Chemical and Biomolecular Engineering Publications

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Ultra-high capacity, multifunctional nanoscale sorbents for PFOA and PFOS treatment
(Springer Nature, 2023) Lee, Junseok; Kim, Changwoo; Liu, Chen; Wong, Michael S.; Cápiro, Natalie L.; Pennell, Kurt D.; Fortner, John D.
Here, we describe surface functionalized, superparamagnetic iron oxide nanocrystals (IONCs) for ultra-high PFAS sorption and precise, low energy (magnetic) separation, considering perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS). As a function of surface coating, sorption capacities described are considerably higher than previous studies using activated carbon, polymers, and unmodified metal/metal oxides, among others. In particular, positively charged polyethyleneimine (PEI) coated IONCs demonstrate extreme sorption capacities for both PFOA and PFOS due to electrostatic and hydrophobic interactions, along with high polymer grafting densities, while remaining stable in water, thus maintaining available surface area. Further, through a newly developed method using a quart crystal microbalance with dissipation (QCM-D), we present real-time, interfacial observations (e.g., sorption kinetics). Through this method, we explore underpinning mechanism(s) for differential PFAS (PFOA vs PFOS) sorption behavior(s), demonstrating that PFAS functional head group strongly influence molecular orientation on/at the sorbent interface. The effects of water chemistry, including pH, ionic composition of water, and natural organic matter on sorption behavior are also evaluated and along with material (treatment) demonstration via bench-scale column studies.
Engineering chirality at wafer scale with ordered carbon nanotube architectures
(Springer Nature, 2023) Doumani, Jacques; Lou, Minhan; Dewey, Oliver; Hong, Nina; Fan, Jichao; Baydin, Andrey; Zahn, Keshav; Yomogida, Yohei; Yanagi, Kazuhiro; Pasquali, Matteo; Saito, Riichiro; Kono, Junichiro; Gao, Weilu; Carbon Hub; Smalley-Curl Institute
Creating artificial matter with controllable chirality in a simple and scalable manner brings new opportunities to diverse areas. Here we show two such methods based on controlled vacuum filtration - twist stacking and mechanical rotation - for fabricating wafer-scale chiral architectures of ordered carbon nanotubes (CNTs) with tunable and large circular dichroism (CD). By controlling the stacking angle and handedness in the twist-stacking approach, we maximize the CD response and achieve a high deep-ultraviolet ellipticity of 40 ± 1 mdeg nm−1. Our theoretical simulations using the transfer matrix method reproduce the experimentally observed CD spectra and further predict that an optimized film of twist-stacked CNTs can exhibit an ellipticity as high as 150 mdeg nm−1, corresponding to a g factor of 0.22. Furthermore, the mechanical rotation method not only accelerates the fabrication of twisted structures but also produces both chiralities simultaneously in a single sample, in a single run, and in a controllable manner. The created wafer-scale objects represent an alternative type of synthetic chiral matter consisting of ordered quantum wires whose macroscopic properties are governed by nanoscopic electronic signatures and can be used to explore chiral phenomena and develop chiral photonic and optoelectronic devices.
The energetics and evolution of oxidoreductases in deep time
(Wiley, 2024) McGuinness, Kenneth N.; Fehon, Nolan; Feehan, Ryan; Miller, Michelle; Mutter, Andrew C.; Rybak, Laryssa A.; Nam, Justin; AbuSalim, Jenna E.; Atkinson, Joshua T.; Heidari, Hirbod; Losada, Natalie; Kim, J. Dongun; Koder, Ronald L.; Lu, Yi; Silberg, Jonathan J.; Slusky, Joanna S. G.; Falkowski, Paul G.; Nanda, Vikas
The core metabolic reactions of life drive electrons through a class of redox protein enzymes, the oxidoreductases. The energetics of electron flow is determined by the redox potentials of organic and inorganic cofactors as tuned by the protein environment. Understanding how protein structure affects oxidation–reduction energetics is crucial for studying metabolism, creating bioelectronic systems, and tracing the history of biological energy utilization on Earth. We constructed ProtReDox (https://protein-redox-potential.web.app), a manually curated database of experimentally determined redox potentials. With over 500 measurements, we can begin to identify how proteins modulate oxidation–reduction energetics across the tree of life. By mapping redox potentials onto networks of oxidoreductase fold evolution, we can infer the evolution of electron transfer energetics over deep time. ProtReDox is designed to include user-contributed submissions with the intention of making it a valuable resource for researchers in this field.
