Into the Facet-Selectivity of Sequenced Amphiphilic Peptoids at the Au-Water Interface

Shape-controlled colloidal nanocrystal syntheses often require aid from facet-selective solution-phase chemical additives to regulate atom addition/migration fluxes or oriented particle attachment. Because of their highly tunable chemical property and robustness to a wide range of experimental conditions, peptoids contribute to a very promising group of next-generation functional chemical additives. To generalize the design philosophy, it is critical to understand the origin of facet selectivity at the molecular level. We employ molecular dynamics simulations and biased sampling methods to investigate the origin of Au(111)-favored adsorption of a peptoid, Nce3Ncp6, that is evidenced to assist the formation of five-fold twinned nanostructures. We find that the facet-selectivity is achieved through a synergistic effect of both molecule-surface and solvent-surface interactions. Extending beyond the single-chain scenario, the order of peptoid-peptoid and peptoid-surface energetics, i.e., peptoid-Au(100) < peptoid-peptoid < peptoid-Au(111), further amplifies the distinct behavior of Nce3Ncp6 chains on different Au surfaces. Our studies set the stage for future peptoid design in shape-controlled nanocrystal syntheses by probing the facet selectivity from various perspectives.

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Thermal Conductivity of Polyethylene Chains Using Molecular Dynamics Simulations

ASME 2008 3rd Energy Nanotechnology International Conference ◽

10.1115/enic2008-53006 ◽

2008 ◽

Author(s):

Asegun Henry ◽

Gang Chen

Keyword(s):

Thermal Conductivity ◽

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Polymer Chains ◽

High Thermal Conductivity ◽

Polymer Materials ◽

Single Chain ◽

Wide Range ◽

Dynamics Simulations ◽

Limiting Case

We used molecular dynamics simulations to calculate the thermal conductivity of polyethylene chains, by employing the widely used Green-Kubo formula. The simulations use the AIREBO potential and employ periodic boundary conditions to mimic the dynamics of an infinite chain. In this limiting case, we observed that when the simulation domain is large enough the thermal conductivity diverges. The results suggest that single polymer chains intrinsically have high thermal conductivity. Although polymers are generally known to have low thermal conductivity, our observation of divergent thermal conductivity in a single chain suggests that high thermal conductivity polymer materials can be engineered, which would be of interest to a wide range of applications.

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General Trend of Negative Transference Number in Li Salt/Ionic Liquid Mixtures

10.26434/chemrxiv.7728545 ◽

2019 ◽

Cited By ~ 1

Author(s):

Nicola Molinari ◽

Jonathan P. Mailoa ◽

Boris Kozinsky

Keyword(s):

Ionic Liquid ◽

Transference Number ◽

Liquid Mixtures ◽

Single Linkage ◽

Self Diffusion ◽

Wide Range ◽

Single Linkage Cluster ◽

Concentrated Solution ◽

The One ◽

Dynamics Simulations

We show that strong cation-anion interactions in a wide range of lithium-salt/ionic liquid mixtures result in a negative lithium transference number, using molecular dynamics simulations and rigorous concentrated solution theory. This behavior fundamentally deviates from the one obtained using self-diffusion coefficient analysis and agrees well with experimental electrophoretic NMR measurements, which accounts for ion correlations. We extend these findings to several ionic liquid compositions. We investigate the degree of spatial ionic coordination employing single-linkage cluster analysis, unveiling asymmetrical anion-cation clusters. Additionally, we formulate a way to compute the effective lithium charge that corresponds to and agrees well with electrophoretic measurements and show that lithium effectively carries a negative charge in a remarkably wide range of chemistries and concentrations. The generality of our observation has significant implications for the energy storage community, emphasizing the need to reconsider the potential of these systems as next generation battery electrolytes.<br>

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Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD

10.26434/chemrxiv.9461462 ◽

2019 ◽

Author(s):

Christopher John ◽

Greg M. Swain ◽

Robert P. Hausinger ◽

Denis A. Proshlyakov

Keyword(s):

