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At least 415 records · Page 23

PySAGES: flexible, advanced sampling methods accelerated with GPUs

Abstract Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of the relevant underlying free energy landscapes. In this sense, software that can be seamlessly adapted to a broad range of complex systems is essential. Building on past efforts to provide open-source community-supported software for advanced sampling, we introduce PySAGES, a Python implementation of the Software Suite for Advanced General Ensemble Simulations (SSAGES) that provides full GPU support for massively parallel applications of enhanced sampling methods such as adaptive biasing forces, harmonic bias, or forward flux sampling in the context of molecular dynamics simulations. By providing an intuitive interface that facilitates the management of a system’s configuration, the inclusion of new collective variables, and the implementation of sophisticated free energy-based sampling methods, the PySAGES library serves as a general platform for the development and implementation of emerging simulation techniques. The capabilities, core features, and computational performance of this tool are demonstrated with clear and concise examples pertaining to different classes of molecular systems. We anticipate that PySAGES will provide the scientific community with a robust and easily accessible platform to accelerate simulations, improve sampling, and enable facile estimation of free energies for a wide range of materials and processes.

Chemistry↗

Advances in Computational Approaches for Estimating Passive Permeability in Drug Discovery

Passive permeation of cellular membranes is a key feature of many therapeutics. The relevance of passive permeability spans all biological systems as they all employ biomembranes for compartmentalization. A variety of computational techniques are currently utilized and under active development to facilitate the characterization of passive permeability. These methods include lipophilicity relations, molecular dynamics simulations, and machine learning, which vary in accuracy, complexity, and computational cost. This review briefly introduces the underlying theories, such as the prominent inhomogeneous solubility diffusion model, and covers a number of recent applications. Various machine-learning applications, which have demonstrated good potential for high-volume, data-driven permeability predictions, are also discussed. Due to the confluence of novel computational methods and next-generation exascale computers, we anticipate an exciting future for computationally driven permeability predictions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanistic Insights into Dinitrogen Reduction to Ammonia in Light-Controlled Nanocrystal:Nitrogenase Complexes

Developing systems that can efficiently capture photon energy and convert this energy into fuels and chemicals requires understanding how to assemble molecular components with diverse functions into complete systems possessing selectivity and efficiency in directing charge carriers to catalytic reactions. There are many challenges to achieving this goal. One promising approach is the development of hybrid systems that combine semiconductor nanocrystals (NCs) for light capture and enzymes as efficient catalysts. Such biohybrid systems capitalize on the tunable electronic and optical properties of NCs while leveraging the unmatched specificity and efficiency of enzymes in catalyzing chemical reactions, thereby offering opportunities to surpass the limitations of each component alone. Here, we focus on recent progress in developing a biohybrid system that combines CdS NCs for photon capture with the enzyme nitrogenase to accomplish light-driven dinitrogen (N 2 ) reduction to ammonia (NH 3 ). Integrating light-harvesting materials with biological catalysts requires a deep understanding of NC properties, protein stability, and electron transfer (ET), making it an inherently multidisciplinary problem. The reduction of N 2 to NH 3 is a challenging reaction, with a high demand in both agriculture and industrial chemical production. This reaction is intrinsically energy intensive, due to the need to activate the N≡N triple bond. The current standard industrial approach to N 2 reduction, the Haber−Bosch reaction, obtains the necessary energy input from fossil fuels, whereas biological systems capable of N 2 reduction utilize the hydrolysis of ATP as their energy source. Replacing these costly, energy-intensive inputs with renewable light energy represents a critical step toward sustainable NH 3 production. Recent progress has demonstrated that semiconductor CdS NCs can be coupled to the catalytic component of nitrogenase, the MoFe protein, to form a biohybrid CdS NC:MoFe protein complex, enabling light-driven N 2 reduction rather than energy input from fossil fuels or ATP. This illustrates how inorganic NCs can functionally replace the natural Fe protein partner, yielding a biohybrid catalyst that enables controlled electron delivery and provides not only light-driven NH 3 production but also new approaches for probing enzyme catalytic function. The CdS NC:MoFe protein biohybrid system enables light-initiated electron delivery at ambient temperature, as well as temperatures below freezing, allowing for stabilization and spectroscopic characterization of key reaction intermediates. These findings highlight how photochemical biohybrids can serve as both functional catalysts and mechanistic probes. Beyond studies of the nitrogenase mechanism, studies of the CdS NC:MoFe system reveal how variables such as NC size, electrostatic binding interactions, and sacrificial electron donors (SEDs) govern complex stability, charge transfer efficiency, and catalytic performance. In addition, studies of nitrogenase and the high activation barrier for N 2 reduction are enabling investigations of new and interesting questions regarding the properties and limitations of NC biocatalysis. In this Account, we describe the key features of CdS NC:MoFe protein biohybrids and the parameters for optimal light-driven N 2 reduction, and how controlling ET with light illuminates the path to new insights into the nitrogenase mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crystal structure of Campylobacter jejuni lipoprotein Cj1090c

