Recent ucm_chem items

Magnetic field weakening carrier secondary recombination in/on amorphous Co0.07Fe0.93Ox co-catalysts to boost BiVO4/Co0.07Fe0.93Ox film photoanodes for solar water splitting

Wed, 3 Jun 2026 00:00:00 +0000

Magnetic field weakening carrier secondary recombination in/on amorphous Co0.07Fe0.93Ox co-catalysts to boost BiVO4/Co0.07Fe0.93Ox film photoanodes for solar water splitting

Wireless Bioelectronic Modulation of Membrane Potential in Glioblastoma Using Carbon Nanotube Porins

Tue, 5 May 2026 00:00:00 +0000

Disruption of membrane potential (V_mem) can activate pathways associated with cancer proliferation. Manipulating ion channels may therefore present an effective strategy for treating cancers that fail to respond to conventional therapies. One approach to target these channels is to manipulate the membrane charge, which involves the use of wireless bipolar electrodes such as carbon nanotube porins (CNTPs) inserted into cell membranes to modulate membrane charge and ionic flux. By utilizing membrane dyes, we observed alterations in V_mem induced by CNTPs and externally applied voltages. Analyses of cellular behaviors and processes indicated that V_mem is more receptive to stimuli in invasive cancers, while it leads to increased metabolism in less invasive cancers, with notable changes in the cell cycle occurring at approximately 48 h post-treatment in Glioblastoma (GB) cell lines. This work shows that CNTPs, in combination and with externally...

Deriving effective electrode–ion interactions from free-energy profiles at electrochemical interfaces

Wed, 15 Apr 2026 00:00:00 +0000

Understanding ion adsorption at electrified metal-electrolyte interfaces is essential for accurate modeling of electrochemical systems. Here, we systematically investigate the free energy profiles of Na+, Cl-, and F- ions at the Au(111)-water interface using enhanced sampling molecular dynamics with both classical force fields and machine-learned interatomic potentials (MLIPs). Our classical metadynamics results reveal a strong dependence of predicted ion adsorption on the Lennard-Jones parameters, highlighting that-without due care-standard mixing rules can lead to qualitatively incorrect descriptions of ion-metal interactions. We present a systematic methodology for tuning the cross term LJ parameters to control adsorption energetics in agreement with more accurate models. As a surrogate for an ab initio model, we employed the recently released Universal Models for Atoms MLIP, which validates classical trends and displays strong specific adsorption for chloride, weak adsorption...

Mechanism and reconstitution of circadian transcription in cyanobacteria

Wed, 25 Feb 2026 00:00:00 +0000

Circadian biological clocks evolved across kingdoms of life as an adaptation to predictable cycles of sunrise and sunset. In the cyanobacterium Synechococcuselongatus, a protein-based clock precisely controls when different genes are turned on and off during the 24-h day but the phasing mechanism remains unclear. Here we show the molecular basis of this regulation and reconstitute clock-controlled transcription in vitro using purified components. Biochemical and structural analyses revealed that the clock-regulated transcription factor RpaA can function as either an activator or a repressor of cyanobacterial RNA polymerase, depending on its binding position relative to core promoter elements. Leveraging the repressor mechanism, we developed a heterologous in vitro system driven by bacteriophage T7 RNA polymerase that sustains circadian transcription for multiple days. These findings explain how a single clock output generates opposite phases of gene expression and define the minimal...

Surface Crowding Effects in Molecular Recognition by Thrombin Binding Aptamers Conjugated to Gold Nanoparticles

Wed, 8 Oct 2025 00:00:00 +0000

This study addresses the challenge of determining how surface immobilization and crowding affect the binding affinity of DNA/RNA aptamers used in nanoparticle-based biosensors. Binding affinity is a critical determinant of biosensor performance. We employed isothermal titration calorimetry (ITC) to directly measure the binding interactions between thrombin and aptamer-functionalized gold nanoparticles. We found that binding affinity improves with increasing aptamer density due to entropic compensation, up to a critical threshold. Beyond this point, steric hindrance diminishes target binding. These findings demonstrate the utility of ITC in characterizing aptamer-target interactions and offer insights for optimizing the sensitivity, limit of detection, and dynamic range of aptamer-based biosensing platforms.

Prokaryotic Circadian Systems: Cyanobacteria and Beyond.

Wed, 8 Oct 2025 00:00:00 +0000

Circadian clocks are biological timekeeping mechanisms that synchronize physiology with the 24-h day-night cycle and provide temporal order to cellular events that recur daily as circadian rhythms. The cyanobacterium Synechococcus elongatus displays robust circadian rhythms and for more than 30 years has served as a model organism for uncovering the principles of prokaryotic timekeeping. The fundamental driving force behind these rhythms is a three-protein oscillator composed of KaiA, KaiB, and KaiC. In this review, we summarize current knowledge of the molecular mechanism of the Kai oscillator and focus on the dynamic conformational changes of these proteins over the period of a day. We also discuss how timing information is relayed from the oscillator to regulate downstream gene expression, thereby influencing cellular physiology. Furthermore, we explore circadian or circadian-like timing systems identified in other prokaryotes. We hope this review can inspire the discovery...

Reconstitution of circadian clock in synthetic cells reveals principles of timekeeping

Wed, 30 Jul 2025 00:00:00 +0000

The cyanobacterial circadian clock maintains remarkable precision and synchrony, even in cells with femtoliter volumes. Here, we reconstitute the KaiABC post-translational oscillator (PTO) in giant unilamellar vesicles (GUVs) to investigate underlying mechanisms of this fidelity. We show that our encapsulation methodology replicates native protein variability. With long-term, single-vesicle tracking of circadian rhythms using fluorescent KaiB and confocal microscopy, we find that oscillator fidelity decreases with lower protein levels and smaller vesicle sizes. KaiB membrane association, observed in cyanobacteria, was recapitulated in GUV membranes. A mathematical model incorporating protein stoichiometry limitations suggests that high expression of PTO components and associated regulators (CikA and SasA) buffers stochastic variations in protein levels. Additionally, while the transcription-translation feedback loop contributes minimally to overall fidelity, it is essential for...

Water, Solute, and Ion Transport in De Novo-Designed Membrane Protein Channels

Tue, 3 Jun 2025 00:00:00 +0000

Biological organisms engineer peptide sequences to fold into membrane pore proteins capable of performing a wide variety of transport functions. Synthetic de novo-designed membrane pores can mimic this approach to achieve a potentially even larger set of functions. Here we explore water, solute, and ion transport in three de novo designed β-barrel membrane channels in the 5-10 Å pore size range. We show that these proteins form passive membrane pores with high water transport efficiencies and size rejection characteristics consistent with the pore size encoded in the protein structure. Ion conductance and ion selectivity measurements also show trends consistent with the pore size, with the two larger pores showing weak cation selectivity. MD simulations of water and ion transport and solute size exclusion are consistent with the experimental trends and provide further insights into structure-function correlations in these membrane pores.

