Chemical Engineering Simulation

We present a new library designed to provide a simple and straightforward way to implement QM/AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) and other polarizable QM/MM (Molecular Mechanics) methods based on induced point dipoles. The library, herein referred to as OpenMMPol, is free and open-sourced and is engineered to address the increasing demand for accurate and efficient QM/MM simulations. OpenMMPol is specifically designed to allow polarizable QM/MM calculations of ground state energies and gradients and excitation properties...

Microdroplets are a class of soft matter that has been extensively employed for chemical, biochemical, and industrial applications. However, fabricating microdroplets with largely controllable contact-area shape and apparent contact angle, a key prerequisite for their applications, is still a challenge. Here, by engineering a type of surface with homocentric closed-loop microwalls/microchannels, we can achieve facile size, shape, and contact-angle tunability of microdroplets on the textured surfaces by design...

Cell adhesion peptides (CAPs) often play a critical role in tissue engineering research. However, the discovery of novel CAPs for diverse applications remains a challenging and time-intensive process. This study presents an efficient computational pipeline integrating sequence embeddings, binding predictors, and molecular dynamics simulations to expedite the discovery of new CAPs. A Pro2vec model, trained on vast CAP data sets, was built to identify RGD-similar tripeptide candidates. These candidates were further evaluated for their binding affinity with integrin receptors using the Mutabind2 machine learning model...

The selective α,β-desaturation of cyclic carbonyl compounds, which are found in the core of many steroid and bioactive molecules, using green chemistry is highly desirable. To achieve this task, we have for the first time described and solved the de novo structure of a member of the cyclohexanone dehydrogenase class of enzymes. The breadth of substrate specificity was investigated by assaying the cyclohexanone dehydrogenase, from Alicycliphilus denitrificans , against several cyclic ketones, lactones and lactams...

Fungal bifunctional terpene synthases (BFTSs) catalyze the formation of numerous di-/sester-/tri-terpenes skeletons. However, the mechanism in controlling the cyclization pattern of terpene scaffolds is rarely deciphered for further application of tuning the catalytic promiscuity of terpene synthases for expanding the chemical space. In this study, we expanded the catalytic promiscuity of Fusarium oxysporum fusoxypene synthase (FoFS) by a single mutation at L89, leading to the production of three new sesterterpenes...

The glass-glass interfaces (GGIs) are in a unique glass phase, while current knowledge on the interfacial phase has not completely established to explain the unprecedented improvements in the ductility of metallic nanoglasses (NGs). In this work, Co-P NGs prepared through the pulse electrodeposition are investigated, whose GGI regions clearly show elemental segregation with chemical composition dominated by element Co. Such compositional heterogeneity is further verified by molecular dynamics (MD) simulation on the formation of GGIs in Co-P NGs and atomic structures of GGIs with Co segregation are found to be less dense than those of glassy grains...

The colorimetric sensor-based electronic nose has been demonstrated to discriminate specific gaseous molecules for various applications, including health or environmental monitoring. However, conventional colorimetric sensor systems rely on RGB sensors, which cannot capture the complete spectral response of the system. This limitation can degrade the performance of machine learning analysis, leading to inaccurate identification of chemicals with similar functional groups. Here, we propose a novel time-resolved hyperspectral (TRH) data set from colorimetric array sensors consisting of 1D spatial, 1D spectral, and 1D temporal axes, which enables hierarchical analysis of multichannel 2D spectrograms via a convolution neural network (CNN)...

Asparagine (Asn) deamidation and aspartic acid (Asp) isomerization are common degradation pathways that affect the stability of therapeutic antibodies. These modifications can pose a significant challenge in the development of biopharmaceuticals. As such, the early engineering and selection of chemically stable monoclonal antibodies (mAbs) can substantially mitigate the risk of subsequent failure. In this study, we introduce a novel in silico approach for predicting deamidation and isomerization sites in therapeutic antibodies by analyzing the structural environment surrounding asparagine and aspartate residues...

With the increasingly serious greenhouse effect, the electrochemical carbon dioxide reduction reaction (CO2 RR) has garnered widespread attention as it is capable of leveraging renewable energy to convert CO2 into value-added chemicals and fuels. However, the performance of CO2 RR can hardly meet expectations because of the diverse intermediates and complicated reaction processes, necessitating the exploitation of highly efficient catalysts. In recent years, with advanced characterization technologies and theoretical simulations, the exploration of catalytic mechanisms has gradually deepened into the electronic structure of catalysts and their interactions with intermediates, which serve as a bridge to facilitate the deeper comprehension of structure-performance relationships...

In this study, numerical simulations are conducted with the goal of exploring the impact of the direction of the moving wall, solute and thermal transport, and entropy production on doubly diffusive convection in a chamber occupied by a Casson liquid. Wall movement has a significant impact on convective flow, which, in turn, affects the rate of mass and heat transfer; this sparked our interest in conducting further analysis. The left and right (upright) walls are preserved with constant (but different) thermal and solutal distributions, while the horizontal boundaries are impermeable to mass transfer and insulated from heat transfer...

