engineers, and other professionals from government and private sector organizations in nine autonomous regions in Spain. Our aim is to identify the key governance practices facilitating or hindering the use of remote sensing (RS) information and to provide recommendations for improving their integration into landscape management and fire suppression activities to reduce wildfire risk. We share several case studies detailing activities and institutional arrangements facilitating the translation of satellite science and research into decision-making environments, with a focus on how this knowledge flows among the various stakeholder categories. Among the barriers faced by fire management teams in Spain, we identified institutional silos, lack of technical skills in satellite data processing and analysis, and the evolving acceptance of satellite data by decision makers.
Introduction to the Special Issue on Large Language Models, Conversational Systems, and Generative AI in Health - Part 1
(ACM, 2025-03-20) Zhou, Jiayu; Gaur, Manas; Rahmani, Amir M.; Chandra Guntuku, Sharath; Jiang, Xiaofan (Fred); Naumann, Tristan
Dialogue systems are designed to offer human users social support or functional services through natural language interactions. Traditional conversation research has put significant emphasis on a system’s response-ability, including its capacity to understand dialogue context and generate appropriate responses. However, the key element of proactive behavior—a crucial aspect of intelligent conversations—is often overlooked in these studies. Proactivity empowers conversational agents to lead conversations towards achieving pre-defined targets or fulfilling specific goals on the system side. Proactive dialogue systems are equipped with advanced techniques to handle complex tasks, requiring strategic and motivational interactions, thus representing a significant step towards artificial general intelligence. Motivated by the necessity and challenges of building proactive dialogue systems, we provide a comprehensive review of various prominent problems and advanced designs for implementing proactivity into different types of dialogue systems, including open-domain dialogues, task-oriented dialogues, and information-seeking dialogues. We also discuss real-world challenges that require further research attention to meet application needs in the future, such as proactivity in dialogue systems that are based on large language models, proactivity in hybrid dialogues, evaluation protocols and ethical considerations for proactive dialogue systems. By providing a quick access and overall picture of the proactive dialogue systems domain, we aim to inspire new research directions and stimulate further advancements towards achieving the next level of conversational AI capabilities, paving the way for more dynamic and intelligent interactions within various application domains.
Introduction to Correlation and Regression Analysis
(SAS Institute, 2008) Stockwell, Ian
SAS® has many tools that can be used for data analysis. From Freqs and Means to Tabulates and Univariates, SAS can present a synopsis of data values relatively easily. However, there is a difference between what the data are, and what the data mean. In order to take this next step, I would like to go beyond the basics and introduce correlation and hypothesis testing using regression models. A brief statistical background will be included, along with coding examples for correlation and linear regression.
Abolishing Poverty: Toward Pluriverse Futures and Politics
(University of Georgia Press, 2023) Lawson, Victoria; Elwood, Sarah; Mendoza, Yolanda González; Reddy, Chandan
Abolishing Poverty argues for a project of relationality that refuses the whiteness of liberal poverty studies and instead centers critiques of the poverty relation and political futures disavowed under liberal governance. In disrupting poverty thinking, the author collective opens space for diverse frameworks for understanding impoverishment and articulating antiracist knowledges and political visions. The book explores new infrastructures of possibilities and political solidarities rooted in accountable relations to each other and from flights to the future that animate diverse communities.This book is boundary and genre crossing, with broad appeal to scholars of such disciplines as human geography, ethnic studies, decolonial theory, and feminist studies. As a volume, the work is unique in its primary field of human geography in the form of its making, its collective authorship, and its investigation of politics that abolish poverty thinking and engage in activism against the poverty relation produced through settler colonialism, heteropatriarchy, white supremacy, and capitalist exploitation.
Integrating Frequency-Domain Representations with Low-Rank Adaptation in Vision-Language Models
(2025-03-08) Khan, Md Azim; Gangopadhyay, Aryya; Wang, Jianwu; Erbacher, Robert F.