Vibrational spectroscopy of single molecules/single entities without plasmonic enhancement

Wed, 23 Apr 2025 00:00:00 +0000

Vibrational spectroscopy of single molecules/single entities without plasmonic enhancement

Unveiling the cold reality of metamorphic proteins

Wed, 26 Mar 2025 00:00:00 +0000

Metamorphic proteins switch reversibly between two differently folded states under a variety of environmental conditions. Their identification and prediction are gaining attention, but the fundamental physicochemical basis for fold switching remains poorly understood. In this Perspective article, we address this problem by surveying the landscape of well-characterized metamorphic proteins and noting that a significant fraction of them display temperature sensitivity. We then make the case that the dependence on temperature, in particular cold-denaturation effects, is likely to be an underlying property of many metamorphic proteins regardless of their ultimate triggering mechanisms, especially those with a single domain. The argument is supported by rigorous analysis of hydrophobic effects in each well-characterized metamorphic protein pair and a description of how these parameters relate to temperature. The conclusion discusses the relevance of these insights to a better understanding...

Protocols for in vitro reconstitution of the cyanobacterial circadian clock

Wed, 19 Mar 2025 00:00:00 +0000

Circadian clocks are intracellular systems that orchestrate metabolic processes in anticipation of sunrise and sunset by providing an internal representation of local time. Because the ~24-h metabolic rhythms they produce are important to health across diverse life forms there is growing interest in their mechanisms. However, mechanistic studies are challenging in vivo due to the complex, that is, poorly defined, milieu of live cells. Recently, we reconstituted the intact circadian clock of cyanobacteria in vitro. It oscillates autonomously and remains phase coherent for many days with a fluorescence-based readout that enables real-time observation of individual clock proteins and promoter DNA simultaneously under defined conditions without user intervention. We found that reproducibility of the reactions required strict adherence to the quality of each recombinant clock protein purified from Escherichia coli. Here, we provide protocols for preparing in vitro clock samples so...

Cannabidiol Toxicity Driven by Hydroxyquinone Formation

Fri, 28 Feb 2025 00:00:00 +0000

Oxidative byproducts of cannabidiol (CBD) are known to be cytotoxic. However, CBD susceptibility to oxidation and resulting toxicity dissolved in two common solvents, ethanol (EtOH) and dimethyl sulfoxide (DMSO), is seldom discussed. Furthermore, CBD products contain a wide range of concentrations, making it challenging to link general health risks associated with CBD cytotoxicity. Here, we report on the effect of CBD and CBD analogues dissolved in EtOH or DMSO at various concentrations. The cells used in these studies were human umbilical vascular endothelial cells (HUVECs). Our findings show significant CBD oxidation to cannabidiol-quinone (CBD-Q) and subsequent cytotoxicity, occurring at 10 μM concentration, regardless of the solution delivery vehicle. Moreover, a new analogue of CBD, cannabidiol-diacetate (CBD-DA), exhibits significantly more stability and reduced toxicity compared with CBD or CBD-Q, respectively. This knowledge is important for determining concentration-dependent...

A Contactless Method for Measuring the Redox Potentials of Metal Nanoparticles

Wed, 8 Jan 2025 00:00:00 +0000

The standard redox potentials of metal nanoparticles are important for understanding their chemical properties. Traditionally, these redox potentials are measured by using voltammetry. Although voltammetry is fast and cost-effective, loading or landing the nanoparticles on electrodes alters their electrochemical properties, posing a challenge for accurately determining their intrinsic redox potentials. Here, a contactless method was developed utilizing chemical assays and the Nernst equation to measure the standard reduction potentials of gold nanoparticles in their colloidal state. To showcase the versatility and accuracy of this Nernstian approach, the reduction potentials were measured for a size range of 5.0-73 nm, revealing their scaling law and dependence on the nanoparticle surface energy.

Nanoscale dynamics of Dynamin 1 helices reveals squeeze-twist deformation mode critical for membrane fission.

Sat, 14 Dec 2024 00:00:00 +0000

Dynamin 1 (Dyn1) GTPase, a principal driver of membrane fission during synaptic endocytosis, self-assembles into short mechanoactive helices cleaving the necks of endocytic vesicles. While structural information about Dyn1 helix is abundant, little is known about the nanoscale dynamics of the helical scaffolding at the moment of fission, complicating mechanistic understanding of Dyn1 action. To address the role of the helix dynamics in fission, we used High-Speed Atomic Force Microscopy (HS-AFM) and fluorescence microscopy to track and compare the spatiotemporal characteristics of the helices formed by wild-type Dyn1 and its K44A mutant impaired in GTP hydrolysis on minimal lipid membrane templates. In the absence of nucleotide, membrane-bound WTDyn1 and K44ADyn1 self-assembled into tubular protein scaffolding of similar diameter encaging the lipid bilayer. In both cases, the GTP addition caused scaffold constriction coupled with formation of 20 to 30 nm nanogaps in the protein...

Intrinsically disordered regions are poised to act as sensors of cellular chemistry

Mon, 9 Dec 2024 00:00:00 +0000

Intrinsically disordered proteins and protein regions (IDRs) are abundant in eukaryotic proteomes and play a wide variety of essential roles. Instead of folding into a stable structure, IDRs exist in an ensemble of interconverting conformations whose structure is biased by sequence-dependent interactions. The absence of a stable 3D structure, combined with high solvent accessibility, means that IDR conformational biases are inherently sensitive to changes in their environment. Here, we argue that IDRs are ideally poised to act as sensors and actuators of cellular physicochemistry. We review the physical principles that underlie IDR sensitivity, the molecular mechanisms that translate this sensitivity to function, and recent studies where environmental sensing by IDRs may play a key role in their downstream function.

Simulating Real-Time Molecular Electron Dynamics Efficiently Using the Time-Dependent Density Matrix Renormalization Group

Fri, 6 Dec 2024 00:00:00 +0000

Compared to ground-state electronic structure optimizations, accurate simulations of molecular real-time electron dynamics are usually much more difficult to perform. To simulate electron dynamics, the time-dependent density matrix renormalization group (TDDMRG) has been shown to offer an attractive compromise between accuracy and cost. However, many simulation parameters significantly affect the quality and efficiency of a TDDMRG simulation. So far, it is unclear whether common wisdom from ground-state DMRG carries over to the TDDMRG, and a guideline on how to choose these parameters is missing. Here, in order to establish such a guideline, we investigate the convergence behavior of the main TDDMRG simulation parameters, such as time integrator, the choice of orbitals, and the choice of matrix-product-state representation for complex-valued nonsinglet states. In addition, we propose a method to select orbitals that are tailored to optimize the dynamics. Lastly, we showcase the...

Disordered proteins interact with the chemical environment to tune their protective function during drying

Thu, 5 Dec 2024 00:00:00 +0000

The conformational ensemble and function of intrinsically disordered proteins (IDPs) are sensitive to their solution environment. The inherent malleability of disordered proteins, combined with the exposure of their residues, accounts for this sensitivity. One context in which IDPs play important roles that are concomitant with massive changes to the intracellular environment is during desiccation (extreme drying). The ability of organisms to survive desiccation has long been linked to the accumulation of high levels of cosolutes such as trehalose or sucrose as well as the enrichment of IDPs, such as late embryogenesis abundant (LEA) proteins or cytoplasmic abundant heat-soluble (CAHS) proteins. Despite knowing that IDPs play important roles and are co-enriched alongside endogenous, species-specific cosolutes during desiccation, little is known mechanistically about how IDP-cosolute interactions influence desiccation tolerance. Here, we test the notion that the protective function...