Active Site ◽

Structural Model ◽

Heme Iron ◽

Chemical Transformations ◽

Experimental Conditions ◽

Strongly Coupled ◽

Non Heme Iron ◽

Reversible Redox ◽

Wide Range ◽

Complex Structural

2-Oxoglutarate (2OG)-dependent dioxygenases catalyze C-H activation while performing a wide range of chemical transformations. In contrast to their heme analogues, non-heme iron centers afford greater structural flexibility with important implications for their diverse catalytic mechanisms. We characterize an <i>in situ</i> structural model of the putative transient ferric intermediate of 2OG:taurine dioxygenase (TauD) by using a combination of spectroelectrochemical and semi-empirical computational methods, demonstrating that the Fe (III/II) transition involves a substantial, fully reversible, redox-linked conformational change at the active site. This rearrangement alters the apparent redox potential of the active site between -127 mV for reduction of the ferric state and 171 mV for oxidation of the ferrous state of the 2OG-Fe-TauD complex. Structural perturbations exhibit limited sensitivity to mediator concentrations and potential pulse duration. Similar changes were observed in the Fe-TauD and taurine-2OG-Fe-TauD complexes, thus attributing the reorganization to the protein moiety rather than the cosubstrates. Redox difference infrared spectra indicate a reorganization of the protein backbone in addition to the involvement of carboxylate and histidine ligands. Quantitative modeling of the transient redox response using two alternative reaction schemes across a variety of experimental conditions strongly supports the proposal for intrinsic protein reorganization as the origin of the experimental observations.

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Exploring siRNA Umpired Nanogels: A Tale of Barrier Combating Carrier

Current Pharmaceutical Design ◽

10.2174/1381612826666200417143800 ◽

2020 ◽

Vol 26 (27) ◽

pp. 3234-3250

Author(s):

Sushil K. Kashaw ◽

Prashant Sahu ◽

Vaibhav Rajoriya ◽

Pradeep Jana ◽

Varsha Kashaw ◽

...

Keyword(s):

Drug Delivery ◽

Biomedical Engineering ◽

Viral Infections ◽

Slow Release ◽

Molecular Level ◽

Release Kinetics ◽

Biologically Active ◽

Release Process ◽

Rapid Release ◽

Wide Range

Potential short interfering RNAs (siRNA) modulating gene expression have emerged as a novel therapeutic arsenal against a wide range of maladies and disorders containing cancer, viral infections, bacterial ailments and metabolic snags at the molecular level. Nanogel, in the current medicinal era, displayed a comprehensive range of significant drug delivery prospects. Biodegradation, swelling and de-swelling tendency, pHsensitive drug release and thermo-sensitivity are some of the renowned associated benefits of nanogel drug delivery system. Global researches have also showed that nanogel system significantly targets and delivers the biomolecules including DNAs, siRNA, protein, peptides and other biologically active molecules. Biomolecules delivery via nanogel system explored a wide range of pharmaceutical, biomedical engineering and agro-medicinal application. The siRNAs and DNAs delivery plays a vivacious role by addressing the hitches allied with chronic and contemporary therapeutic like generic possession and low constancy. They also incite release kinetics approach from slow-release while mingling to rapid release at the targets will be beneficial as interference RNAs delivery carriers. Therefore, in this research, we focused on the latest improvements in the delivery of siRNA loaded nanogels by enhancing the absorption, stability, sensitivity and combating the hindrances in cellular trafficking and release process.