In Gram-negative bacteria, lipopolysaccharide (LPS) is an essential component of the asymmetric outer membrane (OM). LptE is an OM lipoprotein that forms a complex with the β-barrel OM protein, LptD. Incorporation of LPS into the OM outer leaflet is essential for bacterial viability, and mediated by the LptD/E complex. The genome of Campylobacter jejuni, a major foodborne pathogen, contains over 20 putative lipoproteins including Cj1090c. Here, we report the crystal structure of Cj1090c at 2.4 Å resolution, revealing structural evidence for LptE in C. jejuni. The analysis of this crystal structure, along with the genomic context, allows us to propose the C. jejuni LPS transport system for the first time, and also permits for discussion of the features of the LptD/E complex of C. jejuni.

59 BASIC BIOLOGICAL SCIENCES↗

Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar K D

Fluorogenic RNA aptamer tags with high affinity enable RNA purification and imaging. The G-quadruplex (G4) based Mango (M) series of aptamers were selected to bind a thiazole orange based (TO1-Biotin) ligand. Using a chemical biology and reselection approach, we have produced a MII.2 aptamer–ligand complex with a remarkable set of properties: Its unprecedented K D of 45 pM, formaldehyde resistance (8% v/v), temperature stability and ligand photo-recycling properties are all unusual to find simultaneously within a small RNA tag. Crystal structures demonstrate how MII.2, which differs from MII by a single A23U mutation, and modification of the TO1-Biotin ligand to TO1-6A-Biotin achieves these results. MII binds TO1-Biotin heterogeneously via a G4 surface that is surrounded by a stadium of five adenosines. Breaking this pseudo-rotational symmetry results in a highly cooperative and homogeneous ligand binding pocket: A22 of the G4 stadium stacks on the G4 binding surface while the TO1-6A-Biotin ligand completely fills the remaining three quadrants of the G4 ligand binding face. Similar optimization attempts with MIII.1, which already binds TO1-Biotin in a homogeneous manner, did not produce such marked improvements. We use the novel features of the MII.2 complex to demonstrate a powerful optically-based RNA purification system.

59 BASIC BIOLOGICAL SCIENCES↗

Transport and Assembly of Magnetic Surface Rotors**

This minireview focuses on recent advances with surface magnetic rotors, namely field-responsive spherical or anisotropic microparticles that translate close to, or are embedded in a confining surface. The application of external magnetic modulations allows these microscopic wheels to be remotely spun and steered while also tuning their interactions and inducing assembly from a collection of disordered, moving units. With optical microscopy one can observe and characterize the complex collective phenomena that emerge in dissipative colloidal systems driven far from equilibrium by external fields. From a technological point of view, magnetic surface rotors envisage implementation into microfluidic devices, and can be used for drug delivery, mixing as well as a model system for biological active matter.

36 MATERIALS SCIENCE↗

The Interaction of Global Biochemical Cycles

The global biosphere in an exceedingly complex system. To gain an understanding of its structure and dynamic features, it is necessary not only to increase the knowledge about the detailed processes but also to develop models of how global interactions take place. Attempts to analyze the detailed physical, chemical and biological processes in this context need to be guided by an advancement of understanding of the latter. It is necessary to develop a strategy of data gathering that severs both these purposes simultaneously. The following papers deal with critical aspects in the global cycles of carbon, nitrogen, phosphorus and sulfur in details as well as the cycle of water and the flow of energy in the Earth's environment. The objective is to set partly the foundation for the development of mathematical models that allow exploration of the coupled dynamics of the global cycles of carbon, nitrogen, phosphorus, sulfur, as well as energy and water flux.