Implementation of time-dependent Hartree–Fock in real space

Thu, 21 Nov 2024 00:00:00 +0000

Abstract: Time-dependent Hartree–Fock (TDHF) is one of the fundamental post-Hartree–Fock (HF) methods to describe excited states. In its Tamm-Dancoff form, equivalent to Configuration Interaction Singles, it is still widely used and particularly applicable to big molecules where more accurate methods may be unfeasibly expensive. However, it is rarely implemented in real space, mostly because of the expensive nature of the exact-exchange potential in real space. Compared to widely used Gaussian-type orbitals (GTO) basis sets, real space often offers easier implementation of equations and more systematic convergence of Rydberg states, as well as favorable scaling, effective domain parallelization, flexible boundary conditions, and ability to treat model systems. We implemented TDHF in the Octopus real-space code as a step toward linear-response hybrid time-dependent density-functional theory (TDDFT), other post-HF methods, and ensemble density-functional theory...

CT584 Is Not a Protective Vaccine Antigen against Respiratory Chlamydial Challenge in Mice

Sat, 16 Nov 2024 00:00:00 +0000

Background:Chlamydia trachomatis is the most prevalent bacterial sexually transmitted pathogen in humans worldwide. Since chlamydial infection is largely asymptomatic with the potential for serious complications, a preventative vaccine is likely the most viable long-term answer to this public health threat. Cell-free protein synthesis (CFPS) utilizes the cellular protein manufacturing machinery decoupled from the requirement for maintaining cellular viability, offering the potential for flexible, rapid, and decentralized production of recombinant protein vaccine antigens. Methods: Here, we use CFPS to produce the full-length putative chlamydial type three secretion system (T3SS) needle-tip protein, CT584, for evaluation as a vaccine antigen in mouse models. High-speed atomic force microscopy (HS-AFM) (RIBM, Tsukuba, Japan) imaging and computer simulations confirm that CFPS-produced CT584 retains a native-like structure prior to immunization. Female mice were...

Evaluation in mice of cell-free produced CT584 as a Chlamydia vaccine antigen

Wed, 6 Nov 2024 00:00:00 +0000

Chlamydia trachomatis is the most prevalent bacterial sexually transmitted pathogen worldwide. Since chlamydial infection is largely asymptomatic with the potential for serious complications, a preventative vaccine is likely the most viable long-term answer to this public health threat. Cell-free protein synthesis (CFPS) utilizes the cellular protein manufacturing machinery decoupled from the requirement for maintaining cellular viability, offering the potential for flexible, rapid, and de-centralized production of recombinant protein vaccine antigens. Here, we use CFPS to produce the putative chlamydial type three secretion system (T3SS) needle-tip protein, CT584, for use as a vaccine antigen in mouse models. High-speed atomic force microscopy (HS-AFM) imaging and computer simulations confirm that CFPS-produced CT584 retains a native-like structure prior to immunization. Female mice were primed with CT584 adjuvanted with CpG-1826 intranasally (i.n.) or CpG-1826 + Montanide...

Ion transport and ultra-efficient osmotic power generation in boron nitride nanotube porins

Sat, 21 Sep 2024 00:00:00 +0000

Nanotube porins form transmembrane nanomaterial-derived scaffolds that mimic the geometry and functionality of biological membrane channels. We report synthesis, transport properties, and osmotic energy harvesting performance of another member of the nanotube porin family: boron nitride nanotube porins (BNNTPs). Cryo-transmission electron microscopy imaging, liposome transport assays, and DNA translocation experiments show that BNNTPs reconstitute into lipid membranes to form functional channels of ~2-nm diameter. Ion transport studies reveal ion conductance characteristics of individual BNNTPs, which show an unusual C^1/4 scaling with ion concentration and pronounced pH sensitivity. Reversal potential measurements indicate that BNNTPs have strong cation selectivity at neutral pH, attributable to the high negative charge on the channel. BNNTPs also deliver very large power density up to 12 kW/m² in the osmotic gradient transport experiments at neutral...

From Precious to Earth-Abundant Metallic Nanoparticles: A Trend of Interband Transitions in Photocatalyzed Nitrobenzene Reduction

Thu, 12 Sep 2024 00:00:00 +0000

Metallic nanoparticles have been demonstrated to be versatile photocatalysts, as exemplified by those made from noble and precious metals. Transitioning from precious to earth-abundant metals for sustainable photocatalysis requires benchmarking their catalytic performance. In this work, we attempt to compare the photocatalytic activities of Au, Pd, and Co-B nanoparticles in the reduction of nitrobenzene by hydrazine. Despite their different morphologies and surface structures, Co-B nanoparticles offer the highest catalytic enhancement when comparing their reaction rates under irradiation to those under nonirradiation conditions. The trend of improved photocatalytic performance when transitioning from Au to Pd, and then to Co-B, can be explained by the nature of their d-band positions and corresponding hot carriers photogenerated from interband transitions.

Single molecule insights into interfacial molecular recognition for model electrochemical DNA biosensors

Wed, 11 Sep 2024 00:00:00 +0000

Electrochemical sensors that use surface-immobilized DNA to bind analytes and transduce the binding into electrochemical signals, have the potential for rapid, specific, and sensitive detection of bioanalytes via a compact and portable platform. However, accessing the structure of these surfaces/interfaces at the relevant spatial scale (<10 nm), which determines the interfacial interactions and ultimately sensing performance, remains an unsolved challenge. Here, we review studies that have used high resolution atomic force microscope imaging and spatial statistical analysis tools to understand crowding interactions between thiolated DNA probes immobilized on gold electrodes and how such interactions impact target binding. We also review related studies that attempt to control the nanoscale spatial arrangement of the immobilized recognition elements to optimize sensing performance. These efforts have led to new advances in understanding of the structure–function relationships...

One-Step Ligand-Exchange Method to Produce Quantum Dot–DNA Conjugates for DNA-Directed Self-Assembly

Wed, 11 Sep 2024 00:00:00 +0000

To address the current challenges in making bright, stable, and small DNA-functionalized quantum dots (QDs), we have developed a one-step ligand-exchange method to produce QD-DNA conjugates from commonly available hydrophobic QDs. We show that by systematically adjusting the reaction conditions such as ligand-to-nanoparticle molar ratio, pH, and solvent composition, stable and highly photoluminescent water-soluble QD-DNA conjugates with relatively high ligand loadings can be produced. Moreover, by site specifically binding these QD-DNA conjugates to a DNA origami template, we demonstrate that these bioconjugates have sufficient colloidal stability for DNA-directed self-assembly. Fluorescence quenching by an adjacent gold nanoparticle (AuNP) was demonstrated. Such QD-AuNP dimers may serve as biosensors with improved sensitivity and reproducibility. Moreover, our simple method can facilitate the assembly of QDs into more complex superlattices and discrete clusters that may enable...