Niobium Oxide Photocatalytically Oxidizes Ammonia in Water at Ambient Conditions
(SciELO, 2024) Elias, Welman; Clark, Chelsea; Heck, Kimberly; Arredondo, Jacob; Wang, Bo; Toro, Andras; Kürtib, László; Wong, Michael; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment
Ammonia contamination in water is a significant environmental issue since it is toxic and leads to eutrophication. Photocatalysis has been investigated as a strategy for ammonia degradation but can potentially form toxic nitrite (NO2–) and nitrate (NO3–) byproducts. This work reports on the ability of niobium oxide (Nb2O5) to photocatalytically oxidize aqueous-phase ammonia (NH3). Whereas as-synthesized Nb2O5 showed little catalytic activity (< 1% NH3 conversion after 6 h of UV-C irradiation, at room temperature and atmospheric pressure, and under O2 headspace), Nb2O5 treated in basic solution (OH-Nb2O5) was able to photocatalytically degrade NH3 at ca. 9% conversion after six hours, with ca. 70% selectivity to the desired N2, with a first-order rate constant of ca. 12 times higher than the as synthesize catalyst (1.6 × 10–3 min–1 vs. 2.0 × 10–2 min–1). Raman spectroscopic analysis indicated the presence of terminal Nb=O species after base treatment of Nb2O5, implicating them as catalytically active sites. These results underscore how a simple structural modification can significantly affect photocatalytic activity for aqueous ammonia oxidation.
Complete defluorination of per- and polyfluoroalkyl substances — dream or reality?
(Elsevier, 2023) Arana Juve, Jan-Max; Wang, Bo; Wong, Michael S.; Ateia, Mohammed; Wei, Zongsu; The Catalysis and Nanomaterials Laboratory
The consensus of removing per- and polyfluoroalkyl substances (PFAS) from the environment is widely recognized and enlightened by the near-zero standards released from the U.S. Environmental Protection Agency in 2023. The only way to achieve the goal of zero fluoro-pollution is to fully defluorinate or mineralize PFAS, but current technologies only partially defluorinate a limited number of PFAS, which can lead to the creation of potentially more toxic short-chain intermediates. Therefore, we discuss herein the need to broaden the scope of tested PFAS, summarize the state-of-the-art degradation technologies, and provide perspectives to achieve complete defluorination. Besides fundamental knowledge gaps in defluorination reactions, technological gaps in the aspects of water matrix effects, pilot tests, and cost analysis also limit the application and comparison of different treatment technologies. This work would shed light on further research to find solutions in the complete defluorination of PFAS.
Application of magnetic nanoparticles as demulsifiers for surfactant-enhanced oil recovery
(Wiley, 2023) Zhang, Leilei; Bai, Chutian; Zhang, Zhuqing; Wang, Xinglin; Nguyen, Thao Vy; Vavra, Eric; Puerto, Maura; Hirasaki, George J.; Biswal, Sibani Lisa
Nonionic surfactants are increasingly being applied in oil recovery processes due to their stability and low adsorption onto mineral surfaces. However, these surfactants lead to the production of emulsified oil that is extremely stable and difficult to separate by conventional methods. This research characterizes the stability of crude oil mixed with a nonionic surfactant, L24–22, in a brine solution. When subjected to gravity separation, a middle oil-rich and bottom water-rich emulsion are generated for various water–oil ratios. Thermal treatments can effectively break oil-rich emulsions, but the bottom water layer remains contaminated with micron-sized crude oil droplets. A magnetic nanoparticle treatment is shown to demulsify the crude oil emulsions, dropping the total organic carbon (TOC) in the water layer from 1470 to 30 ppm.