Moore, B., III↗

The case for planetary sample return missions. 2. History of Mars

Principal science goals for exploration of Mars are to establish the chemical, isotopic, and physical state of Martian material, the nature of major surface-forming processes and their time scales, and the past and present biological potential of the planet. Many of those goals can only be met by detailed analyses of atmospheric gases and carefully selected samples of fresh rocks, weathered rocks, soils, sediments, and ices. The high-fidelity mineral separations, complex chemical treatments, and ultrasensitive instrument systems required for key measurements, as well as the need to adapt analytical strategies to unanticipated results, point to Earth-based laboratory analyses on returned Martian samples as the best means for meeting the stated objectives.

NASA Center ARC↗

Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem

Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The current study unveiled the core microbial methanogenic metabolisms in anaerobic vessel ecosystems by applying combined genome-centric metagenomics and metatranscriptomics. Here, we demonstrate that an enriched natural system, fueled only with acetate, could support a bacteria-dominated microbiota employing a multi-trophic methanogenic process. Moreover, significant changes, in terms of microbial structure and function, were recorded after the system was supplemented with additional H 2 . Methanosarcina thermophila, the predominant methanogen prior to H 2 addition, simultaneously performed acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. The methanogenic pattern changed after the addition of H 2 , which immediately stimulated Methanomicrobia-activity and was followed by a slow enrichment of Methanobacteria members. Interestingly, the essential genes involved in the Wood-Ljungdahl pathway were not expressed in bacterial members. The high expression of a glycine cleavage system indicated the activation of alternative metabolic pathways for acetate metabolism, which were reconstructed in the most abundant bacterial genomes. Moreover, as evidenced by predicted auxotrophies, we propose that specific microbes of the community were forming symbiotic relationships, thus reducing the biosynthetic burden of individual members. These results provide new information that will facilitate future microbial ecology studies of interspecies competition and symbiosis in methanogenic niches.

59 BASIC BIOLOGICAL SCIENCES↗

Intelligent Consequence Control by Aerial Reconnoiter Using Unmanned Systems

In a nuclear accident, or in the aftermath of an improvised nuclear device or radiological dispersal device detonation, radioactive materials may pose a severe health threat to individuals near the site of the incident. The Intelligent Consequence Control by Aerial Reconnoiter Using Unmanned Systems (ICARUS) does the dull, dirty, and dangerous (and, sometimes, deep) work of mapping and characterizing valuable information to enable a safe and appropriate response. ICARUS provides timely answers to the questions, “What is it?” “Where is it?”, and “How far does it extend?” Using commercial, off-the-shelf proven components, the integrated chemical, biological, radiological, nuclear, and explosives detection architecture for our drones provides a solution for collecting radiological, chemical, and optical information on developing complex situations, returning actionable data for determining if it is safe for further response efforts. ICARUS can determine and transmit the location, identity, and intensity of radionuclide contamination to a remote base station. It can deliver on the unexpected.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

North‐East Peri‐Tethyan Water Column Deoxygenation and Euxinia at the Paleocene Eocene Thermal Maximum

Abstract The Paleocene–Eocene Thermal Maximum (PETM) is associated with climatic change and biological turnover. It shares features with the Oceanic Anoxic Events (OAEs) of the Mesozoic, such as transient global warming and biogeochemical perturbations. However, the PETM experienced a more muted expansion of marine anoxia compared to the Mesozoic OAEs (especially OAE2), with geographically limited evidence for photic zone euxinia (PZE). We explore the extent and drivers of marine deoxygenation during the PETM using biomarkers for water column euxinia and anoxia as well as an intermediate complexity Earth system model (cGEnIE). These reveal that the water column in the North‐East Peri‐Tethys became anoxic, with euxinic conditions reaching the photic zone (PZE) during the PETM. Our model shows that euxinia developed due to a global increase in the ocean nutrient inventory with concomitant oxygen consumption, similar to findings for OAE2. The particularly strong regional response in the NE Peri‐Tethys appears to arise from a combination of global CO 2 ‐weathering forcing, regionally restricted circulation and upwelling of sulphidic thermocline waters. Unlike OAE2, anoxia and PZE do not become widespread in our PETM simulations, consistent with new and existing geochemical and biological proxy data. This globally muted response could result from reduced biogeochemical feedbacks to climate forcing relative to the mid‐Cretaceous climate. Our observations suggest that similar mechanisms operated in response to disparate Cenozoic (PETM) and Mesozoic (OAEs) transient global warming events, while also highlighting that background conditions are crucial in modulating the sensitivity of Earth's system to them.

