Experimental and simulation study of reverse micelles formed by aerosol-OT and water in non-polar solvents.

The formation of reverse micelles by aerosol-OT [sodium bis(2-ethylhexyl) sulfosuccinate] in hydrocarbon solvents, and in the presence of water, is studied using a combination of atomistic molecular-dynamics simulations and small-angle neutron scattering (SANS). There have been many previous studies of aerosol-OT and its self-assembly in both water and non-aqueous solvents, but this work is focused on a combined experimental and simulation study of reverse-micelle formation. The effects of hydration (with water-to-surfactant molar ratios in the range 0-60) and solvent (cyclohexane and -dodecane) are investigated.

Dynamics of magnetization growth and relaxation in ferrofluids.

The dynamics of the growth and relaxation of the magnetization in ferrofluids are determined using theory based on the Fokker-Planck-Brown equation, and Brownian-dynamics simulations. Magnetization growth starting from an equilibrium nonmagnetized state in zero field, and following an instantaneous application of a uniform field of arbitrary strength, is studied with and without interparticle interactions. Similarly, magnetization relaxation is studied starting from an equilibrium magnetized state in a field of arbitrary strength, and following instantaneous removal of the field.

Structure and dynamics in suspensions of magnetic platelets.

In this research, we employ Brownian dynamics simulations, density functional theory, and mean-field theory to explore the profound influence of shape anisotropy of magnetic nanoplatelets on suspension magnetic response. Each platelet is modelled as an oblate cylinder with a longitudinal point dipole, with an emphasis on strong dipolar interactions conducive to self-assembly. We investigate static structural and magnetic properties, characterising the system through pair distribution function, static structure factor, and cluster-size distribution.

Polymeric surfactants at liquid-liquid interfaces: Dependence of structural and thermodynamic properties on copolymer architecture.

Polymeric surfactants are amphiphilic molecules with two or more different types of monomers. If one type of monomer interacts favorably with a liquid, and another type of monomer interacts favorably with another, immiscible liquid, then polymeric surfactants adsorb at the interface between the two liquids and reduce the interfacial tension. The effects of polymer architecture on the structural and thermodynamic properties of the liquid-liquid interface are studied using molecular simulations.

Experimental and simulation study of self-assembly and adsorption of glycerol monooleate in -dodecane with varying water content onto iron oxide.

The self-assembly and surface adsorption of glycerol monooleate (GMO) in -dodecane are studied using a combination of experimental and molecular dynamics simulation techniques. The self-assembly of GMO to form reverse micelles, with and without added water, is studied using small-angle neutron scattering and simulations. A large-scale simulation is also used to investigate the self-assembly kinetics.

MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile.

Background: Identification of pathogenic bacteria from clinical specimens and evaluating their antimicrobial resistance (AMR) are laborious tasks that involve in vitro cultivation, isolation, and susceptibility testing. Recently, a number of methods have been developed that use machine learning algorithms applied to the whole-genome sequencing data of isolates to approach this problem. However, making AMR assessments from more easily available metagenomic sequencing data remains a big challenge.

Magnetization relaxation dynamics in polydisperse ferrofluids.

When a ferrofluid is magnetized in a strong magnetic field, and then the field is switched off, the magnetization decays from its saturation value to zero. The dynamics of this process are controlled by the rotations of the constituent magnetic nanoparticles, and for the Brownian mechanism, the respective rotation times are strongly influenced by the particle size and the magnetic dipole-dipole interactions between the particles. In this work, the effects of polydispersity and interactions on the magnetic relaxation are studied using a combination of analytical theory and Brownian dynamics simulations.

Measurements of large optical rotary dispersion in the adipose eyelid of Atlantic mackerel ().

Collagen is the most prevalent of Nature's structural proteins, and is found in the extracellular matrices of animals. The structures of collagen molecules and aggregates are chiral, which leads to the rotation of transmitted, plane-polarized light. Here, it is shown that the concentrations of chiral molecules and aggregates in the optically transparent, adipose eyelid of Atlantic mackerel () can be so high, that plane-polarized light in the visible spectrum is rotated by tens to hundreds of degrees, depending on wavelength (the optical rotatory dispersion (ORD)).