Evaluation of outbreak persistence caused by multidrug-resistant and echinocandin-resistant Candida parapsilosis using multidimensional experimental and epidemiological approaches

Thu, 15 Aug 2024 00:00:00 +0000

Candida parapsilosis is known to cause severe and persistent outbreaks in clinical settings. Patients infected with multidrug-resistant C. parapsilosis (MDR Cp) isolates were identified in a large Turkish hospital from 2017-2020. We subsequently identified three additional patients infected with MDR Cp isolates in 2022 from the same hospital and two echinocandin-resistant (ECR) isolates from a single patient in another hospital. The increasing number of MDR and ECR isolates contradicts the general principle that the severe fitness cost associated with these phenotypes could prevent their dominance in clinical settings. Here, we employed a multidimensional approach to systematically assess the fitness costs of MDR and ECR C. parapsilosis isolates. Whole-genome sequencing revealed a novel MDR genotype infecting two patients in 2022. Despite severe in vitro defects, the levels and tolerances of the biofilms of our ECR and MDR isolates were generally comparable...

Approaching periodic systems in ensemble density functional theory via finite one-dimensional models

Sat, 3 Aug 2024 00:00:00 +0000

Ensemble density functional theory (EDFT) is a generalization of ground-state DFT, which is based on an exact formal theory of finite collections of a system’s ground and excited states. EDFT in various forms has been shown to improve the accuracy of calculated energy level differences in isolated model systems, atoms, and molecules, but it is not yet clear how EDFT could be used to calculate band gaps for periodic systems. We extend the application of EDFT toward periodic systems by estimating the thermodynamic limit with increasingly large finite one-dimensional ‘particle in a box’ systems, which approach the uniform electron gas (UEG). Using ensemble-generalized Hartree and local spin density approximation exchange-correlation functionals, we find that corrections go to zero in the infinite limit, as expected for a metallic system. However, there is a correction to the effective mass, with results comparable to other calculations on 1D, 2D, and 3D UEGs, which indicates promise...

Mechanism of DNA origami folding elucidated by mesoscopic simulations

Thu, 1 Aug 2024 00:00:00 +0000

Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design...

Formation of Linear Plasmonic Heterotrimers Using Nanoparticle Docking to DNA Origami Cages

Wed, 31 Jul 2024 00:00:00 +0000

The fabrication of complex assemblies with interesting collective properties from plasmonic nanoparticles (NPs) is often challenging. While DNA-directed self-assembly has emerged as one of the most promising approaches to forming such complex assemblies, the resulting structures tend to have large variability in gap sizes and shapes, as the DNA strands used to organize these particles are flexible, and the polydispersity of the NPs leads to variability in these critical structural features. Here, we use a new strategy termed docking to DNA origami cages (D-DOC) to organize spherical NPs into a linear heterotrimer with a precisely defined geometrical arrangement. Instead of binding NPs to the exterior of the DNA templates, D-DOC binds the NPs to either the interior or the opening of a 3D cage, which significantly reduces the variability of critical structural features by incorporating multiple diametrically arranged capture strands to tether NPs. Additionally, such a spatial arrangement...

Computation of the expectation value of the spin operator S^2 for the spin-flip Bethe–Salpeter equation

Sat, 22 Jun 2024 00:00:00 +0000

Spin-flip (SF) methods applied to excited-state approaches like the Bethe-Salpeter equation allow access to the excitation energies of open-shell systems, such as molecules and defects in solids. The eigenstates of these solutions, however, are generally not eigenstates of the spin operator Formula presented. Even for simple cases where the excitation vector is expected to be, for example, a triplet state, the value of ⟨Formula presented⟩ may be found to differ from 2.00; this difference is called ‘spin contamination’. The expectation values ⟨Formula presented⟩ must be computed for each excitation vector, to assist with the characterization of the particular excitation and to determine the amount of spin contamination of the state. Our aim is to provide for the first time in the SF methods literature a comprehensive resource on the derivation of the formulas for ⟨Formula presented⟩ as well as its computational implementation. After a brief discussion of the theory of the SF Bethe-Salpeter...

A substitutional quantum defect in WS2 discovered by high-throughput computational screening and fabricated by site-selective STM manipulation

Thu, 16 May 2024 00:00:00 +0000

Point defects in two-dimensional materials are of key interest for quantum information science. However, the parameter space of possible defects is immense, making the identification of high-performance quantum defects very challenging. Here, we perform high-throughput (HT) first-principles computational screening to search for promising quantum defects within WS2, which present localized levels in the band gap that can lead to bright optical transitions in the visible or telecom regime. Our computed database spans more than 700 charged defects formed through substitution on the tungsten or sulfur site. We found that sulfur substitutions enable the most promising quantum defects. We computationally identify the neutral cobalt substitution to sulfur (CoS0$${\rm{Co}}_{{{{{{{{\rm{S}}}}}}}}}^{0}$$) and fabricate it with scanning tunneling microscopy (STM). The CoS0$${\rm{Co}}_{{{{{{{{\rm{S}}}}}}}}}^{0}$$ electronic structure measured by STM agrees with first principles and showcases...

Size-dependent errors in real-time electron density propagation

Tue, 7 May 2024 00:00:00 +0000

Real-time (RT) electron density propagation with time-dependent density functional theory (TDDFT) or Hartree-Fock (TDHF) is one of the most popular methods to model the charge transfer in molecules and materials. However, both RT-TDHF and RT-TDDFT within the adiabatic approximation are known to produce inaccurate evolution of the electron density away from the ground state in model systems, leading to large errors in charge transfer and erroneous shifting of peaks in absorption spectra. Given the poor performance of these methods with small model systems and the widespread use of the methods with larger molecular and material systems, here we bridge the gap in our understanding of these methods and examine the size-dependence of errors in RT density propagation. We analyze the performance of RT density propagation for systems of increasing size during the application of a continuous resonant field to induce Rabi-like oscillations, during charge-transfer dynamics, and for peak...

Structural biases in disordered proteins are prevalent in the cell

Sat, 4 May 2024 00:00:00 +0000

Intrinsically disordered proteins and protein regions (IDPs) are prevalent in all proteomes and are essential to cellular function. Unlike folded proteins, IDPs exist in an ensemble of dissimilar conformations. Despite this structural plasticity, intramolecular interactions create sequence-specific structural biases that determine an IDP ensemble’s three-dimensional shape. Such structural biases can be key to IDP function and are often measured in vitro, but whether those biases are preserved inside the cell is unclear. Here we show that structural biases in IDP ensembles found in vitro are recapitulated inside human-derived cells. We further reveal that structural biases can change in a sequence-dependent manner due to changes in the intracellular milieu, subcellular localization, and intramolecular interactions with tethered well-folded domains. We propose that the structural sensitivity of IDP ensembles can be leveraged for biological function, can be the underlying cause of...

Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography

Mon, 15 Apr 2024 00:00:00 +0000

Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp¹⁷ ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated...