Situational awareness applications rely heavily on real-time processing of visual and textual data to provide actionable insights. Vision language models (VLMs) have become essential tools for interpreting complex environments by connecting visual inputs with natural language descriptions. However, these models often face computational challenges, especially when required to perform efficiently in real environments. This research presents a novel vision language model (VLM) framework that leverages frequency domain transformations and low-rank adaptation (LoRA) to enhance feature extraction, scalability, and efficiency. Unlike traditional VLMs, which rely solely on spatial-domain representations, our approach incorporates Discrete Fourier Transform (DFT) based low-rank features while retaining pretrained spatial weights, enabling robust performance in noisy or low visibility scenarios. We evaluated the proposed model on caption generation and Visual Question Answering (VQA) tasks using benchmark datasets with varying levels of Gaussian noise. Quantitative results demonstrate that our model achieves evaluation metrics comparable to state-of-the-art VLMs, such as CLIP ViT-L/14 and SigLIP. Qualitative analysis further reveals that our model provides more detailed and contextually relevant responses, particularly for real-world images captured by a RealSense camera mounted on an Unmanned Ground Vehicle (UGV).
Information Theory of Composite Sequence Motifs: Mutational and Biophysical Determinants of Complex Molecular Recognition
(2024-11-15) Mascolo, Elia; Erill, Ivan
The recognition of nucleotide sequence patterns is a fundamental biological process that controls the start sites of replication, transcription and translation, as well as transcriptional and translational regulation. Foundational work on the evolution of biological information showed that the amount of information encoded in the target nucleotide sequence patterns, a quantity named Rsequence, evolves by natural selection to match a predictable quantity called Rfrequency. In this work, we propose a generalization of this canonical framework that can describe composite sequence motifs: motifs composed of a series of sequence patterns at some variable (not necessarily conserved) distance from each other. We find that some information can be encoded through the conservation of the distance between sequence patterns, a quantity we named Rspacer, and that - to be functional - biological systems require the sum of Rsequence and Rspacer to be constant. We empirically validate our mathematical results through evolutionary simulations. We apply this general framework to demonstrate that the pre-recruitment of regulatory complexes to target sites has intrinsic advantages over in situ recruitment in terms of energy dissipation and search efficiency, and that realistic values of protein flexibility co-evolve with the target composite motifs to match their spacer size variability. Lastly, we show that the relative advantage of encoding information in sequence patterns or in spacers depends on the balance between nucleotide substitutions and insertions/deletions, with known estimates for the rates of these mutation types favoring the evolution of composite motifs with highly conserved spacer length.
Information is primary and central to meaning-making
(University of Tartu Press, 2024-12-31) Cárdenas-García, Jaime F.
There is the misconception that the concept of information is not applicable to meaning-making in living beings. What is more generally believed is that Peircean semiosis provides a more robust framework to explain meaning-making. This involves the production, exchange, and interpretation of signs as the basis for meaning to an organism. Semiosis establishes a continuous and developing occurrence of triadic relations between a representamen (sign), an object (the other), and an interpretant as the organism engages with its umwelt, resulting in the appearance of meaning as a factor in its life. However, it is not clear that Peircean semiosis is the most fundamental process by which meaning-making may be instantiated in nature. Here we show that information defined by Gregory Bateson as ‘a difference which makes a difference’ can more fundamentally serve as a basis for meaning-making. Both its etymological origins and Bateson’s dictum naturalize the concept of information to identify its cybernetic dynamic motivated by constitutive absence, or the ability of an organism to find in its environment what it teleologically deems missing. This implies an ability to interpret its environmental surroundings. Furthermore, detecting a difference is the most fundamental of acts, revealing that information is the basis for meaning-making for an organism, allowing any level of intricacy in its interpretative capabilities. Indeed, Peircean semiosis is shown to be a special case of informatic meaning-making. In short, information provides a firm foundation for meaning-making for living beings.