The development of new three-dimensional (3D) biomaterials with advanced versatile properties is critical to the success of tissue engineering (TE) applications. Here, (a) bioactive decellularized tendon extracellular matrix (dECM) with a sol-gel transition feature at physiological temperature, (b) halloysite nanotubes (HNT) with known mechanical properties and bioactivity, and (c) magnetic nanoparticles (MNP) with superparamagnetic and osteogenic properties were combined to develop a new scaffold that could be used in prospective bone TE applications...

CONTEXT: Gallium, renowned for its notably low melting point and unique property of becoming liquid at room temperature, is a valuable constituent in phase change materials. In this study, we investigate the solid-liquid phase transition of gallium using the modified embedded atom method (MEAM) potential. It addresses the technique to compute the free energy difference between the solid and liquid without using a reference state. We examine various thermodynamic and dynamic properties, including density, specific heat capacity, diffusivity, and radial distribution functions...

The rapid development of synthetic biology has significantly improved the capabilities of mono-culture systems in converting different substrates into various value-added bio-chemicals through metabolic engineering. However, overexpression of biosynthetic pathways in recombinant strains can impose a heavy metabolic burden on the host, resulting in imbalanced energy distribution and negatively affecting both cell growth and biosynthesis capacity. Synthetic consortia, consisting of two or more microbial species or strains with complementary functions, have emerged as a promising and efficient platform to alleviate the metabolic burden and increase product yield...

Design of next-generation membranes requires a nanoscopic understanding of the effect of biologically inspired heterogeneous surface chemistries and topologies (roughness) on local water and solute behavior. In particular, the rejection of small, neutral solutes, such as boric acid, poses a heretofore unsolved challenge. In prior work, a computational inverse design technique using an evolutionary optimization successfully uncovered new surface design strategies for optimized transport of water over solutes in smooth, model pores consisting of two surface chemistries...

Temporal analysis of products (TAP) reactors enable experiments that probe numerous kinetic processes within a single set of experimental data through variations in pulse intensity, delay, or temperature. Selecting additional TAP experiments often involves an arbitrary selection of reaction conditions or the use of chemical intuition. To make experiment selection in TAP more robust, we explore the efficacy of model-based design of experiments (MBDoE) for precision in TAP reactor kinetic modeling. We successfully applied this approach to a case study of synthetic oxidative propane dehydrogenation (OPDH) that involves pulses of propane and oxygen...

This review provides a comprehensive and accessible literature review on the integration of nanoparticles into biolubricants to enhance wear and friction regulation, thus improving the overall lubricated system performance. Nanotechnology has significantly impacted various industries, particularly in lubrication. Nanobiolubricants offer promising avenues for enhancing tribological properties. This review focuses on oxide nanoparticles, such as zinc oxide (ZnO), aluminum oxide (Al2 O3 ), copper oxide (CuO), titanium dioxide (TiO2 ), zirconium dioxide (ZrO2 ), and graphene oxide (GO) nanoparticles, for their ability to enhance lubricant performance...

Low permeability is a key geological factor constraining the development of shale gas, and reservoir modification to improve its permeability is a prerequisite. Controlled shock wave fracturing can induce the formation of complex fractures in reservoirs and is expected to become an important means of reservoir modification. However, the mechanism of controlled shock wave fracturing in shale and the geological engineering control factors are unclear. Therefore, this article reveals the mechanism and effect of shock wave modification through small-scale experiments and large-scale numerical simulations...

Irregular coal pillars inevitably appear in the layout of the current long-wall mining method, which easily forms stress concentrations and becomes a heavy disaster area of rock burst. In order to solve the impact risk of irregular coal pillar working face, it is necessary to study the instability mechanism of the coal pillar and put forward effective prevention and control measures. Based on the research background of 14320 working face of the Dongtan Coal Mine in the Yanzhou mining area of China, this paper studies the prediction and prevention of rock bursts in this kind of coal pillar by means of theoretical calculation, numerical simulation, engineering analogy, and field monitoring...

Multispecies water quality modeling is critical for simulating complex chemical reactions in drinking water distribution systems. An updated EPANET 2.2-compatible version of EPANET multi-species eXtension (EPANET-MSX) was used, which included dispersion and improved mass balance reporting, to simulate an experimental study. The use of EPANET-MSX was supplemented by an automated Python script to process experimental data, handle model execution, and analyze results. Nicotine-associated chlorine loss in drinking water-initially investigated from a drinking water security perspective-modeled with EPANET-MSX was compared with bottle test and test injection data...

Structure-guided engineering of a CHMO from Amycolatopsis methanolica (AmCHMO) was performed for asymmetric sulfoxidation activity and stereoselectivity toward omeprazole sulfide. Initially, combinatorial active-site saturation test (CASTing) and iteratively saturation mutagenesis (ISM) were performed on 5 residues at the "bottleneck" of substrate tunnel, and MT3 was successfully obtained with a specific activity of 46.19 U/g and R-stereoselectivity of 99% toward OPS. Then, 4 key mutations affecting the stereoselectivity were identified through multiple rounds of ISM on residues at the substrate binding pocket region, resulting MT8 with an inversed stereoselectivity from 99% (R) to 97% (S)...