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Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents

International Journal of Molecular Sciences ◽

10.3390/ijms22157879 ◽

2021 ◽

Vol 22 (15) ◽

pp. 7879

Author(s):

Yingxia Gao ◽

Yi Zheng ◽

Léon Sanche

Keyword(s):

Condensed Phase ◽

Genetic Material ◽

High Energy ◽

Dna Lesions ◽

Low Energy ◽

Experimental Investigations ◽

Experimental Conditions ◽

Strand Breaks ◽

Sequence Of Events ◽

Wide Range

The complex physical and chemical reactions between the large number of low-energy (0–30 eV) electrons (LEEs) released by high energy radiation interacting with genetic material can lead to the formation of various DNA lesions such as crosslinks, single strand breaks, base modifications, and cleavage, as well as double strand breaks and other cluster damages. When crosslinks and cluster damages cannot be repaired by the cell, they can cause genetic loss of information, mutations, apoptosis, and promote genomic instability. Through the efforts of many research groups in the past two decades, the study of the interaction between LEEs and DNA under different experimental conditions has unveiled some of the main mechanisms responsible for these damages. In the present review, we focus on experimental investigations in the condensed phase that range from fundamental DNA constituents to oligonucleotides, synthetic duplex DNA, and bacterial (i.e., plasmid) DNA. These targets were irradiated either with LEEs from a monoenergetic-electron or photoelectron source, as sub-monolayer, monolayer, or multilayer films and within clusters or water solutions. Each type of experiment is briefly described, and the observed DNA damages are reported, along with the proposed mechanisms. Defining the role of LEEs within the sequence of events leading to radiobiological lesions contributes to our understanding of the action of radiation on living organisms, over a wide range of initial radiation energies. Applications of the interaction of LEEs with DNA to radiotherapy are briefly summarized.

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Review of the Upright Balance Assessment Based on the Force Plate

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18052696 ◽

2021 ◽

Vol 18 (5) ◽

pp. 2696

Author(s):

Baoliang Chen ◽

Peng Liu ◽

Feiyun Xiao ◽

Zhengshi Liu ◽

Yong Wang

Keyword(s):

Postural Balance ◽

Force Plate ◽

Assessment Method ◽

Balance Assessment ◽

Experimental Conditions ◽

Methodological Research ◽

Assessment Tests ◽

Wide Range ◽

Foot Posture ◽

Plate System

Quantitative assessment is crucial for the evaluation of human postural balance. The force plate system is the key quantitative balance assessment method. The purpose of this study is to review the important concepts in balance assessment and analyze the experimental conditions, parameter variables, and application scope based on force plate technology. As there is a wide range of balance assessment tests and a variety of commercial force plate systems to choose from, there is room for further improvement of the test details and evaluation variables of the balance assessment. The recommendations presented in this article are the foundation and key part of the postural balance assessment; these recommendations focus on the type of force plate, the subject’s foot posture, and the choice of assessment variables, which further enriches the content of posturography. In order to promote a more reasonable balance assessment method based on force plates, further methodological research and a stronger consensus are still needed.

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Molecular-Level Investigation of Cycloaliphatic Epoxidised Ionic Liquids as a New Generation of Monomers for Versatile Poly(Ionic Liquids)

Polymers ◽

10.3390/polym13091512 ◽

2021 ◽

Vol 13 (9) ◽

pp. 1512

Author(s):

Baris Demir ◽

Gabriel Perli ◽

Kit-ying Chan ◽

Jannick Duchet-Rumeau ◽

Sébastien Livi

Keyword(s):

Ionic Liquids ◽

Molecular Level ◽

Computational Approach ◽

Polymer Materials ◽

Chemical Structures ◽

Cycloaliphatic Epoxy ◽

Polymer Models ◽

Mechanical Performances ◽

Dynamics Simulations ◽

New Generation

Recently, a new generation of polymerised ionic liquids with high thermal stability and good mechanical performances has been designed through novel and versatile cycloaliphatic epoxy-functionalised ionic liquids (CEILs). From these first promising results and unexplored chemical structures in terms of final properties of the PILs, a computational approach based on molecular dynamics simulations has been developed to generate polymer models and predict the thermo–mechanical properties (e.g., glass transition temperature and Young’s modulus) of experimentally investigated CEILs for producing multi-functional polymer materials. Here, a completely reproducible and reliable computational protocol is provided to design, test and tune poly(ionic liquids) based on epoxidised ionic liquid monomers for future multi-functional thermoset polymers.

