CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published.

Specialized Listeria monocytogenes produce tailocins to provide a population-level competitive growth advantage.

Tailocins are phage tail-like bacteriocins produced by various bacterial species to kill kin competitors. Given that tailocin release is dependent upon cell lysis, regulation of tailocin production at the single-cell and population level remains unclear. Here we used flow cytometry, competition assays and structural characterization of tailocin production in a human bacterial pathogen, Listeria monocytogenes.

Coherent Phonon Dynamics in Plasmonic Gold Tetrahedral Nanoparticle Ensembles.

Coherent phonon modes supported by plasmonic nanoparticles offer prospective applications in chemical and biological sensing. Whereas the characterization of these phonon modes often requires single-particle measurements, synthetic routes to narrow size distributions of nanoparticles permit ensemble investigations. Recently, the synthesis of highly monodisperse gold tetrahedral nanoparticles with tunable edge lengths and corner sharpnesses has been developed.

Tailoring the characteristics of polyacrylonitrile nanofiltration membranes for nickel removal from wastewater: The influence of binary solvents and pore-forming agents.

This work presents the results of an investigation on the physiochemical and structural characteristics of polyacrylonitrile (PAN) nanofiltration (NF) membranes prepared using a novel concept of binary solvents for nickel (Ni) removal from wastewater streams. The thermodynamic and kinetic aspects are emphasized aiming to optimize dope formulation, membrane performance, and durability. The fabricated membranes were characterized by scanning electron microscopy (SEM), porosimetry, tensile stress/strain, and flux and rejection.

Vitamin D and gut microbiome in preterm infants.

Background: The incidence of vitamin D deficiency among pregnant women remains high and is associated with vitamin D deficiency in infants. In normally breastfed infants, Bifidobacteriaceae and Lactobacillaceae are known to help in maintaining immunotolerance and prevent infection. Vitamin D in the gastrointestinal tract plays a role in determining the composition and function of intestinal bacteria.

Femtosecond pulse amplification on a chip.

Femtosecond laser pulses enable the synthesis of light across the electromagnetic spectrum and provide access to ultrafast phenomena in physics, biology, and chemistry. Chip-integration of femtosecond technology could revolutionize applications such as point-of-care diagnostics, bio-medical imaging, portable chemical sensing, or autonomous navigation. However, current chip-integrated pulse sources lack the required peak power, and on-chip amplification of femtosecond pulses has been an unresolved challenge.

Pneumolysin-responsive liposomal platform for selective treatment of Streptococcus pneumoniae.

The bacterium Streptococcus pneumoniae has become a leading cause of meningitis, sepsis, and bacterial pneumonia worldwide, with increased prevalence of antibiotic-resistant serotypes serving to exacerbate the issue. The main factor responsible for colonization and immune response escape in pneumococcal infections is the secreted molecule pneumolysin, which is a subset within a family of related toxins that form transmembrane pores in biological membranes through cholesterol recognition and binding. The conserved activity and structure of pneumolysin between all observed S.

PBAT/PLA-Based Electrospun Nanofibrous Protective Clothes with Superhydrophobicity, Permeability, and Thermal Insulation Characteristics for Individuals with Disabilities.

This study presents the development of multifunctional protective clothing for disabled individuals using PBAT/PLA biopolymeric-based electrospun nanofibrous membranes. The fabric consists of a superhydrophobic electrospun nanofibrous cloth reinforced with silica nanoparticles. The resulting nanofiber membranes were characterized using FE-SEM, a CA goniometer, breathability and hydrostatic pressure resistance tests, UV-vis spectroscopy, thermal infrared photography, tensile tests, and nanoindentation.

Continuous Focusing of Particles by AC-Electroosmosis and Induced Dipole Interactions.

Continuous particle focusing by using microfluidics is an effective method for separating particles, cells, or droplets for analytical purposes. Previously, it was shown that an alternating current across rectangular microchannels with slightly deformed side walls results in vortex flow patterns caused by alternating current electroosmosis (AC-EOF) and could lead to particle focusing. In this work, we explore this mechanism by experimentally studying the particle focusing behavior for various fluid flow velocities through a microchannel.

Adhesion of retinal cells to gold surfaces by biomimetic molecules.

Background: Neural cell-electrode coupling is crucial for effective neural and retinal prostheses. Enhancing this coupling can be achieved through surface modification and geometrical design to increase neuron-electrode proximity. In the current research, we focused on designing and studying various biomolecules as a method to elicit neural cell-electrode adhesion via cell-specific integrin mechanisms.

How bulk liquid viscosity shapes capillary suspensions.

Hypothesis: Capillary suspensions offer a new approach to generate novel materials. They are ternary liquid-liquid-solid systems characterized by particles connected by liquid bridges of one fluid suspended in a second immiscible bulk fluid. The viscosity of the bulk liquid can be modulated to customize the structure and rheological properties of capillary suspensions.

Rapid Spreading of Yield-Stress Liquids.