Prelithiation Effects in Enhancing Silicon-Based Anodes for Full-Cell Lithium-Ion Batteries Using Stabilized Lithium Metal Particles
(American Chemical Society, 2023) Nguyen, Quan Anh; Haridas, Anulekha K.; Terlier, Tanguy; Biswal, Sibani Lisa
Silicon (Si) has been considered as one of the most promising replacements for graphite anodes in next-generation lithium-ion batteries due to its superior specific capacity. However, the irreversible consumption of lithium (Li) ions in Si-based anodes, which is associated with a large volume expansion upon lithiation and the continuous formation of the solid electrolyte interphase (SEI), is especially detrimental to full-cell batteries, whose Li-ion reserve is limited. This study demonstrates the application of stabilized lithium metal particles (SLMPs) as a prelithiation method for Si anodes that can be readily incorporated into large-scale industrial battery manufacturing. Particularly, a surfactant-stabilized SLMP dispersion was designed to be spray-coated onto prefabricated Si composite anodes, forming a uniformly distributed and well-adhered SLMP layer for in situ prelithiation. In full-cells with lithium iron phosphate (LFP) cathodes, the Si-based anodes demonstrated an improved 1st cycle Coulombic efficiency and cycle life with SLMP prelithiation using capacity-control cycling. However, when cycling over the full potential range, prelithiation with high SLMP loading was found to initially increase battery capacity while inducing accelerated fading in later cycles. This phenomenon was caused by Li trapping in the Li–Si alloy associated with higher SLMP-enabled Li diffusion kinetics. Additionally, cycled Si anodes from full-cells were also examined by surface analysis techniques, X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS), demonstrating SLMP effects in modifying the SEI by increasing the inorganic content, particularly LiF, which had been widely credited with improving SEI morphology and Li-ion diffusion through the interphase. Our findings provide valuable insights into the design of prelithiation and cycling strategies for high-capacity Si-based full-cell batteries to utilize the benefits of SLMP while avoiding the Li trapping phenomenon.
Three-dimensional covalent organic frameworks with pto and mhq-z topologies based on Tri- and tetratopic linkers
(Springer Nature, 2023) Zhu, Dongyang; Zhu, Yifan; Chen, Yu; Yan, Qianqian; Wu, Han; Liu, Chun-Yen; Wang, Xu; Alemany, Lawrence B.; Gao, Guanhui; Senftle, Thomas P.; Peng, Yongwu; Wu, Xiaowei; Verduzco, Rafael
Three-dimensional (3D) covalent organic frameworks (COFs) possess higher surface areas, more abundant pore channels, and lower density compared to their two-dimensional counterparts which makes the development of 3D COFs interesting from a fundamental and practical point of view. However, the construction of highly crystalline 3D COF remains challenging. At the same time, the choice of topologies in 3D COFs is limited by the crystallization problem, the lack of availability of suitable building blocks with appropriate reactivity and symmetries, and the difficulties in crystalline structure determination. Herein, we report two highly crystalline 3D COFs with pto and mhq-z topologies designed by rationally selecting rectangular-planar and trigonal-planar building blocks with appropriate conformational strains. The pto 3D COFs show a large pore size of 46 Å with an extremely low calculated density. The mhq-z net topology is solely constructed from totally face-enclosed organic polyhedra displaying a precise uniform micropore size of 1.0 nm. The 3D COFs show a high CO2 adsorption capacity at room temperature and can potentially serve as promising carbon capture adsorbents. This work expands the choice of accessible 3D COF topologies, enriching the structural versatility of COFs.
Revealing the Dual-Layered Solid Electrolyte Interphase on Lithium Metal Anodes via Cryogenic Electron Microscopy
(American Chemical Society, 2023) Wi, Tae-Ung; Park, Sung O; Yeom, Su Jeong; Kim, Min-Ho; Kristanto, Imanuel; Wang, Haotian; Kwak, Sang Kyu; Lee, Hyun-Wook
It is crucial to comprehend the effect of the solid electrolyte interphase (SEI) on battery performance to develop stable Li metal batteries. Nonetheless, the exact nanostructure and working mechanisms of the SEI remain obscure. Here, we have investigated the relationship between electrolyte components and the structural configuration of interfacial layers using an optimized cryogenic transmission electron microscopy (Cryo-TEM) analysis and theoretical calculation. We revealed a unique dual-layered inorganic-rich nanostructure, in contrast to the widely known simple specific component-rich SEI layers. The origin of stable Li cycling is closely related to the Li-ion diffusion mechanism via diverse crystalline grains and numerous grain boundaries in the fine crystalline-rich SEI layer. The results can elucidate a particular issue pertaining to the chemical structure of SEI layers that can induce uniform Li diffusion and rapid Li-ion conduction on Li metal anodes, developing stable Li metal batteries.
