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Protein footprinting is a new methodology that is based on probing, typically with the use of mass spectrometry, of reactivity of different aminoacid residues to a modifying reagent. Data thus obtained allow one to make inferences about…

Molecular Networks · Quantitative Biology 2010-12-21 Pasquale Moio , Arman Kulyyassov , Damien Vertut , Luc Camoin , Erlan Ramankulov , Marc Lipinski , Vasily Ogryzko

The knowledge of absolute fluxes of reactive species such as radicals or energetic ions to the surface is crucial for understanding the growth or etching of thin films. These species have due to their high reactivity very low densities and…

Plasma Physics · Physics 2011-05-16 Jan Benedikt , Dirk Ellerweg , Achim von Keudell

Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex natural products, and commodity chemicals at scale. However, the adoption of biocatalysis is limited by our ability to select enzymes that will catalyze…

Biomolecules · Quantitative Biology 2022-04-06 Samuel Goldman , Ria Das , Kevin K. Yang , Connor W. Coley

Enzyme mining is rapidly evolving as a data-driven strategy to identify biocatalysts with tailored functions from the vast landscape of uncharacterized proteins. The integration of machine learning into these workflows enables…

Biomolecules · Quantitative Biology 2025-07-11 Yanzi Zhang , Felix Moorhoff , Sizhe Qiu , Wenjuan Dong , David Medina-Ortiz , Jing Zhao , Mehdi D. Davari

This work establishes a protocol to study via Molecular Dynamics simulation the degradation of Per-and Polyfluoroalkyl Substances (PFAS) in water by hydroxyl radical. To achieve this, molecular dynamics simulations are carried out, using…

Chemical Physics · Physics 2025-07-25 Axel Richard , Pascal Brault , Nicolas Froloff , Olivier Aubry , Dunpin Hong , Hervé Rabat

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…

Biomolecules · Quantitative Biology 2015-06-04 Jeremy Schofield , Paul Inder , Raymond Kapral

A combination of experiments and extensive modelling, including a chemical kinetics analysis, was performed for a CO$_2$/H$_2$O plasma in a dielectric barrier discharge. This provides a better understanding of the mechanisms related to the…

Chemical Physics · Physics 2016-06-15 Ramses Snoeckx , Alp Ozkan , Robby Aerts , Thierry Dufour , François Reniers , Annemie Bogaerts

Nanoparticles (NPs) make for intriguing heterogeneous catalysts due to their large active surface area and excellent and often size-dependent catalytic properties that emerge from a multitude of chemically different surface reaction sites.…

Low-temperature plasmas are partially ionized gases, where ions and neutrals coexist in a highly reactive environment. This creates a rich chemistry, which is often difficult to understand in its full complexity. In this work, we develop a…

Plasma Physics · Physics 2024-09-13 Diogo R. Ferreira , Alexandre Lança , Luís Lemos Alves

The physicochemical mechanisms underlying the pyrolysis of n-hexane in a high temperature Ar-H2 environment were investigated for plasma pyrolysis process. An optimal chemical kinetics model was developed using the Reaction Mechanism…

Plasma Physics · Physics 2025-06-18 Subin Choi , Chanmi Jung , Dae Hoon Lee , Jeongan Choi , Jaekwang Kim

Flexible microfluidics have found extensive utility in the biological and biomedical fields. A leading substrate material for compliant devices is polydimethylsiloxane (PDMS). Despite its many advantages, PDMS is inherently hydrophobic and…

In plasma X ray photoelectron spectroscopy emerges as a powerful platform for real time, in situ chemical analysis under conditions relevant to semiconductor processing and other plasma enabled technologies. This study investigates the…

Palladium (Pd) catalysts have been extensively studied for the direct synthesis of H2O through the hydrogen oxidation reaction at ambient conditions. This heterogeneous catalytic reaction not only holds considerable practical significance…

Materials Science · Physics 2024-04-23 Yukun Liu , Kunmo Koo , Zugang Mao , Xianbiao Fu , Xiaobing Hu , Vinayak P. Dravid

Concern of toxic compounds and their, potentially more harmful degradation products, present in aquatic environment alarmed scientific community and research on the development of novel technologies for wastewater treatment had become of…

Plasma Physics · Physics 2022-03-22 Barbara Topolovec , Nikola Skoro , Nevena Puac , Mira Petrovic

Commercial titanium dioxide is successfully plasma-treated under ambient conditions for different time periods, leading to reduced crystallite size and the creation of oxygen vacancies. Density functional theory-based calculations reveal…

Applied Physics · Physics 2024-04-26 C. Ugwumadu , I. Olaniyan , H. K. Jeong , D. A. Drabold

A wide variety of feed gases are used to generate low-temperature plasmas for the microelectronics and the sustainability applications. These plasmas often have a complex combination of reactive and non-reactive species which may have…

Advancements in differential pumping and electron optics over the past few decades have enabled x-ray photoelectron spectroscopy (XPS) measurements at (near-)ambient pressures, bridging the pressure gap for characterizing realistic sample…

Plasma Physics · Physics 2025-02-27 J. Trey Diulus , Ashley R. Head , Jorge Anibal Boscoboinik , Andrei Kolmakov

Biological nanomachines are nanometer-size macromolecular complexes that catalyze chemical reactions in the presence of substrate molecules. The catalytic functions carried out by such nanomachines in the cytoplasm, and biological membranes…

Soft Condensed Matter · Physics 2022-11-22 Yuto Hosaka , Shigeyuki Komura

High density polyethylene surfaces were exposed to the atmospheric post-discharge of a radiofrequency plasma torch supplied in helium and oxygen. Dynamic water contact angle measurements were performed to evaluate changes in surface…

Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…

Biomolecules · Quantitative Biology 2025-01-07 Martin Vögele , Neil J. Thomson , Sang T. Truong , Jasper McAvity , Ulrich Zachariae , Ron O. Dror
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