Behrooz, L.↗

Assembly and Analysis of Cell-Scale Membrane Envelopes

The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms-a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An Activity-Based Sensing Approach to Monitor Nanomaterial-Promoted Changes in Labile Metal Pools in Living Systems

Metal-based nanoparticles are a promising class of materials for diagnosis and treatment of cancer and other diseases. However, mechanisms of action of these nanomedicines remain insufficiently understood due in large part to our limited understanding of the dynamic equilibria between solid metal nanoparticles and labile metal ions generated from these nanoparticles within complex biological milieus. Here, we apply activitybased sensing to directly identify and investigate the fate of labile copper pools with metal and oxidation state-specificity generated by anticancer copper nanomedicines. We found that treatment of cells with copper-releasing nanoparticles alter labile Cu(I)/Cu(II) ratios through an increase in labile Cu(II), while overall labile copper levels decrease. Labile copper release triggers compensatory responses in two major antioxidant pathways, glutathione (GSH) and nuclear factor erythroid 2-related factor 2 (NRF2), as well as in metal homeostasis to limit copper availability via regulation of copper export (ATP7B) and copper import (CTR1) proteins. These findings establish the value of activity-based sensing as a generalizable approach for labile metal imaging to help decipher molecular mechanisms of bioactive metal nanoparticles and guide the development of more effective nanomedicine diagnostics and therapies to target metal-dependent disease vulnerabilities.

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Biology Inspired Approach for Communal Behavior in Sensor Networks

Research in wireless sensor network technology has exploded in the last decade. Promises of complex and ubiquitous control of the physical environment by these networks open avenues for new kinds of science and business. Due to the small size and low cost of sensor devices, visionaries promise systems enabled by deployment of massive numbers of sensors working in concert. Although the reduction in size has been phenomenal it results in severe limitations on the computing, communicating, and power capabilities of these devices. Under these constraints, research efforts have concentrated on developing techniques for performing relatively simple tasks with minimal energy expense assuming some form of centralized control. Unfortunately, centralized control does not scale to massive size networks and execution of simple tasks in sparsely populated networks will not lead to the sophisticated applications predicted. These must be enabled by new techniques dependent on local and autonomous cooperation between sensors to effect global functions. As a step in that direction, in this work we detail a technique whereby a large population of sensors can attain a global goal using only local information and by making only local decisions without any form of centralized control.

Jones, Kennie H.↗

Unimodal Imaging of Monovalent Metal-Chelator Complexes and Lipids by MALDI Imaging Mass Spectrometry

Careful regulation of monovalent metal ions (M + ) is necessary to maintain a functional cellular system. Of these ions, appropriate sodium (Na + ) and potassium (K + ) concentrations are particularly integral for electrochemical signaling, as well as the secondary transport of nutrients and waste. Dysregulation of M + homeostasis can disrupt these mechanisms, potentially influencing the metabolism of downstream biomolecules such as lipids. Thus, the relationship between M + abundances and related biomolecular distributions must be elucidated to better understand the physiology of healthy and disordered tissues. Traditional techniques for imaging biological metal distributions include SIMS, LA-ICP-MS, and XRF; however, these capabilities are limited to elemental analysis or the analysis of molecular fragments and must be paired with other modalities to visualize distributions of more complex biomolecules within the same or similar samples. Conversely, matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful tool often used for mapping such biomolecular distributions, but current methods are unable to detect metals within tissue. This study illustrates a novel methodology that adds metal detection to the MALDI IMS repertoire through which the simultaneous detection of M + metals and lipids is achievable. Using a robotic sprayer for homogeneous application, on-tissue deposition of the chelator deferiprone (DEF) enables subsequent detection of the ionizable metal-chelator complex by MALDI without hindering lipid detection. Our work provides proof-of-concept data for the simultaneous detection of K + , Na + , and intact lipids using MALDI IMS.