High Strength Titanium with Fibrous Grain for Advanced Bone Regeneration
(Wiley, 2023) Wang, Ruohan; Wang, Mingsai; Jin, Rongrong; Wang, Yanfei; Yi, Min; Li, Qinye; Li, Juan; Zhang, Kai; Sun, Chenghua; Nie, Yu; Huang, Chongxiang; Mikos, Antonios G.; Zhang, Xingdong
Pure titanium is widely used in clinical implants, but its bioinert properties (poor strength and mediocre effect on bone healing) limit its use under load-bearing conditions. Modeling on the structure of collagen fibrils and specific nanocrystal plane arrangement of hydroxyapatite in the natural bone, a new type of titanium (Ti) with a highly aligned fibrous-grained (FG) microstructure is constructed. The improved attributes of FG Ti include high strength (≈950 MPa), outstanding affinity to new bone growth, and tight bone-implant contact. The bone-mimicking fibrous grains induce an aligned surface topological structure conducive to forming close contact with osteoblasts and promotes the expression of osteogenic genes. Concurrently, the predominant Ti(0002) crystal plane of FG Ti induces the formation of hydrophilic anatase titanium oxide layers, which accelerate biomineralization. In conclusion, this bioinspired FG Ti not only proves to show mechanical and bone-regenerative improvements but it also provides a new strategy for the future design of metallic biomaterials.
Design and fabrication of a Preformed Thixotropic-Viscoelastic Nanocomposite hydrogel system (PNCH) for controlling sand production in reservoirs
(Elsevier, 2023) Saghandali, Farzin; Baghban Salehi, Mahsa; Taghikhani, Vahid
In this study, the performance of preformed dual crosslinked nanocomposite hydrogels (PNCH) consisting of acrylamide, 2-acrylamide-2-methylpropane sulfonic acid, maleic acid, and acrylic acid in sand control was investigated. Also, the effects of three nanoparticles (NPs) of iron (PNCH1), silicon (PNCH2), and bentonite (PNCH3) on the PNCH structure were studied. The morphology, equilibrium swelling ratio (ESR), rheology, thermal strength, zeta potential, and compressive strength were experimentally analyzed. According to the XRD results, the NPs were completely dispersed in all three samples. The results of SEM and EDS tests confirmed the presence of NPs within the PNCHs with a dense, homogeneous, and porous structure. The results of the ESR at distilled and formation water at ambient temperature for PNCHs (1), (2), and (3) were (13.9,4.55), (15.45, 6.35), and (12.9, 4.8), also at reservoir temperatures ESR results were reported (78, 17.5), (89, 13), and (70,12.9) respectively. From the TGA results, structure destruction of PNCHs starts at 222, 225, and 202 °C respectively so the addition of 1 wt% of NPs increased the structure destruction from nearly 80 °C to more than 200 °C. Based on the results of the strain sweep test, structures of PNCHs can cause viscoelastic behavior with the maximum elastic modulus of 29,000, 8430, and 10,800, and critical strain of (10%, 19.3%, and 10.8%) respectively. The loop test results confirmed the time-dependent viscoelastic properties of thixotropic in all structures. Finally, in compressive strength test revealed that adding 0.5 pore volume of 1 wt% of PNCH into the sandpack increased its strength by 980%.