When a liquid drop makes initial contact with any surface, an unbalanced surface tension force drives the contact line, causing spreading. For Newtonian liquids, either liquid inertia or viscosity dictates these early regimes of spreading, albeit with different power-law behaviors of the evolution of the dynamic spreading radius. In this work, we investigate the early regimes of spreading for yield-stress liquids.

A DNA Aptamer for 2-Aminopurine: Binding-Induced Fluorescence Quenching.

2-Aminopurine (2AP) is a fluorescent analog of adenine, and its unique properties make it valuable in various biochemical and biotechnological applications. Its fluorescence property probes local dynamics in DNA and RNA because stacking with the surrounding bases quench its fluorescence. 2AP-labeled DNA or RNA sequences have been used for the detection of genetic mutations, viral RNA, or other nucleic acid-based markers associated with diseases like cancer and infectious diseases.

A biodegradable microgrooved and tissue mechanocompatible citrate-based scaffold improves bladder tissue regeneration.

Chronic bladder dysfunction due to bladder disease or trauma is detrimental to affected patients as it can lead to increased risk of upper urinary tract dysfunction. Current treatment options include surgical interventions that enlarge the bladder with autologous bowel tissue to alleviate pressure on the upper urinary tract. This highly invasive procedure, termed bladder augmentation enterocystoplasty (BAE), significantly increases the risk of patient morbidity and mortality due to the incompatibility between bowel and bladder tissue.

Interplay between element-specific distortions and electrocatalytic oxygen evolution for cobalt-iron hydroxides.

A microscopic understanding of how Fe-doping of Co(OH) improves electrocatalytic oxygen evolution remains elusive. We study two Co Fe (OH) series that differ in fabrication protocol and find composition alone poorly correlates to catalyst performance. Structural descriptors extracted using X-ray diffraction, X-ray absorption spectroscopy, and Raman spectroscopy reveal element-specific distortions in Co Fe (OH).

Integrated analysis of facial microbiome and skin physio-optical properties unveils cutotype-dependent aging effects.

Background: Our facial skin hosts millions of microorganisms, primarily bacteria, crucial for skin health by maintaining the physical barrier, modulating immune response, and metabolizing bioactive materials. Aging significantly influences the composition and function of the facial microbiome, impacting skin immunity, hydration, and inflammation, highlighting potential avenues for interventions targeting aging-related facial microbes amidst changes in skin physiological properties.

Results: We conducted a multi-center and deep sequencing survey to investigate the intricate interplay of aging, skin physio-optical conditions, and facial microbiome.

Hierarchical electrodes with superior cycling performance using porous material based on cellulose nanofiber as flexible substrate.

The development and application of flexible electrodes with extended cycle life have long been a focal point in the field of energy research. In this study, positively charged polyethylene imine (PEI) and conductive polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) with negative charge were alternately deposited onto a cellulose nanofiber (CNF) porous material utilizing pressure gradient-assisted layer-by-layer (LbL) self-assembly technology. The flexible substrate, characterized by a three-dimensional porous structure reinforced with stiff CNF, not only facilitated high charge storage but also enhanced the electrode's cycling life by reducing the volume changes of PEDOT:PSS.

Gold Nanoparticles in Serum and Milk and Their Effect for Label-Free Colorimetric Sensing of DNA.

Label-free gold nanoparticle (AuNP)-based colorimetric biosensors have been widely used for the detection of DNA. However, the effect of the biological sample matrix has not been fully explored. In this work, we investigated the salt-induced aggregation of AuNPs as well as DNA adsorption in serum and milk.

Stabilized Cu-OH species on in situ reconstructed Cu nanoparticles for CO-to-CH conversion in neutral media.

Achieving large-scale electrochemical CO reduction to multicarbon products with high selectivity using membrane electrode assembly (MEA) electrolyzers in neutral electrolyte is promising for carbon neutrality. However, the unsatisfactory multicarbon products selectivity and unclear reaction mechanisms in an MEA have hindered its further development. Here, we report a strategy that manipulates the interfacial microenvironment of Cu nanoparticles in an MEA to suppress hydrogen evolution reaction and enhance CH conversion.

Interplay of Na Substitution in Magnetic Interaction and Photocatalytic Properties of CaNaTiTaO Perovskite Nanoparticles.

This research paper delves into the enhancement of wastewater treatment through the design and synthesis of advanced photocatalytic materials, focusing on the effects of sodium (Na) substitution in CaNaTaTiO perovskites. By employing various analytical techniques such as X-ray diffraction, Field Emission Scanning Electron Microscopy, Transmission Electron Microscopy and UV-vis spectroscopy, the study examines the transition of these perovskites from tetragonal to orthorhombic structures and observes a reduction in Ca content with Na substitution, which also favors the cubic phase formation and inhibits secondary phases. Significantly, magnetic property analysis uncovers an unexpected ferromagnetic ordering in these perovskites, including compositions traditionally viewed as non-magnetic.