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My thesis mostly focusses on the systems of porphyrin molecules adsorbed on single-crystalline metallic surfaces. Cyclic tetrapyrrole porphyrins play key roles in many important chemical and biological processes, such as oxygen transport in…

Atomic and Molecular Clusters · Physics 2022-01-25 Qiushi Zhang

Several methods are constructed for large-scale electronic structure calculations. Test calculations are carried out with up to 10^7 atoms. As an application, cleavage process of silicon is investigated by molecular dynamics simulation with…

Materials Science · Physics 2007-05-23 T. Hoshi , R. Takayama , Y. Iguchi , T. Fujiwara

Electron energy loss spectroscopy is consolidating as a powerful tool to explore electronic (as well as vibrational) excitations of matter, including molecules. Performed in a scanning transmission electron microscope, this technique is…

Chemical Physics · Physics 2021-03-05 Ciro A. Guido , Enzo Rotunno , Matteo Zanfrognini , Stefano Corni , Vincenzo Grillo

Superresolution microscopy has become a powerful tool to investigate the internal structure of complex colloidal and polymeric systems, such as microgels, at the nanometer scale. The ability to monitor microgels response to temperature…

A new, more comprehensive model of gas-grain chemistry in hot molecular cores is presented, in which nondiffusive reaction processes on dust-grain surfaces and in ice mantles are implemented alongside traditional diffusive surface/bulk-ice…

Astrophysics of Galaxies · Physics 2022-02-23 Robin T. Garrod , Mihwa Jin , Kayla A. Matis , Dylan Jones , Eric R. Willis , Eric Herbst

Despite many advantages associated with the use of spherical particles, in practice, non-spherical particles are the main ingredient in sintering-based processing techniques, like selective-laser-sintering, where their shape and surface…

Soft Condensed Matter · Physics 2019-12-12 Amirmehdi Salehi , Gholamreza Pircheraghi

This paper presents for the first time an innovative instrument called an inverted scanning microwave microscope (iSMM), which is capable of noninvasive and label-free imaging and characterization of intracellular structures of a live cell…

Molecules are the smallest unit in matters that can exist independently, relatively stable, and maintain physical and chemical activities. The atomic species, alignment commands, and chemical bonds are key factors to dominate their…

Chemical Physics · Physics 2023-08-11 Liangfei Duan , Tong Zhou , Huiqin Yang , Weihua Mu , Zhongshan Deng , Jing Liu , Qingju Liu

Electrospray ion-beam deposition (ES-IBD) is a versatile tool to study structure and reactivity of molecules from small metal clusters to large protein assemblies. It brings molecules gently into the gas phase where they can be accurately…

Materials exhibit geometric structures across mesoscopic to microscopic scales, influencing macroscale properties such as appearance, mechanical strength, and thermal behavior. Capturing and modeling these multiscale structures is…

Graphics · Computer Science 2025-04-15 Bojja Venu , Adam Bosak , Juan Raul Padron-Griffe

The engineering of quantum materials requires the development of tools able to address various synthesis and characterization challenges. These include the establishment and refinement of growth methods, material manipulation, and defect…

Materials Science · Physics 2023-07-13 Ondrej Dyck , Andrew R. Lupini , Stephen Jesse

The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…

Computational Physics · Physics 2025-10-03 Simon Gravelle , Cecilia M. S. Alvares , Jacob R. Gissinger , Axel Kohlmeyer

Aqueous solid-liquid interfaces (SLI) are ubiquitous in nature and technology, often hosting molecular-level processes with macroscopic consequences. Molecular dynamics (MD) simulations offer a tool of choice to investigate interfacial…

Soft Condensed Matter · Physics 2025-08-12 Mahdi Tavakol , Kislon Voïtchovsky

A multiscale QM/classical approach is presented, that is able to model the optical properties of complex nanostructures composed of a molecular system adsorbed on metal nanoparticles. The latter are described by a combined…

Chemical Physics · Physics 2024-10-29 Pablo Grobas Illobre , Piero Lafiosca , Luca Bonatti , Tommaso Giovannini , Chiara Cappelli

Semiconductor devices continue to press into the nanoscale regime, and new applications have emerged for which the quantum properties of dopant atoms act as the functional part of the device, underscoring the necessity to probe the quantum…

Mesoscale and Nanoscale Physics · Physics 2015-05-13 I. Kuljanishvili , C. Kayis , J. F. Harrison , C. Piermarocchi , T. A. Kaplan , S. H. Tessmer , L. N. Pfeiffer , K. W. West

We examine the organization and dynamics of binary colloidal monolayers composed of micron-scale silica particles interspersed with smaller-diameter silica particles that serve as minority component impurities. These binary monolayers are…

Soft Condensed Matter · Physics 2023-05-22 Jonathan G. Raybin , Rebecca B. Wai , Naomi S. Ginsberg

We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…

Chemical Physics · Physics 2025-08-22 Indranil Mal , Milan Kočí , Paolo Nicolini , Prokop Hapala

Conventional lithography methods involving pattern transfer through resist templating face challenges of material compatibility with various process solvents. Other approaches of direct material writing often compromise pattern complexity…

Materials Science · Physics 2024-07-19 Shuangshuang Zeng , Tian Tian , Jiwoo Oh , Chih-Jen Shih

Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…

Soft Condensed Matter · Physics 2016-08-08 I. Nezbeda , J. Jirsák , F. Moučka , W. R. Smith

We demonstrate a novel single molecule technique that is compatible with high precision measurements and obtain the spectrum of two molecular ion species. While the current result yields modest spectral resolution due to a broad light…

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