Gradient copolymers block copolymers: self-assembly in solution and surface adsorption.

The structures of amphiphilic block and gradient copolymers in solution and adsorbed onto surfaces are surveyed using molecular-dynamics simulations. A bead-spring model is used to identify the general effects of the different architectures: block and gradient copolymers have equal numbers of solvophilic and solvophobic beads, and the gradient copolymer is represented by a linear concentration profile along the chain. Each type of isolated copolymer forms a structure with a globular head of solvophobic beads, and a coil-like tail of solvophilic beads.

SEQ2MGS: an effective tool for generating realistic artificial metagenomes from the existing sequencing data.

Assessment of bioinformatics tools for the metagenomics analysis from the whole genome sequencing data requires realistic benchmark sets. We developed an effective and simple generator of artificial metagenomes from real sequencing experiments. The tool (SEQ2MGS) analyzes the input FASTQ files, precomputes genomic content, and blends shotgun reads from different sequenced isolates, or spike isolate(s) in real metagenome, in desired proportions.

User-Centered Evaluation of a Visual Annotation Tool for Rapid Assessment of Pediatric Weight Entry Errors.

Weight entry errors can cause significant patient harm in pediatrics due to pervasive weight-based dosing practices. While computerized algorithms can assist in error detection, they have not achieved high sensitivity and specificity to be further developed as a clinical decision support tool. To train an advanced algorithm, expert-annotated weight errors are essential but difficult to collect.

How chains and rings affect the dynamic magnetic susceptibility of a highly clustered ferrofluid.

The dynamic magnetic susceptibility, χ(ω), of a model ferrofluid at a very low concentration (volume fraction, approximately 0.05%), and with a range of dipolar coupling constants (1≤λ≤8), is examined using Brownian dynamics simulations. With increasing λ, the structural motifs in the system change from unclustered particles, through chains, to rings.

Influence of size polydispersity on magnetic field tunable structures in magnetic nanofluids containing superparamagnetic nanoparticles.

We probe the influence of particle size polydispersity on field-induced structures and structural transitions in magnetic fluids (ferrofluids) using phase contrast optical microscopy, light scattering and Brownian dynamics simulations. Three different ferrofluids containing superparamagnetic nanoparticles of different polydispersity indices (PDIs) are used. In a ferrofluid with a high PDI (∼0.

Effects of interactions on magnetization relaxation dynamics in ferrofluids.

The dynamics of magnetization relaxation in ferrofluids are studied with statistical-mechanical theory and Brownian dynamics simulations. The particle dipole moments are initially perfectly aligned, and the magnetization is equal to its saturation value. The magnetization is then allowed to decay under zero-field conditions toward its equilibrium value of zero.

Disordered Filaments Mediate the Fibrillogenesis of Type I Collagen in Solution.

Collagen type I is one of the major structural proteins in mammals, providing tissues such as cornea, tendon, bone, skin, and dentin with mechanical stability, strength, and toughness. Collagen fibrils are composed of collagen molecules arranged in a quarter-stagger array that gives rise to a periodicity of 67 nm along the fibril axis, with a 30 nm overlap zone and a 37 nm gap zone. The formation of such highly organized fibrils is a self-assembly process where electrostatic and hydrophobic interactions play a critical role in determining the staggering of the molecules with 67 nm periodicity.

Observation of soft glassy behavior in a magnetic colloid exposed to an external magnetic field.

We provide the first experimental evidence for soft glassy behavior in a sterically stabilized magnetic colloid (ferrofluid) of relatively low volume fraction (φ = 0.037) when a uniform magnetic field is applied at a sufficiently high rate (fast quench). Fast magnetic-field quenches favor structural arrest of field-induced aggregates, owing to insufficient time to settle into lower energy states, thereby pushing the system to a frustrated metastable configuration like a repulsive glass.

Prediction of Antimicrobial Resistance in Gram-Negative Bacteria From Whole-Genome Sequencing Data.

Background: Early detection of antimicrobial resistance in pathogens and prescription of more effective antibiotics is a fast-emerging need in clinical practice. High-throughput sequencing technology, such as whole genome sequencing (WGS), may have the capacity to rapidly guide the clinical decision-making process. The prediction of antimicrobial resistance in Gram-negative bacteria, often the cause of serious systemic infections, is more challenging as genotype-to-phenotype (drug resistance) relationship is more complex than for most Gram-positive organisms.