59 BASIC BIOLOGICAL SCIENCES↗

Virus-Like Particles (VLPs) as a Platform for Hierarchical Compartmentalization

Hierarchically self-assembled structures are common in biology, but it is often challenging to design and fabricate synthetic analogs. The archetypal cell is defined by hierarchically organized multicompartmentalized structures with boundaries that delineate the interior from exterior environments and is an inspiration for complex functional materials. Here, we have demonstrated an approach to the design and construction of a nested protein cage system that can additionally incorporate the packing of other functional macromolecules and exhibit some of the features of a minimal synthetic cell-like material. We have demonstrated a strategy for controlled co-packaging of subcompartments, ferritin (Fn) cages, together with active cellobiose-hydrolyzing β-glycosidase enzyme macromolecules, CelB, inside the sequestered volume of the bacteriophage P22 capsid. Using controlled in vitro assembly, we were able to modulate the stoichiometry of Fn cages and CelB encapsulated inside the P22 to control the degree of compartmentalization. The co-encapsulated enzyme CelB showed catalytic activity even when packaged at high total macromolecular concentrations comparable to an intracellular environment. Here, this approach could be used as a model to create synthetic protein-based protocells that can confine smaller functionalized proto-organelles and additional macromolecules to support a range of biochemical reactions.

59 BASIC BIOLOGICAL SCIENCES↗

Closure of Regenerative Life Support Systems: Results of the Lunar-Mars Life Support Test Project

Future long duration human exploration missions away from Earth will require closed-loop regenerative life support systems to reduce launch mass, reduce dependency on resupply and increase the level of mission self sufficiency. Such systems may be based on the integration of biological and physiocochemical processes to produce potable water, breathable atmosphere and nutritious food from metabolic and other mission wastes. Over the period 1995 to 1998 a series of ground-based tests were conducted at the National Aeronautics and Space Administration, Johnson Space Center, to evaluate the performance of advanced closed-loop life support technologies with real human metabolic and hygiene loads. Named the Lunar-Mars Life Support Test Project (LMLSTP), four integrated human tests were conducted with increasing duration, complexity and closure. The first test, LMLSTP Phase I, was designed to demonstrate the ability of higher plants to revitalize cabin atmosphere. A single crew member spent 15 days within an atmospherically closed chamber containing 11.2 square meters of actively growing wheat. Atmospheric carbon dioxide and oxygen levels were maintained by control of the rate of photosynthesis through manipulation of light intensity or the availability of carbon dioxide and included integrated physicochemical systems. During the second and third tests, LMLSTP Phases II & IIa, four crew members spent 30 days and 60 days, respectively, in a larger sealed chamber. Advanced physicochemical life support hardware was used to regenerate the atmosphere and produce potable water from wastewater. Air revitalization was accomplished by using a molecular sieve and a Sabatier processor for carbon dioxide absorption and reduction, respectively, with oxygen generation performed by water hydrolysis. Production of potable water from wastewater included urine treatment (vapor compression distillation), primary treatment (ultrafiltration/reverse osmosis and multi-filtration) and post processing. For the Phase II test the water recovery rate ranged from 95 to 98%, depending on the processor. LMLSTP Phase III, the fourth test of the series, had a duration of 91 days and included four crew members. The test demonstrated an integration of physicochemical and biological technologies for air revitalization, water recovery and waste processing. Wheat supplemented the physicochemical air revitalization systems by providing approximately 25% of the oxygen required for the 4-person crew. The water recovery system included immobilized cell and trickling filter bioreactors for primary water treatment, reverse osmosis and air evaporation systems for secondary water treatment, followed by post processing. The 8 day initial supply of water was recycled through the chamber and crew 10 times over the course of the test. Grain from the wheat together with fresh lettuce from a small growth chamber within the crew chamber provided supplementation to the stored food system, but at a level less than 5% of the crew s caloric requirement. An incinerator was used to demonstrate mineralization of the crew s solid waste, with the combustion products (mainly carbon dioxide) returned to the wheat for conversion to oxygen.

Barta, Daniel↗

Crystallization of ApoA1 and ApoE4 Nanolipoprotein Particles and Initial XFEL-Based Structural Studies

Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via high-density lipoprotein (HDL) and low-density lipoprotein (LDL) maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics, and to develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.

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