In-depth analysis of LISA Pathfinder performance results: Time evolution, noise projection, physical models, and implications for LISA
(APS, 2024-08-21) LISA Pathfinder Collaboration; Armano, M.; Audley, H.; Baird, J.; Binetruy, P.; Born, M.; Bortoluzzi, D.; Castelli, Eleonora; Cavalleri, A.; Cesarini, A.; Chiavegato, V.; Cruise, A. M.; Dal Bosco, D.; Danzmann, K.; De Deus Silva, M.; Diepholz, I.; Dixon, G.; Dolesi, R.; Ferraioli, L.; Ferroni, V.; Fitzsimons, E. D.; Freschi, M.; Gesa, L.; Giardini, D.; Gibert, F.; Giusteri, R.; Grimani, C.; Grzymisch, J.; Harrison, I.; Hartig, M. S.; Heinzel, G.; Hewitson, M.; Hollington, D.; Hoyland, D.; Hueller, M.; Inchauspé, H.; Jennrich, O.; Jetzer, P.; Johlander, B.; Karnesis, N.; Kaune, B.; Korsakova, N.; Killow, C. J.; Lobo, J. A.; López-Zaragoza, J. P.; Maarschalkerweerd, R.; Mance, D.; Martín, V.; Martin-Polo, L.; Martin-Porqueras, F.; Martino, J.; McNamara, P. W.; Mendes, J.; Mendes, L.; Meshksar, N.; Nofrarias, M.; Paczkowski, S.; Perreur-Lloyd, M.; Petiteau, A.; Plagnol, E.; Ramos-Castro, J.; Reiche, J.; Rivas, F.; Robertson, D. I.; Russano, G.; Sala, L.; Slutsky, J.; Sopuerta, C. F.; Sumner, T.; Texier, D.; Thorpe, J. I.; Vetrugno, D.; Vitale, S.; Wanner, G.; Ward, H.; Wass, P.; Weber, W. J.; Wissel, L.; Wittchen, A.; Zanoni, C.; Zweifel, P.
We present an in-depth analysis of the LISA Pathfinder differential acceleration performance over the entire course of its science operations, spanning approximately 500 days. We find: (1) The evolution of the Brownian noise that dominates the acceleration amplitude spectral density (ASD), for frequencies 𝑓≳1 mHz, is consistent with the decaying pressure due to the outgassing of a single gaseous species. (2) Between 𝑓=36 μ⁢Hz and 1 mHz, the acceleration ASD shows a 1/𝑓 tail in excess of the Brownian noise of almost constant amplitude, with ≃20% fluctuations over a period of a few days, with no particular time pattern over the course of the mission. (3) At the lowest considered frequency of 𝑓=18 μ⁢Hz, the ASD significantly deviates from the 1/𝑓 behavior, because of temperature fluctuations that appear to modulate a quasistatic pressure gradient, sustained by the asymmetries of the outgassing pattern. We also present the results of a projection of the observed acceleration noise on the potential sources for which we had either a direct correlation measurement or a quantitative estimate from dedicated experiments. These sources account for approximately 40% of the noise power in the 1/𝑓 tail. Finally, we analyze the possible sources of the remaining unexplained fraction and identify the possible measures that may be taken to keep those under control in LISA.
Improvisational Computational Storytelling in Open Worlds
(Springer Nature, 2016-10-22) Martin, Lara J.; Harrison, Brent; Riedl, Mark O.
Improvisational storytelling involves one or more people interacting in real-time to create a story without advanced notice of topic or theme. Human improvisation occurs in an open-world that can be in any state and characters can perform any behaviors expressible through natural language. We propose the grand challenge of computational improvisational storytelling in open-world domains. The goal is to develop an intelligent agent that can sensibly co-create a story with one or more humans through natural language. We lay out some of the research challenges and propose two agent architectures that can provide the basis for exploring the research issues surrounding open-world human-agent interactions.

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