Labile assembly of a tardigrade protein induces biostasis

Thu, 11 Apr 2024 00:00:00 +0000

Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar to that of intermediate filament assembly. We show that in vitro, gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fibrillar networks during osmotic stress. Fibrillar networking of CAHS D improves survival of osmotically shocked cells. We observe two emergent properties...

Coupled cluster theory on modern heterogeneous supercomputers.

Tue, 5 Mar 2024 00:00:00 +0000

This study examines the computational challenges in elucidating intricate chemical systems, particularly through ab-initio methodologies. This work highlights the Divide-Expand-Consolidate (DEC) approach for coupled cluster (CC) theory-a linear-scaling, massively parallel framework-as a viable solution. Detailed scrutiny of the DEC framework reveals its extensive applicability for large chemical systems, yet it also acknowledges inherent limitations. To mitigate these constraints, the cluster perturbation theory is presented as an effective remedy. Attention is then directed towards the CPS (D-3) model, explicitly derived from a CC singles parent and a doubles auxiliary excitation space, for computing excitation energies. The reviewed new algorithms for the CPS (D-3) method efficiently capitalize on multiple nodes and graphical processing units, expediting heavy tensor contractions. As a result, CPS (D-3) emerges as a scalable, rapid, and precise solution for computing molecular...

Tandem manganese catalysis for the chemo-, regio-, and stereoselective hydroboration of terminal alkynes: in situ precatalyst activation as a key to enhanced chemoselectivity

Thu, 29 Feb 2024 00:00:00 +0000

The manganese(ii) complex [Mn(^iPrPNP)Cl₂] (^iPrPNP = 2,6-bis(diisopropylphosphinomethyl)pyridine) was found to catalyze the stereo- and regioselective hydroboration of terminal alkynes employing HBPin (pinacolborane). In the absence of in situ activators, mixtures of alkynylboronate and E-alkenylboronate esters were formed, whereas when NaHBEt₃ was employed as the in situ activator, E-alkenylboronate esters were exclusively accessed. Mechanistic studies revealed a tandem C-H borylation/semihydrogenation pathway accounting for the formation of the products. Stoichiometric reactions hint toward reaction of a Mn-H active species with the terminal alkyne as the catalyst entry pathway to the cycle, whereas reaction with HBPin led to catalyst deactivation.

The inner workings of an ancient biological clock

Thu, 25 Jan 2024 00:00:00 +0000

Circadian clocks evolved in diverse organisms as an adaptation to the daily swings in ambient light and temperature that derive from Earth's rotation. These timing systems, based on intracellular molecular oscillations, synchronize organisms' behavior and physiology with the 24-h environmental rhythm. The cyanobacterial clock serves as a special model for understanding circadian rhythms because it can be fully reconstituted in vitro. This review summarizes recent advances that leverage new biochemical, biophysical, and mathematical approaches to shed light on the molecular mechanisms of cyanobacterial Kai proteins that support the clock, and their homologues in other bacteria. Many questions remain in circadian biology, and the tools developed for the Kai system will bring us closer to the answers.

Solutal Marangoni effect determines bubble dynamics during electrocatalytic hydrogen evolution

Wed, 15 Nov 2023 00:00:00 +0000

Understanding and manipulating gas bubble evolution during electrochemical water splitting is a crucial strategy for optimizing the electrode/electrolyte/gas bubble interface. Here gas bubble dynamics are investigated during the hydrogen evolution reaction on a well-defined platinum microelectrode by varying the electrolyte composition. We find that the microbubble coalescence efficiency follows the Hofmeister series of anions in the electrolyte. This dependency yields very different types of H2 gas bubble evolution in different electrolytes, ranging from periodic detachment of a single H2 gas bubble in sulfuric acid to aperiodic detachment of small H2 gas bubbles in perchloric acid. Our results indicate that the solutal Marangoni convection, induced by the anion concentration gradient developing during the reaction, plays a critical role at practical current density conditions. The resulting Marangoni force on the H2 gas bubble and the bubble departure diameter therefore depend...

Structural Preferences Shape the Entropic Force of Disordered Protein Ensembles

Thu, 26 Oct 2023 00:00:00 +0000

Intrinsically disordered protein regions (IDRs) make up over 30% of the human proteome and exist in a dynamic conformational ensemble instead of a native, well-folded structure. Tethering IDRs to a surface (for example, the surface of a well-folded region of the same protein) can reduce the number of accessible conformations in these ensembles. This reduces the ensemble's conformational entropy, generating an effective entropic force that pulls away from the point of tethering. Recent experimental work has shown that this entropic force causes measurable, physiologically relevant changes to protein function. But how the magnitude of this force depends on IDR sequence remains unexplored. Here, we use all-atom simulations to analyze how structural preferences in IDR ensembles contribute to the entropic force they exert upon tethering. We show that sequence-encoded structural preferences play an important role in determining the magnitude of this force: compact, spherical ensembles...

Revisiting the Effect of the Air–Water Interface of Ultrasonically Atomized Water Microdroplets on H2O2 Formation

Thu, 12 Oct 2023 00:00:00 +0000

Studying chemical processes at the air-water interface is always challenging. A recent report claimed that H₂O₂ was formed spontaneously on the surface of condensed water microdroplets. However, a newer report concluded that the detected H₂O₂ in the previous report could originate in part from the water vapor source that involved ultrasonic atomization of liquid water. Here, this phenomenon is reinvestigated regarding the influence of ultrasonic cavitation, surface modification of droplets, and solutes in the bulk liquid on H₂O₂ production. When the droplet surfaces were modified by surfactants, H₂O₂ production did not change, whereas adding gases or inorganic compounds to the bulk solution caused significant changes in H₂O₂ production. These results confirm that H₂O₂ formation originates from cavitation in bulk solutions. It is concluded that the...

Real-time dynamics of carbon nanotube porins in supported lipid membranes visualized by high-speed atomic force microscopy

Wed, 11 Oct 2023 00:00:00 +0000

In-plane mobility of proteins in lipid membranes is one of the fundamental mechanisms supporting biological functionality. Here we use high-speed atomic force microscopy (HS-AFM) to show that a novel type of biomimetic channel-carbon nanotube porins (CNTPs)-is also laterally mobile in supported lipid membranes, mimicking biological protein behaviour. HS-AFM can capture real-time dynamics of CNTP motion in the supported lipid bilayer membrane, build long-term trajectories of the CNTP motion and determine the diffusion coefficients associated with this motion. Our analysis shows that diffusion coefficients of CNTPs fall into the same range as those of proteins in supported lipid membranes. CNTPs in HS-AFM experiments often exhibit 'directed' diffusion behaviour, which is common for proteins in live cell membranes.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.

