ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling.

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems.

Abnormal clinical presentation and surgical outcome of an intraventricular cavernoma of the third ventricle.

We present a unique case of a man presenting with progressive short-term memory deficits over 10+ years who was found to have a large intraventricular cavernoma in the anterior wall of the third ventricle with invasion of medial limbic structures. Identifying intraventricular cavernomas early is crucial to prevent substantial growth and to increase the chance of successful patient outcomes.

First Dark Matter Search Results from the LUX-ZEPLIN (LZ) Experiment.

The LUX-ZEPLIN experiment is a dark matter detector centered on a dual-phase xenon time projection chamber operating at the Sanford Underground Research Facility in Lead, South Dakota, USA. This Letter reports results from LUX-ZEPLIN's first search for weakly interacting massive particles (WIMPs) with an exposure of 60 live days using a fiducial mass of 5.5 t.

Bacterial Membranes Are More Perturbed by the Asymmetric Versus Symmetric Loading of Amphiphilic Molecules.

Characterizing the biophysical properties of bacterial membranes is critical for understanding the protective nature of the microbial envelope, interaction of biological membranes with exogenous materials, and designing new antibacterial agents. Presented here are molecular dynamics simulations for two cationic quaternary ammonium compounds, and the anionic and nonionic form of a fatty acid molecule interacting with a bacterial inner membrane. The effect of the tested materials on the properties of the model membranes are evaluated with respect to various structural properties such as the lateral pressure profile, lipid tail order parameter, and the bilayer's electrostatic potential.

Dispersal of female and male Aedes aegypti from discarded container habitats using a stable isotope mark-capture study design in South Texas.

Aedes aegypti is the main vector of arboviral diseases such as dengue, chikungunya and Zika. A key feature for disease transmission modeling and vector control planning is adult mosquito dispersal. We studied Ae aegypti adult dispersal by conducting a mark-capture study of naturally occurring Ae.

Stable Isotope Marking of Laboratory-Reared Aedes aegypti (Diptera: Culicidae).

The use of stable isotope enrichment to mark mosquitoes has provided a tool to study the biology of vector species. In this study, we evaluated isotopic marking of Aedes aegypti (L.) (Diptera: Culicidae) in a laboratory setting.

Laboratory evaluation of stable isotope labeling of Culicoides (Diptera: Ceratopogonidae) for adult dispersal studies.

Background: Stable isotope labeling is a promising method for use in insect mark-capture and dispersal studies. Culicoides biting midges, which transmit several important animal pathogens, including bluetongue virus (BTV) and epizootic hemorrhagic disease virus (EHDV), are small flies that develop in various semi-aquatic habitats. Previous Culicoides dispersal studies have suffered from the limitations of other labeling techniques, and an inability to definitively connect collected adult midges to specific immature development sites.

Solvation Dynamics of HEHEHP Ligand at the Liquid-Liquid Interface.

Actinide-lanthanide separation (ALSEP) has been a topic of interest in recent years as it has been shown to selectively extract problematic metals from spent nuclear fuel. However, the process suffers from slow kinetics, prohibiting it from being applied to nuclear facilities. In an effort to improve the process, many fundamental studies have been performed, but the majority have only focused on the thermodynamics of separation.

Correction: Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism - a gas-phase ab initio study.

Correction for 'Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism - a gas-phase ab initio study' by Vivek S. Bharadwaj et al., Phys.

Overview: Nucleation of clathrate hydrates.

Molecular level knowledge of nucleation and growth of clathrate hydrates is of importance for advancing fundamental understanding on the nature of water and hydrophobic hydrate formers, and their interactions that result in the formation of ice-like solids at temperatures higher than the ice-point. The stochastic nature and the inability to probe the small length and time scales associated with the nucleation process make it very difficult to experimentally determine the molecular level changes that lead to the nucleation event. Conversely, for this reason, there have been increasing efforts to obtain this information using molecular simulations.

Quantum-Mechanical Study of the Reaction Mechanism for 2π-2π Cycloaddition of Fluorinated Methylene Groups.

Perfluorocyclobutyl polymers are thermally and chemically stable, may be produced without a catalyst via thermal 2π-2π cycloaddition, and can form block structures, making them suitable for commercialization of specialty polymers. Thermal 2π-2π cycloaddition is a rare reaction that begins in the singlet state and proceeds through a triplet intermediate to form an energetically stable four-membered ring in the singlet state. This reaction involves two changes in spin state and, thus, two spin-crossover transitions.

A Novel Optical Diagnostic for In Situ Measurements of Lithium Polysulfides in Battery Electrolytes.

An optical diagnostic technique to determine the order and concentration of lithium polysulfides in lithium-sulfur (Li-S) battery electrolytes has been developed. One of the major challenges of lithium-sulfur batteries is the problem of polysulfide shuttling between the electrodes, which leads to self-discharge and loss of active material. Here we present an optical diagnostic for quantitative in situ measurements of lithium polysulfides using attenuated total reflection Fourier transform infrared (FT-IR) spectroscopy.

