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Chemotactic bacteria sense and respond to temporal and spatial gradients of chemical cues in their surroundings. This phenomenon plays a critical role in many microbial processes such as groundwater bioremediation, microbially enhanced oil recovery, nitrogen fixation in legumes, and pathogenesis of the disease. Chemical heterogeneity in these natural systems may produce numerous competing signals from various directions. Predicting the migration behavior of bacterial populations under such conditions is necessary for designing effective treatment schemes. In this study, experimental studies and mathematical models are reported for the chemotactic response of Escherichia coli to a combination of attractant (α‐methylaspartate) and repellent (NiCl2), which bind to the same transmembrane receptor complex. The model describes the binding of chemoeffectors and phosphorylation of the kinase in the signal transduction mechanism. Chemotactic parameters of E. coli (signaling efficiency σ, stimuli sensitivity coefficient γ, and repellent sensitivity coefficient κ) were determined by fitting the model with experimental results for individual stimuli. Interestingly, our model naturally identifies NiCl2 as a repellent for κ>1. The model is capable of describing quantitatively the response to the individual attractant and repellent, and correctly predicts the change in direction of bacterial population migration for competing stimuli with a twofold increase in repellent concentration. [ABSTRACT FROM AUTHOR]

MXenes exhibit excellent capacitance at high scan rates in sulfuric acid aqueous electrolytes, but the narrow potential window of aqueous electrolytes limits the energy density. Organic electrolytes and room‐temperature ionic liquids (RTILs) can provide higher potential windows, leading to higher energy density. The large cation size of RTIL hinders its intercalation in‐between the layers of MXene limiting the specific capacitance in comparison to aqueous electrolytes. In this work, different chain lengths alkylammonium (AA) cations are intercalated into Ti3C2Tx, producing variation of MXene interlayer spacings (d‐spacing). AA‐cation‐intercalated Ti3C2Tx (AA‐Ti3C2), exhibits higher specific capacitances, and cycling stabilities than pristine Ti3C2Tx in 1 m 1‐ethly‐3‐methylimidazolium bis‐(trifluoromethylsulfonyl)‐imide (EMIMTFSI) in acetonitrile and neat EMIMTFSI RTIL electrolytes. Pre‐intercalated MXene with an interlayer spacing of ≈2.2 nm, can deliver a large specific capacitance of 257 F g−1 (1428 mF cm−2 and 492 F cm−3) in neat EMIMTFSI electrolyte leading to high energy density. Quasi elastic neutron scattering and electrochemical impedance spectroscopy are used to study the dynamics of confined RTIL in pre‐intercalated MXene. Molecular dynamics simulations suggest significant differences in the structures of RTIL ions and AA cations inside the Ti3C2Tx interlayer, providing insights into the differences in the observed electrochemical behavior. [ABSTRACT FROM AUTHOR]

We introduce a new Python interface for the Cassandra Monte Carlo software, molecular simulation design framework (MoSDeF) Cassandra. MoSDeF Cassandra provides a simplified user interface, offers broader interoperability with other molecular simulation codes, enables the construction of programmatic and reproducible molecular simulation workflows, and builds the infrastructure necessary for high‐throughput Monte Carlo studies. Many of the capabilities of MoSDeF Cassandra are enabled via tight integration with MoSDeF. We discuss the motivation and design of MoSDeF Cassandra and proceed to demonstrate both simple use‐cases and more complex workflows, including adsorption in porous media and a combined molecular dynamics – Monte Carlo workflow for computing lateral diffusivity in graphene slit pores. The examples presented herein demonstrate how even relatively complex simulation workflows can be reduced to, at most, a few files of Python code that can be version‐controlled and shared with other researchers. We believe this paradigm will enable more rapid research advances and represents the future of molecular simulations. [ABSTRACT FROM AUTHOR]

Open-source molecular modeling software in chemical engineering focusing on the Molecular Simulation Design Framework Keywords: adsorption/gas; computer simulations (MC and MD); simulation, molecular; thermodynamics/statistical EN adsorption/gas computer simulations (MC and MD) simulation, molecular thermodynamics/statistical 1 12 12 02/24/21 20210301 NES 210301 GLO:44H/01mar21:aic17206-toc-0001.jpg PHOTO (COLOR): . gl BACKGROUND Molecular simulation has emerged as an important sub-field of chemical engineering, due in no small part to the leadership of Keith Gubbins. The downside of open-source software is that, since there is no revenue stream in the usual sense (sale of software), the sustainability of an open-source code over decades can be questionable. This collaboration is resulting in increasing integration with HOOMD-blue, integration with MC codes Cassandra and GOMC, and the first principles MD/MC code CP2K; additionally, MoSDeF has been integrated more closely with Michigan's signac workflow management tools. [Extracted from the article]

Keith E. Gubbins is the Worley H. Clark Jr. Distinguished University Professor Emeritus in the Department of Chemical and Biomolecular Engineering at North Carolina State University (NCSU), a member of the National Academy of Engineering (1989), and a fellow of the American Institute of Chemical Engineers (AIChE, 2003). Applications (Oxford University Press, 2011),11 which was published three decades later, focuses on significant theoretical developments in the interim years for treating associating liquids (e.g., those with hydrogen-bonding networks) and inhomogeneous systems such as fluid-fluid and fluid-solid interfaces, and the assessment of the adequacy of these theories with molecular simulation. Keith and his team also wrote two highly cited reviews on phase transitions in porous materials that are now considered standard references on the subject.32,33 Developing realistic models for porous materials has been another major theme of Keith's research at NCSU. 28 Radhakrishnan R, Gubbins KE, Watanabe A, Kaneko K. Freezing of simple fluids in microporous activated carbon fibers: comparison of simulation and experiment. [Extracted from the article]