Water-ion permselectivity of narrow-diameter carbon nanotubes

Tue, 10 Oct 2023 00:00:00 +0000

Carbon nanotube (CNT) pores, which mimic the structure of the aquaporin channels, support extremely high water transport rates that make them strong candidates for building artificial water channels and high-performance membranes. Here, we measure water and ion permeation through 0.8-nm-diameter CNT porins (CNTPs)-short CNT segments embedded in lipid membranes-under optimized experimental conditions. Measured activation energy of water transport through the CNTPs agrees with the barrier values typical for single-file water transport. Well-tempered metadynamics simulations of water transport in CNTPs also report similar activation energy values and provide molecular-scale details of the mechanism for water entry into these channels. CNTPs strongly reject chloride ions and show water-salt permselectivity values comparable to those of commercial desalination membranes.

Membrane fusion and drug delivery with carbon nanotube porins

Tue, 10 Oct 2023 00:00:00 +0000

Drug delivery mitigates toxic side effects and poor pharmacokinetics of life-saving therapeutics and enhances treatment efficacy. However, direct cytoplasmic delivery of drugs and vaccines into cells has remained out of reach. We find that liposomes studded with 0.8-nm-wide carbon nanotube porins (CNTPs) function as efficient vehicles for direct cytoplasmic drug delivery by facilitating fusion of lipid membranes and complete mixing of the membrane material and vesicle interior content. Fusion kinetics data and coarse-grained molecular dynamics simulations reveal an unusual mechanism where CNTP dimers tether the vesicles, pull the membranes into proximity, and then fuse their outer and inner leaflets. Liposomes containing CNTPs in their membranes and loaded with an anticancer drug, doxorubicin, were effective in delivering the drug to cancer cells, killing up to 90% of them. Our results open an avenue for designing efficient drug delivery carriers compatible with a wide range of...

Carbon nanotube porin diffusion in mixed composition supported lipid bilayers

Tue, 10 Oct 2023 00:00:00 +0000

Carbon nanotube porins (CNTPs), short pieces of carbon nanotubes capable of self-inserting into a lipid bilayer, represent a simplified model of biological membrane channels. We have used high-speed atomic force microscopy (HS-AFM) and all-atom molecular dynamics (MD) simulations to study the behavior of CNTPs in a mixed lipid membrane consisting of DOPC lipid with a variable percentage of DMPC lipid added to it. HS-AFM data reveal that the CNTPs undergo diffusive motion in the bilayer plane. Motion trajectories extracted from the HS-AFM movies indicate that CNTPs exhibit diffusion coefficient values broadly similar to values reported for membrane proteins in supported lipid bilayers. The data also indicate that increasing the percentage of DMPC leads to a marked slowing of CNTP diffusion. MD simulations reveal a CNTP-lipid assembly that diffuses in the membrane and show trends that are consistent with the experimental observations.

Comparing time-dependent density functional theory with many-body perturbation theory for semiconductors: Screened range-separated hybrids and the GW plus Bethe-Salpeter approach

Tue, 26 Sep 2023 00:00:00 +0000

We present band structure and optical absorption spectra obtained from density functional theory (DFT) and linear response time-dependent DFT (TDDFT) calculations using a screened range-separated hybrid (SRSH) functional, including spin-orbit coupling, for seven prototypical semiconductors. The results are compared to those obtained from highly converged many-body perturbation theory calculations using the GW approximation and the GW plus Bethe-Salpeter equation (GW-BSE) approaches. We use a single empirical parameter for our SRSH calculations, fit such that the SRSH band gap reproduces the GW band gap at the Γ point. We then find that ground-state generalized Kohn-Sham SRSH eigenvalues accurately reproduce the band structure obtained from GW calculations, typically to within 0.1–0.2 eV, and optical absorption spectra obtained using TDDFT with the SRSH functional agree well with those of GW-BSE, with a mean deviation of 0.03 and 0.11 eV for the location of the first and second...

Exchange-Driven Intermixing of Bulk and Topological Surface States by Chiral Excitons in Bi2Se3

Tue, 26 Sep 2023 00:00:00 +0000

Topological surface states (TSS) in the prototypical topological insulator (TI) Bi_{2}Se_{3} are frequently characterized using optical probes, but electron-hole interactions and their effect on surface localization and optical response of the TSS remain unexplored. Here, we use ab initio calculations to understand excitonic effects in the bulk and surface of Bi_{2}Se_{3}. We identify multiple series of chiral excitons that exhibit both bulk and TSS character, due to exchange-driven mixing. Our results address fundamental questions about the degree to which electron-hole interactions can relax the topological protection of surface states and dipole selection rules for circularly polarized light in TIs by elucidating the complex intermixture of bulk and surface states excited in optical measurements and their coupling to light.

Cooperative KaiA–KaiB–KaiC Interactions Affect KaiB/SasA Competition in the Circadian Clock of Cyanobacteria

Mon, 18 Sep 2023 00:00:00 +0000

The circadian oscillator of cyanobacteria is composed of only three proteins, KaiA, KaiB, and KaiC. Together, they generate an autonomous ~24-h biochemical rhythm of phosphorylation of KaiC. KaiA stimulates KaiC phosphorylation by binding to the so-called A-loops of KaiC, whereas KaiB sequesters KaiA in a KaiABC complex far away from the A-loops, thereby inducing KaiC dephosphorylation. The switch from KaiC phosphorylation to dephosphorylation is initiated by the formation of the KaiB-KaiC complex, which occurs upon phosphorylation of the S431 residues of KaiC. We show here that formation of the KaiB-KaiC complex is promoted by KaiA, suggesting cooperativity in the initiation of the dephosphorylation complex. In the KaiA-KaiB interaction, one monomeric subunit of KaiB likely binds to one face of a KaiA dimer, leaving the other face unoccupied. We also show that the A-loops of KaiC exist in a dynamic equilibrium between KaiA-accessible exposed and KaiA-inaccessible buried positions....

Photocatalysis of Metallic Nanoparticles: Interband vs Intraband Induced Mechanisms

Mon, 11 Sep 2023 00:00:00 +0000

Photocatalysis induced by localized surface plasmon resonance of metallic nanoparticles has been studied for more than a decade, but photocatalysis originating from direct interband excitations is still under-explored. The spectral overlap and the coupling of these two optical regimes also complicate the determination of hot carriers' energy states and eventually hinder the accurate assignment of their catalytic role in studied reactions. In this Featured Article, after reviewing previous studies, we suggest classifying the photoexcitation via intra- and interband transitions where the physical states of hot carriers are well-defined. Intraband transitions are featured by creating hot electrons above the Fermi level and suitable for reductive catalytic pathways, whereas interband transitions are featured by generating hot d-band holes below the Fermi level and better for oxidative catalytic pathways. Since the contribution of intra- and interband transitions are different in the...

A protein fold switch joins the circadian oscillator to clock output in cyanobacteria

Sat, 9 Sep 2023 00:00:00 +0000

Organisms are adapted to the relentless cycles of day and night, because they evolved timekeeping systems called circadian clocks, which regulate biological activities with ~24-hour rhythms. The clock of cyanobacteria is driven by a three-protein oscillator composed of KaiA, KaiB, and KaiC, which together generate a circadian rhythm of KaiC phosphorylation. We show that KaiB flips between two distinct three-dimensional folds, and its rare transition to an active state provides a time delay that is required to match the timing of the oscillator to that of Earth's rotation. Once KaiB switches folds, it binds phosphorylated KaiC and captures KaiA, which initiates a phase transition of the circadian cycle, and it regulates components of the clock-output pathway, which provides the link that joins the timekeeping and signaling functions of the oscillator.