Nucleosome Breathing Facilitates the Search for Hidden DNA Sites by Pioneer Transcription Factors
(American Chemical Society, 2023) Mondal, Anupam; Felipe, Cayke; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physics
Transfer of genetic information starts with transcription factors (TFs) binding to specific sites on DNA. But in living cells, DNA is mostly covered by nucleosomes. There are proteins, known as pioneer TFs, that can efficiently reach the DNA sites hidden by nucleosomes, although the underlying mechanisms are not understood. Using the recently proposed idea of interaction-compensation mechanism, we develop a stochastic model for the target search on DNA with nucleosome breathing. It is found that nucleosome breathing can significantly accelerate the search by pioneer TFs in comparison to situations without breathing. We argue that this is the result of the interaction-compensation mechanism that allows proteins to enter the inner nucleosome region through the outer DNA segment. It is suggested that nature optimized pioneer TFs to take advantage of nucleosome breathing. The presented theoretical picture provides a possible microscopic explanation for the successful invasion of nucleosome-buried genes.
Theoretical understanding of evolutionary dynamics on inhomogeneous networks
(IOP Publishing, 2023) Teimouri, Hamid; Khavas, Dorsa Sattari; Spaulding, Cade; Li, Christopher; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physics
Evolution is the main feature of all biological systems that allows populations to change their characteristics over successive generations. A powerful approach to understand evolutionary dynamics is to investigate fixation probabilities and fixation times of novel mutations on networks that mimic biological populations. It is now well established that the structure of such networks can have dramatic effects on evolutionary dynamics. In particular, there are population structures that might amplify the fixation probabilities while simultaneously delaying the fixation events. However, the microscopic origins of such complex evolutionary dynamics remain not well understood. We present here a theoretical investigation of the microscopic mechanisms of mutation fixation processes on inhomogeneous networks. It views evolutionary dynamics as a set of stochastic transitions between discrete states specified by different numbers of mutated cells. By specifically considering star networks, we obtain a comprehensive description of evolutionary dynamics. Our approach allows us to employ physics-inspired free-energy landscape arguments to explain the observed trends in fixation times and fixation probabilities, providing a better microscopic understanding of evolutionary dynamics in complex systems.
Mesoscale Modeling of Distributed Water Systems Enables Policy Search
(Wiley, 2023) Zhou, Xiangnan; Duenas-Osorio, Leonardo; Doss-Gollin, James; Liu, Lu; Stadler, Lauren; Li, Qilin; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment
It is widely acknowledged that distributed water systems (DWSs), which integrate distributed water supply and treatment with existing centralized infrastructure, can mitigate challenges to water security from extreme events, climate change, and aged infrastructure. However, it is unclear which are beneficial DWS configurations, i.e., where and at what scale to implement distributed water supply. We develop a mesoscale representation model that approximates DWSs with reduced backbone networks to enable efficient system emulation while preserving key physical realism. Moreover, system emulation allows us to build a multiobjective optimization model for computational policy search that addresses energy utilization and economic impacts. We demonstrate our models on a hypothetical DWS with distributed direct potable reuse (DPR) based on the City of Houston's water and wastewater infrastructure. The backbone DWS with greater than 92% link and node reductions achieves satisfactory approximation of global flows and water pressures, to enable configuration optimization analysis. Results from the optimization model reveal case-specific as well as general opportunities, constraints, and their interactions for DPR allocation. Implementing DPR can be beneficial in areas with high energy intensities of water distribution, considerable local water demands, and commensurate wastewater reuse capacities. The mesoscale modeling approach and the multiobjective optimization model developed in this study can serve as practical decision-support tools for stakeholders to search for alternative DWS options in urban settings.
Coiling of semiflexible paramagnetic colloidal chains
(Royal Society of Chemistry, 2023) Spatafora-Salazar, Aldo; Kuei, Steve; Cunha, Lucas H.P.; Biswal, Sibani Lisa
Semiflexible filaments deform into a variety of configurations that dictate different phenomena manifesting at low Reynolds number. Harnessing the elasticity of these filaments to perform transport-related processes at the microfluidic scale requires structures that can be directly manipulated to attain controllable geometric features during their deformation. The configuration of semiflexible chains assembled from paramagnetic colloids can be readily controlled upon the application of external time-varying magnetic fields. In circularly rotating magnetic fields, these chains undergo coiling dynamics in which their ends close into loops that wrap inward, analogous to the curling of long nylon filaments under shear. The coiling is promising for the precise loading and targeted transport of small materials, however effective implementation requires an understanding of the role that field parameters and chain properties play on the coiling features. Here, we investigate the formation of coils in semiflexible paramagnetic chains using numerical simulations. We demonstrate that the size and shape of the initial coils are governed by the Mason and elastoviscous numbers, related to the field parameters and the chain bending stiffness. The size of the initial coil follows a nonmonotonic behavior with Mason number from which two regions are identified: (1) an elasticity-dependent nonlinear regime in which the coil size decreases with increasing field strength and for which loop shape tends to be circular, and (2) an elasticity-independent linear regime where the size increases with field strength and the shape become more elliptical. From the time scales associated to these regimes, we identify distinct coiling mechanisms for each case that relate the coiling dynamics to two other configurational dynamics of paramagnetic chains: wagging and folding behaviors.