Molecular dynamics simulations of room temperature ionic liquid (RTIL) [emim][TFSI] at stepped graphite electrodes were performed to investigate the influence of the thickness of the electrode surface step on the microstructure of interfacial RTILs. A strong correlation was observed between the interfacial RTIL structure and the step thickness in electrode surface as well as the ion size. Specifically, when the step thickness is commensurate with ion size, the interfacial layering of cation/anion is more evident; whereas, the layering tends to be less defined when the step thickness is close to the half of ion size. Furthermore, two-dimensional microstructure of ion layers exhibits different patterns and alignments of counterion/co-ion lattice at neutral and charged electrodes. As the cation/anion layering could impose considerable effects on ion diffusion, the detailed information of interfacial RTILs at stepped graphite presented here would help to understand the molecular mechanism of RTIL-electrode interfaces in supercapacitors. © 2015 American Institute of Chemical Engineers AIChE J, 61: 3022-3028, 2015 [ABSTRACT FROM AUTHOR]

The expansion of porous carbon electrodes in a room temperature ionic liquid (RTIL) is studied using in situ atomic force microscopy (AFM). The effect of carbon surface area and pore size/pore size distribution on the observed strain profile and ion kinetics is examined. Additionally, the influence of the potential scan rate on the strain response is investigated. By analyzing the strain data at various potential scan rates, information on ion kinetics in the different carbon materials is obtained. Molecular dynamics (MD) simulations are performed to compare with and provide molecular insights into the experimental results; this is the first MD work investigating the pressure exerted on porous electrodes under applied potential in a RTIL electrolyte. Using MD, the pressure exerted on the pore wall is calculated as a function of potential/charge for both a micropore (1.2 nm) and a mesopore (7.0 nm). The shape of the calculated pressure profile matches closely with the strain profiles observed experimentally. [ABSTRACT FROM AUTHOR]

This Eighth Founders Tribute of the Journal recognizes Keith E. Gubbins, a towering figure in Chemical Engineering, who has been instrumental in bringing modern statistical mechanics theory and molecular simulation into the mainstream of the field. Chemical engineering molecular thermodynamics/simulation is a welcoming, inclusive field, thanks to the stewardship shown by Keith Gubbins. The breadth of the papers published herein reflects Keith's extraordinary impact on the Chemical Engineering profession, and its molecular thermodynamics community in particular. [Extracted from the article]

The article discusses the simulation of the molecular dynamics of nanoconfined fluids to compare the results to that in experiments. The availability of computational resources helps increase the rigor and fidelity of the simulations. The critical value for the surface separation of linear alkane n-dodecane and cyclohexane undergoes an abrupt transition to the solid form. The simulations provide evidence of the phase transitions of nanoconfined alkanes in mica sheets.

Assuming aromaticity (cyclic continuous conjugation, planarity, and obeying the Hückel 4n + 2 rule), nucleophilic (N), and electrophilic (ω) characters are anticipated to alternate for σ2 and π2 singlet 3‐, 5‐, 7, and 9‐membered silylenes, 1sσ2 (N?), 2sπ2 (ω?), 3sσ2 (N?), and 4sπ2 (ω?), respectively. Our calculations show silacyclopropenylidene (1sσ2) and silacyclopenta‐2,4‐dienylidene (2sπ2) as N and ω, respectively, for exhibiting all the above criteria, at B3LYP/6‐311++G**, B3LYP/6‐311++G(2df,2p), and M06/6‐311++G** levels of theory. Silacyclohepta‐2,4,6‐trienylidene (3sσ2) meets our prediction of being N, despite deviating from planarity. Contrary to our expectation, silacyclonona‐2,4,6,8‐tetraenylidene (4sπ2) not only does not turn out to be ω but also because of its intrinsic angle strain and boat‐like structure, turns out as the most N among singlet silylenes. In all cases, singlet silylenes appear as ground states, exhibiting more stability than their corresponding triplet states. In contrast to our previous report on the 3‐, 5‐, 7‐, and 9‐membered carbenes (Kassaee, et al, Tetrahedron, 1985), all the above singlet and triplet silylenes appear as minima on their energy surfaces. Besides, no allenic isomer is found as a minimum in the silylene series, and finally, 2sπ2 appears planar while its carbenic analog is nonplanar. Nucleophilicity for singlets increases as a function of the ring size 4s > 3s > 2s > 1s, and it decreases as the aromaticity increases. Our triplet silylenes show higher N than their corresponding singlet structures. [ABSTRACT FROM AUTHOR]

A practical and efficient method is developed for efficient synthesis of quinazoline derivatives through condensation reaction of 2‐aminoaryl ketone, an aldehyde, and ammonium acetate, over magnetic Fe3O4@SiO2‐PrNH2‐Fe3+ NPs as a recyclable nanocatalyst, under solvent‐free conditions. The as‐prepared nanocatalyst was characterized using Fourier transform infrared spectroscopy (FT‐IR), X‐ray diffraction (XRD), field emission scanning electron microscopy (FE‐SEM), transmission electron microscopy (TEM), thermogravimetric analysis (TGA), and vibrating sample magnetometer (VSM). Mild conditions, easy work up, high purity of the products, recyclability, readily availability, nontoxicity, economical, and environmental‐friendly nature of the iron catalyst are the attractive features of this methodology. Fe3O4@SiO2‐PrNH2‐Fe3+ has been introduced as a recyclable nanocatalyst, which exhibits outstanding catalytic activity in synthesis of quinazoline derivatives as one of the most important nitrogen heterocycles. [ABSTRACT FROM AUTHOR]