Modern metal-catalyzed and organocatalytic methods for synthesis of coumarin derivatives: a review

Tue, 29 Aug 2023 00:00:00 +0000

Coumarin is an important pharmaceutical structural motif, abundantly found in numerous commonly used drugs. Compounds containing this core show a broad spectrum of medicinal properties and biological activities. The increasing importance and wide usages of coumarin derivatives have drawn attention to its synthetic methods, among which metal-catalyzed and organocatalytic methods have proved the most effective. Several metal-catalyzed and/or organocatalytic synthetic strategies for coumarin have been investigated and reported in recent decades. This review focuses on more recent reports on catalysis methods for synthesizing coumarin and coumarin-like structures (including light-mediated methods and nano-catalysts), exploring the mechanistic aspects, simplicity, efficiency, repeatability, and other advantages and disadvantages of these methods.

Osmotic Pressure Enables High-Yield Assembly of Giant Vesicles in Solutions of Physiological Ionic Strengths

Thu, 17 Aug 2023 00:00:00 +0000

Giant unilamellar vesicles (GUVs) are micrometer-scale minimal cellular mimics that are useful for bottom-up synthetic biology and drug delivery. Unlike assembly in low-salt solutions, assembly of GUVs in solutions with ionic concentrations of 100-150 mM Na/KCl (salty solutions) is challenging. Chemical compounds deposited on the substrate or incorporated into the lipid mixture could assist in the assembly of GUVs. Here, we investigate quantitatively the effects of temperature and chemical identity of six polymeric compounds and one small molecule compound on the molar yields of GUVs composed of three different lipid mixtures using high-resolution confocal microscopy and large data set image analysis. All the polymers moderately increased the yields of GUVs either at 22 or 37 °C, whereas the small molecule compound was ineffective. Low-gelling temperature agarose is the singular compound that consistently produces yields of GUVs of greater than 10%. We propose a free energy model...

Electrochemically Driven Hydrogen Atom Transfer Catalysis: A Tool for C(sp³)/Si-H Functionalization and Hydrofunctionalization of Alkenes.

Mon, 14 Aug 2023 00:00:00 +0000

Electrochemically driven hydrogen atom transfer (HAT) catalysis provides a complementary approach for the transformation of redox-inactive substrates that would be inaccessible to conventional electron transfer (ET) catalysis. Moreover, electrochemically driven HAT catalysis could promote organic transformations with either hydrogen atom abstraction or donation as the key step. It provides a versatile and effective tool for the direct functionalization of C(sp³)-H/Si-H bonds and the hydrofunctionalization of alkenes. Despite these attractive properties, electrochemically driven HAT catalysis has been largely overlooked due to the lack of understanding of both the catalytic mechanism and how catalyst selection should occur. In this Review, we give an overview of the HAT catalysis applications in the direct C(sp³)-H/Si-H functionalization and hydrofunctionalization of alkenes. The mechanistic pathways, physical properties of the HAT mediators, and state-of-the-art...

Experimental and Thermodynamic Viewpoints on Claims of a Spontaneous H2O2 Formation at the Air–Water Interface

Thu, 13 Jul 2023 00:00:00 +0000

Recent claims of the spontaneous H₂O₂ formation at the air-water interface of water microdroplets have sparked debates on its feasibility. New results from different research groups have provided more insight into these claims, but conclusive proofs are still far from realized. In this Perspective, thermodynamic viewpoints, potential experiments, and theoretical approaches are presented as references for future studies. We suggest that future work should seek for H₂ byproduct as indirect evidence to confirm the feasibility of this phenomenon. Examining potential energy surfaces for H₂O₂ formation reaction when moving from the bulk to the interface under the influence of the local electric fields is also critical to establish this phenomenon.

Coupling of distant ATPase domains in the circadian clock protein KaiC

Mon, 3 Jul 2023 00:00:00 +0000

The AAA+ family member KaiC is the central pacemaker for circadian rhythms in the cyanobacterium Synechococcus elongatus. Composed of two hexameric rings of adenosine triphosphatase (ATPase) domains with tightly coupled activities, KaiC undergoes a cycle of autophosphorylation and autodephosphorylation on its C-terminal (CII) domain that restricts binding of clock proteins on its N-terminal (CI) domain to the evening. Here, we use cryogenic-electron microscopy to investigate how daytime and nighttime states of CII regulate KaiB binding on CI. We find that the CII hexamer is destabilized during the day but takes on a rigidified C2-symmetric state at night, concomitant with ring-ring compression. Residues at the CI-CII interface are required for phospho-dependent KaiB association, coupling ATPase activity on CI to cooperative KaiB recruitment. Together, these studies clarify a key step in the regulation of cyanobacterial circadian rhythms by KaiC phosphorylation.

Electronic control of H+ current in a bioprotonic device with carbon nanotube porins

Wed, 28 Jun 2023 00:00:00 +0000

Hybrid biotic abiotic devices can be used to interface electronics with biological systems for novel therapies or to increase device functionality beyond silicon. Many strategies exist to merge the electronic and biological worlds, one dominated by electrons and holes as charge carriers, the other by ions. In the biological world, lipid bilayers and ion channels are essential to compartmentalize the cell machinery and regulate ionic fluxes across the cell membrane. Here, we demonstrate a bioelectronic device in which a lipid bilayer supported on H+-conducting Pd/PdHx contacts contains carbon nanotubes porin (CNTP) channels. This bioelectronic device uses CNTPs to control of H+ flow across the lipid bilayer with a voltage applied to the Pd/PdHx contacts. Potential applications of these devices include local pH sensing and control.

Author Correction: High permeability sub-nanometre sieve composite MoS2 membranes

Wed, 28 Jun 2023 00:00:00 +0000

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

High permeability sub-nanometre sieve composite MoS2 membranes

Wed, 28 Jun 2023 00:00:00 +0000

Two-dimensional membranes have gained enormous interest due to their potential to deliver precision filtration of species with performance that can challenge current desalination membrane platforms. Molybdenum disulfide (MoS2) laminar membranes have recently demonstrated superior stability in aqueous environment to their extensively-studied analogs graphene-based membranes; however, challenges such as low ion rejection for high salinity water, low water flux, and low stability over time delay their potential adoption as a viable technology. Here, we report composite laminate multilayer MoS2 membranes with stacked heterodimensional one- to two-layer-thick porous nanosheets and nanodisks. These membranes have a multimodal porous network structure with tunable surface charge, pore size, and interlayer spacing. In forward osmosis, our membranes reject more than 99% of salts at high salinities and, in reverse osmosis, small-molecule organic dyes and salts are efficiently filtered....