An interactive online dashboard for tracking COVID-19 in U.S. counties, cities, and states in real time.

Objective: The study sought to create an online resource that informs the public of coronavirus disease 2019 (COVID-19) outbreaks in their area.

Materials And Methods: This R Shiny application aggregates data from multiple resources that track COVID-19 and visualizes them through an interactive, online dashboard.

Results: The Web resource, called the COVID-19 Watcher, can be accessed online (https://covid19watcher.

Experimental and simulation study of the high-pressure behavior of squalane and poly-α-olefins.

The equation of state, dynamical properties, and molecular-scale structure of squalane and mixtures of poly-α-olefins at room temperature are studied with a combination of state-of-the-art, high-pressure experiments and molecular-dynamics simulations. Diamond-anvil cell experiments indicate that both materials are non-hydrostatic media at pressures above ∼1 GPa. The equation of state does not exhibit any sign of a first-order phase transition.

Bioinformatics Approaches to the Understanding of Molecular Mechanisms in Antimicrobial Resistance.

Antimicrobial resistance (AMR) is a major health concern worldwide. A better understanding of the underlying molecular mechanisms is needed. Advances in whole genome sequencing and other high-throughput unbiased instrumental technologies to study the molecular pathogenicity of infectious diseases enable the accumulation of large amounts of data that are amenable to bioinformatic analysis and the discovery of new signatures of AMR.

Static magnetization of immobilized, weakly interacting, superparamagnetic nanoparticles.

The magnetization curve and initial susceptibility of immobilized superparamagnetic nanoparticles are studied using statistical-mechanical theory and Monte Carlo computer simulations. The nanoparticles are considered to be distributed randomly within an implicit solid matrix, but with the easy axes distributed according to particular textures: these are aligned parallel or perpendicular to an external magnetic field, or randomly distributed. The magnetic properties are calculated as functions of the magnetic crystallographic anisotropy barrier (measured with respect to the thermal energy by a parameter σ), and the Langevin susceptibility (related to the dipolar coupling constant and the volume fraction).

DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data.

Methods for single-cell RNA sequencing (scRNA-seq) have greatly advanced in recent years. While droplet- and well-based methods have increased the capture frequency of cells for scRNA-seq, these technologies readily produce technical artifacts, such as doublet cell captures. Doublets occurring between distinct cell types can appear as hybrid scRNA-seq profiles, but do not have distinct transcriptomes from individual cell states.

Self-assembly and adsorption of cetyltrimethylammonium bromide and didodecyldimethylammonium bromide surfactants at the mica-water interface.

The self-assembly and adsorption of the surfactants cetyltrimethylammonium bromide (CTAB) and didodecyldimethylammonium bromide (DDAB) at the muscovite mica-water interface are studied using molecular-dynamics simulations. Adsorption takes place by an ion-exchange mechanism, in which K+ ions are replaced by the organic alkylammonium cations from the solution. Simulations are performed with and without the surface K+ ions, with pure water, and with the surfactants in aqueous solution.

Development and Preliminary Evaluation of a Visual Annotation Tool to Rapidly Collect Expert-Annotated Weight Errors in Pediatric Growth Charts.

Patient weights can be entered incorrectly into electronic health record (EHR) systems. These weight errors can cause significant patient harm especially in pediatrics where weight-based dosing is pervasively used. Determining weight errors through manual chart reviews is impractical in busy clinics, and current EHR alerts are rudimentary.

Interactions between Friction Modifiers and Dispersants in Lubricants: The Case of Glycerol Monooleate and Polyisobutylsuccinimide-Polyamine.

The structural and frictional properties of 10 wt % solutions of the amphiphilic molecules glycerol monooleate (GMO) and polyisobutylsuccinimide-polyamine (PIBSA-PAM) in squalane are studied using molecular dynamics simulations in bulk and under confinement between iron oxide surfaces. GMO is a friction modifier, PIBSA-PAM is a dispersant, and squalane is a good model for typical base oils. A range of liquid compositions and applied pressures is explored, and the formation and stability of reverse micelles are determined under quiescent and shear conditions.