Impregnation of KOAc on PdAu/SiO2 causes Pd-acetate formation and metal restructuring
(Royal Society of Chemistry, 2023) Jacobs, Hunter P.; Elias, Welman C.; Heck, Kimberly N.; Dean, David P.; Dodson, Justin J.; Zhang, Wenqing; Arredondo, Jacob H.; Breckner, Christian J.; Hong, Kiheon; Botello, Christopher R.; Chen, Laiyuan; Mueller, Sean G.; Alexander, Steven R.; Miller, Jeffrey T.; Wong, Michael S.
Potassium-promoted, oxide-supported PdAu is catalytically active for the gas-phase acetoxylation of ethylene to form vinyl acetate monomer (VAM), in which the potassium improves long-term activity and VAM selectivity. The alkali metal is incorporated into the catalyst via wet impregnation of its salt solution, and it is generally assumed that this common catalyst preparation step has no effect on the catalyst structure. However, in this work, we report evidence to the contrary. We synthesized a silica-supported PdAu (PdAu/SiO2, 8 wt% Pd, 4 wt% Au) model catalyst containing Pd-rich PdAu alloy and pure Au phases. Impregnation with potassium acetate (KOAc) aqueous solution and subsequent drying did not cause XRD-detectible changes to the bimetal structure. However, DRIFTS indicated the presence of Pd3(OAc)6 species, which is correlated to up to 2% Pd loss after washing of the dried KOAc-promoted PdAu/SiO2. Carrying out the impregnation step with an AcOH-only solution and subsequent drying caused significant enlargement of the pure Au grain size and generated a smaller amount of Pd3(OAc)6. During co-impregnation of AcOH and KOAc, grain sizes were enlarged slightly, and substantial amounts of K2Pd2(OAc)6 and Pd3(OAc)6 were detected by DRIFTS and correlated to up to 32% Pd loss after washing. Synchrotron XAS analysis showed that approximately half the Pd atoms were oxidized, corroborating the presence of the Pd-acetate species. These results indicate wet-impregnation-induced metal leaching can occur and be substantial during catalyst preparation.
Precise Cation Separations with Composite Cation-Exchange Membranes: Role of Base Layer Properties
(American Chemical Society, 2023) DuChanois, Ryan M.; Mazurowski, Lauren; Fan, Hanqing; Verduzco, Rafael; Nir, Oded; Elimelech, Menachem; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment (NEWT)
Separation of specific ions from water could enable recovery and reuse of essential metals and nutrients, but established membrane technologies lack the high-precision selectivity needed to facilitate a circular resource economy. In this work, we investigate whether the cation/cation selectivity of a composite cation-exchange membrane (CEM), or a thin polymer selective layer on top of a CEM, may be limited by the mass transfer resistance of the underlying CEM. In our analysis, we utilize a layer-by-layer technique to modify CEMs with a thin polymer selective layer (∼50 nm) that has previously shown high selectivity toward copper over similarly sized metals. While these composite membranes have a CuCl2/MgCl2 selectivity up to 33 times larger than unmodified CEMs in diffusion dialysis, our estimates suggest that eliminating resistance from the underlying CEM could further increase selectivity twofold. In contrast, the CEM base layer has a smaller effect on the selectivity of these composite membranes in electrodialysis, although these effects could become more pronounced for ultrathin or highly conductive selective layers. Our results highlight that base layer resistance prevents selectivity factors from being comparable across diffusion dialysis and electrodialysis, and CEMs with low resistance are necessary for providing highly precise separations with composite CEMs.