Control of the Hedgehog pathway by compartmentalized PKA in the primary cilium

Sat, 24 Jun 2023 00:00:00 +0000

The Hedgehog (Hh) signaling is one of the essential signaling pathways during embryogenesis and in adults. Hh signal transduction relies on primary cilium, a specialized cell surface organelle viewed as the hub of cell signaling. Protein kinase A (PKA) has been recognized as a potent negative regulator of the Hh pathway, raising the question of how such a ubiquitous kinase specifically regulates one signaling pathway. We reviewed recent genetic, molecular and biochemical studies that have advanced our mechanistic understanding of PKA’s role in Hh signaling in vertebrates, focusing on the compartmentalized PKA at the centrosome and in the primary cilium. We outlined the recently developed genetic and optical tools that can be harvested to study PKA activities during the course of Hh signal transduction.

Simulations of Subnanometer Scale Image Contrast in Atomic Force Microscopy of Self-Assembled Monolayers in Water

Wed, 7 Jun 2023 00:00:00 +0000

Achieving high-resolution images using dynamic atomic force microscopy (AFM) requires understanding how chemical and structural features of the surface affect image contrast. This understanding is particularly challenging when imaging samples in water. An initial step is to determine how well-characterized surface features interact with the AFM tip in wet environments. Here, we use molecular dynamics simulations of a model AFM tip apex oscillating in water above self-assembled monolayers (SAMs) with different chain lengths and functional groups. The amplitude response of the tip is characterized across a range of vertical distances and amplitude set points. Then relative image contrast is quantified as the difference of the amplitude response of the tip when it is positioned directly above a SAM functional group vs positioned between two functional groups. Differences in contrast between SAMs with different lengths and functional groups are explained in terms of the vertical deflection...

Cell-free production of a functional oligomeric form of a Chlamydia major outer-membrane protein (MOMP) for vaccine development

Fri, 12 May 2023 00:00:00 +0000

Chlamydia is a prevalent sexually transmitted disease that infects more than 100 million people worldwide. Although most individuals infected with Chlamydia trachomatis are initially asymptomatic, symptoms can arise if left undiagnosed. Long-term infection can result in debilitating conditions such as pelvic inflammatory disease, infertility, and blindness. Chlamydia infection, therefore, constitutes a significant public health threat, underscoring the need for a Chlamydia-specific vaccine. Chlamydia strains express a major outer-membrane protein (MOMP) that has been shown to be an effective vaccine antigen. However, approaches to produce a functional recombinant MOMP protein for vaccine development are limited by poor solubility, low yield, and protein misfolding. Here, we used an Escherichia coli-based cell-free system to express a MOMP protein from the mouse-specific species Chlamydia muridarum (MoPn-MOMP or mMOMP). The codon-optimized...

Mechanistic Basis for Regioselection and Regiodivergence in Nickel-Catalyzed Reductive Couplings

Tue, 18 Apr 2023 00:00:00 +0000

The control of regiochemistry is a considerable challenge in the development of a wide array of catalytic processes. Simple π-components such as alkenes, alkynes, 1,3-dienes, and allenes are among the many classes of substrates that present complexities in regioselective catalysis. Considering an internal alkyne as a representative example, when steric and electronic differences between the two substituents are minimal, differentiating among the two termini of the alkyne presents a great challenge. In cases where the differences between the alkyne substituents are substantial, overcoming those biases to access the regioisomer opposite that favored by substrate biases often presents an even greater challenge. Nickel-catalyzed reductive couplings of unsymmetrical π-components make up a group of reactions where control of regiochemistry presents a challenging but important objective. In the course of our studies of aldehyde-alkyne reductive couplings, complementary solutions to challenges...

Fluids and Electrolytes under Confinement in Single-Digit Nanopores

Sun, 16 Apr 2023 00:00:00 +0000

Confined fluids and electrolyte solutions in nanopores exhibit rich and surprising physics and chemistry that impact the mass transport and energy efficiency in many important natural systems and industrial applications. Existing theories often fail to predict the exotic effects observed in the narrowest of such pores, called single-digit nanopores (SDNs), which have diameters or conduit widths of less than 10 nm, and have only recently become accessible for experimental measurements. What SDNs reveal has been surprising, including a rapidly increasing number of examples such as extraordinarily fast water transport, distorted fluid-phase boundaries, strong ion-correlation and quantum effects, and dielectric anomalies that are not observed in larger pores. Exploiting these effects presents myriad opportunities in both basic and applied research that stand to impact a host of new technologies at the water-energy nexus, from new membranes for precise separations and water purification...

Synchronization of the circadian clock to the environment tracked in real time

Wed, 29 Mar 2023 00:00:00 +0000

The circadian system of the cyanobacterium Synechococcus elongatus PCC 7942 relies on a three-protein nanomachine (KaiA, KaiB, and KaiC) that undergoes an oscillatory phosphorylation cycle with a period of ~24 h. This core oscillator can be reconstituted in vitro and is used to study the molecular mechanisms of circadian timekeeping and entrainment. Previous studies showed that two key metabolic changes that occur in cells during the transition into darkness, changes in the ATP/ADP ratio and redox status of the quinone pool, are cues that entrain the circadian clock. By changing the ATP/ADP ratio or adding oxidized quinone, one can shift the phase of the phosphorylation cycle of the core oscillator in vitro. However, the in vitro oscillator cannot explain gene expression patterns because the simple mixture lacks the output components that connect the clock to genes. Recently, a high-throughput in vitro system termed the in vitro clock (IVC) that...

Good Vibrations: Calculating Excited-State Frequencies Using Ground-State Self-Consistent Field Models

Wed, 29 Mar 2023 00:00:00 +0000

The use of Δ-self-consistent field (SCF) approaches for studying excited electronic states has received a renewed interest in recent years. In this work, the use of this scheme for calculating excited-state vibrational frequencies is examined. Results from Δ-SCF calculations for a set of representative molecules are compared with those obtained using configuration interaction with single substitutions (CIS) and time-dependent density functional theory (TD-DFT) methods. The use of an approximate spin purification model is also considered for cases where the excited-state SCF solution is spin-contaminated. The results of this work demonstrate that an SCF-based description of an excited-state potential energy surface can be an accurate and cost-effective alternative to CIS and TD-DFT methods.

Spinor GW/Bethe-Salpeter calculations in BerkeleyGW: Implementation, symmetries, benchmarking, and performance

Thu, 2 Mar 2023 00:00:00 +0000

Computing the GW quasiparticle band structure and Bethe-Salpeter equation (BSE) absorption spectra for materials with spin-orbit coupling have commonly been done by treating GW corrections and spin-orbit coupling (SOC) as separate perturbations to density-functional theory. However, accurate treatment of materials with strong spin-orbit coupling (such as many topological materials of recent interest, and thermoelectrics) often requires a nonperturbative approach using spinor wave functions in the Kohn-Sham equation and GW/BSE. Such calculations have only recently become available, in particular for the BSE. We have implemented this approach in the plane-wave pseudopotential GW/BSE code BerkeleyGW, which is highly parallelized and widely used in the electronic-structure community. We present reference results for quasiparticle band structures and optical absorption spectra of solids with different strengths of spin-orbit coupling, including Si, Ge, GaAs, GaSb, CdSe, Au, and Bi2Se3....

Aligning course materials to improve student learning in an introductory physics laboratory