Impact of Water-Dilution on the Solvation Properties of the Ionic Liquid 1-Methyltriethoxy-3-ethylimidazolium Acetate for Model Biomass Molecules.

Many studies have suggested that the processing of lignocellulosic biomass could provide a renewable feedstock to supplant much of the current demand on petroleum sources. Currently, alkyl imidazolium-based ionic liquids (ILs) have shown considerable promise in the pretreatment, solvation, and hydrolysis of lignocellulosic materials although their high cost and unfavorable viscosity has limited their widespread use. Functionalizing these ILs with an oligo(ethoxy) tail has previously been shown through experiment to decrease the IL's viscosity resulting in enhanced mass transport characteristics, in addition to other favorable traits including decreased inhibition of some enzymes.

Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II.

The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II.

Dynamic free energy surfaces for sodium diffusion in type II silicon clathrates.

Earth abundant semiconducting type II Si clathrates have attracted attention as photovoltaic materials due to their wide band gaps. To realize the semiconducting properties of these materials, guest species that arise during the synthesis process must be completely evacuated from the host cage structure post synthesis. A common guest species utilized in the synthesis of Si clathrates is Na (metal), which templates the clathrate cage formation.

Genome-wide analysis and expression profiling of the PIN auxin transporter gene family in soybean (Glycine max).

Background: The plant phytohormone auxin controls many aspects of plant growth and development, which largely depends on its uneven distribution in plant tissues. Transmembrane proteins of the PIN family are auxin efflux facilitators. They play a key role in polar auxin transport and are associated with auxin asymmetrical distribution in plants.

Molecular Simulations of Fatty-Acid Methyl Esters and Representative Biodiesel Mixtures.

Despite the importance of fatty-acid methyl esters (FAMEs) as key components of various green solvents, detergents, plasticizers, and biodiesels, our understanding of these systems at the molecular level is limited. An enhanced molecular-level perspective of FAMEs will enable a detailed analysis of the polymorph and crystallization phenomena that adversely impact flow properties at low temperatures. Presented here, is the parameterization and validation of a charge-modified generalized amber force field (GAFF) for eight common FAMEs and two representative biodiesel mixtures.

The impact of active site protonation on substrate ring conformation in Melanocarpus albomyces cellobiohydrolase Cel7B.

The ability to utilize biomass as a feedstock for liquid fuel and value-added chemicals is dependent on the efficient and economic utilization of lignin, hemicellulose, and cellulose. In current bioreactors, cellulases are used to convert crystalline and amorphous cellulose to smaller oligomers and eventually glucose by means of cellulase enzymes. A critical component of the enzyme catalyzed hydrolysis reaction is the degree to which the enzyme can facilitate substrate ring deformation from the chair to a more catalytically active conformation (e.

Elucidating the conformational energetics of glucose and cellobiose in ionic liquids.

A major challenge for the utilization of lignocellulosic feedstocks for liquid fuels and other value added chemicals has been the recalcitrant nature of crystalline cellulose to various hydrolysis techniques. Ionic liquids (ILs) are considered to be a promising solvent for the dissolution and conversion of cellulose to simple sugars, which has the potential to facilitate the unlocking of biomass as a supplement and/or replacement for petroleum as a feedstock. Recent studies have revealed that the orientation of the hydroxymethyl group, described via the ω dihedral, and the glycosidic bond, described via the φ-ψ dihedrals, are significantly modified in the presence of ILs.

Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism--a gas-phase ab initio study.

The fumarate addition reaction mechanism is central to the anaerobic biodegradation pathway of various hydrocarbons, both aromatic (e.g., toluene, ethyl benzene) and aliphatic (e.

Electronic structure and spectroscopic analysis of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ion pair.

Electronic and structural properties of the room temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulonyl)imide are studied using density functional theory (DFT) methods in addition to infrared and UV-vis spectroscopy. The DFT methods were conducted for both gas phase and solution phase using the integral equation formalism polarizable continuum model, while optical absorption experiments were conducted using neat and dilute methanol solutions. Three energetically similar conformers were obtained for each of the gas phase and solution phase DFT calculations.

Structural insight into activity enhancement and inhibition of H64A carbonic anhydrase II by imidazoles.

Human carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the hydration and dehydration of CO2 and HCO3 (-), respectively. The reaction follows a ping-pong mechanism, in which the rate-limiting step is the transfer of a proton from the zinc-bound solvent (OH(-)/H2O) in/out of the active site via His64, which is widely believed to be the proton-shuttling residue. The decreased catalytic activity (∼20-fold lower with respect to the wild type) of a variant of CA II in which His64 is replaced with Ala (H64A CA II) can be enhanced by exogenous proton donors/acceptors, usually derivatives of imidazoles and pyridines, to almost the wild-type level.

Do differences make the heart grow fonder? Associations between differential peer experiences on adolescent sibling conflict and relationship quality.

Though it is known that different familial relationships influence one another (e.g., Yu & Gamble, 2008) the influence of outside relationships (i.