Bacteria-Specific Feature Selection for Enhanced Antimicrobial Peptide Activity Predictions Using Machine-Learning Methods
(American Chemical Society, 2023) Teimouri, Hamid; Medvedeva, Angela; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physics
There are several classes of short peptide molecules, known as antimicrobial peptides (AMPs), which are produced during the immune responses of living organisms against various infections. In recent years, substantial progress has been achieved in applying machine-learning methods to predict the activities of AMPs against bacteria. In most investigated cases, however, the outcome is not bacterium-specific since the specific features of bacteria, such as chemical composition and structure of membranes, are not considered. To overcome this problem, we developed a new computational approach that allowed us to train several supervised machine-learning models using a specific set of data associated with peptides targeting E. coli bacteria. LASSO regression and Support Vector Machine techniques have been utilized to select, among more than 1500 physicochemical descriptors, the most important features that can be used to classify a peptide as antimicrobial or ineffective against E. coli. We then performed the classification of active versus inactive AMPs using the Support Vector classifiers, Logistic Regression, and Random Forest methods. This computational study allows us to make recommendations of how to design more efficient antibacterial drug therapies.
Tunable calcium phosphate cement formulations for predictable local release of doxycycline
(Elsevier, 2023) Liu, Qian; Lodoso-Torrecilla, Irene; Gunnewiek, Raquel Klein; Harhangi, Harry R.; Mikos, Antonios G.; van Niftrik, Laura; Jansen, John A.; Chen, Lili; Beucken, Jeroen J.J.P. van den
Background Osteomyelitis is a bacterial infection, which leads to bone loss. Local treatment focuses on elimination of bacteria, which is preferable for simultaneous management of the bone defect after sequestrectomy and bone reconstruction in one-stage treatment of osteomyelitis. Calcium phosphate cements (CPCs) have attracted increased attention as bone substitute material because of their injectability and in situ self-setting properties, which allow for minimally invasive surgical procedures and local drug delivery. Methods We herein established a system to achieve different release profiles of the antibiotic drug doxycycline from CPC by finetuning their formulation. These CPC formulations were generated via facile addition of hydrolytically degrading PLGA particles, varying doses of doxycycline, and addition of the lubricant CMC. Results The CPC formulations exhibited appropriate handling properties in terms of injectability and setting time. Furthermore, doxycycline release profiles showed an adequate burst release followed by a cumulative release of up to 100% over a period of 8 weeks. Importantly, the released doxycycline retained its antibacterial activity against Staphylococcus aureus, the major pathogen causing osteomyelitis. Using an in vivo implantation model, antibacterial efficacy was demonstrated by a rapid decrease of inoculated S. aureus at the CPC surface and within surrounding tissues. Conclusions Our data show the versatility of the CPC system toward local antibacterial therapy, extending its application beyond bone substitution.
Dynamics of chemical reactions on single nanocatalysts with heterogeneous active sites
(AIP Publishing, 2023) Chaudhury, Srabanti; Jangid, Pankaj; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physics
Modern chemical science and industries critically depend on the application of various catalytic methods. However, the underlying molecular mechanisms of these processes still remain not fully understood. Recent experimental advances that produced highly-efficient nanoparticle catalysts allowed researchers to obtain more quantitative descriptions, opening the way to clarify the microscopic picture of catalysis. Stimulated by these developments, we present a minimal theoretical model that investigates the effect of heterogeneity in catalytic processes at the single-particle level. Using a discrete-state stochastic framework that accounts for the most relevant chemical transitions, we explicitly evaluated the dynamics of chemical reactions on single heterogeneous nanocatalysts with different types of active sites. It is found that the degree of stochastic noise in nanoparticle catalytic systems depends on several factors that include the heterogeneity of catalytic efficiencies of active sites and distinctions between chemical mechanisms on different active sites. The proposed theoretical approach provides a single-molecule view of heterogeneous catalysis and also suggests possible quantitative routes to clarify some important molecular details of nanocatalysts.

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