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Polymer cyclization for the emergence of hierarchical nanostructures

Nature Communications ◽

10.1038/s41467-021-24222-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Chaojian Chen ◽

Manjesh Kumar Singh ◽

Katrin Wunderlich ◽

Sean Harvey ◽

Colette J. Whitfield ◽

...

Keyword(s):

Self Assembly ◽

Three Dimensional ◽

Hierarchical Structures ◽

Structural Similarity ◽

Vital Role ◽

Nanomaterial Synthesis ◽

Wide Range ◽

Linear Poly ◽

Polymer Folding ◽

Dynamics Simulations

AbstractThe creation of synthetic polymer nanoobjects with well-defined hierarchical structures is important for a wide range of applications such as nanomaterial synthesis, catalysis, and therapeutics. Inspired by the programmability and precise three-dimensional architectures of biomolecules, here we demonstrate the strategy of fabricating controlled hierarchical structures through self-assembly of folded synthetic polymers. Linear poly(2-hydroxyethyl methacrylate) of different lengths are folded into cyclic polymers and their self-assembly into hierarchical structures is elucidated by various experimental techniques and molecular dynamics simulations. Based on their structural similarity, macrocyclic brush polymers with amphiphilic block side chains are synthesized, which can self-assemble into wormlike and higher-ordered structures. Our work points out the vital role of polymer folding in macromolecular self-assembly and establishes a versatile approach for constructing biomimetic hierarchical assemblies.

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Towards Reduced CNNs for De-Noising Phase Images Corrupted with Speckle Noise

Photonics ◽

10.3390/photonics8070255 ◽

2021 ◽

Vol 8 (7) ◽

pp. 255

Author(s):

Marie Tahon ◽

Silvio Montresor ◽

Pascal Picart

Keyword(s):

Phase Error ◽

Speckle Noise ◽

Experimental Conditions ◽

Benchmark Data ◽

Wide Range ◽

Phase Images ◽

Different Depths ◽

Phase Data ◽

Do So

Digital holography is a very efficient technique for 3D imaging and the characterization of changes at the surfaces of objects. However, during the process of holographic interferometry, the reconstructed phase images suffer from speckle noise. In this paper, de-noising is addressed with phase images corrupted with speckle noise. To do so, DnCNN residual networks with different depths were built and trained with various holographic noisy phase data. The possibility of using a network pre-trained on natural images with Gaussian noise is also investigated. All models are evaluated in terms of phase error with HOLODEEP benchmark data and with three unseen images corresponding to different experimental conditions. The best results are obtained using a network with only four convolutional blocks and trained with a wide range of noisy phase patterns.

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Subinhibitory Antimicrobial Concentrations: A Review of In Vitro and In Vivo Data

Canadian Journal of Infectious Diseases ◽

10.1155/1992/793607 ◽

1992 ◽

Vol 3 (4) ◽

pp. 193-201 ◽

Cited By ~ 14

Author(s):

George G Zhanel ◽

Daryl J Hoban ◽

Godfrey KM Harding

Keyword(s):

Antimicrobial Activity ◽

Animal Studies ◽

Molecular Level ◽

Bacterial Virulence ◽

Antibacterial Effects ◽

Wide Range ◽

Immune Defences

Antimicrobial activity is not an ‘all or none’ effect. An increase in the rate and extent of antimicrobial action is usually observed over a wide range of antimicrobial concentrations. Subinhibitory antimicrobial concentrations are well known to produce significant antibacterial effects, and various antimicrobials at subinhibitory concentrations have been reported to inhibit the rate of bacterial growth. Bacterial virulence may be increased or decreased by subinhibitory antimicrobial concentrations by changes in the ability of bacteria to adhere to epithelial cells or by alterations in bacterial susceptibility to host immune defences. Animal studies performed in rats, hamsters and rabbits demonstrate decreased bacterial adherence, reduced infectivity and increased survival of animals treated with subinhibitory antimicrobial concentrations compared to untreated controls. The major future role of investigation of subinhibitory antimicrobial concentrations will be to define more fully, at a molecular level, how antimicrobials exert their antibacterial effects.

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