scholarly journals Direct method for MD simulations of collision-induced absorption: Application to an Ar–Xe gas mixture

2021 ◽  
Vol 276 ◽  
pp. 107926
Author(s):  
Wissam Fakhardji ◽  
Péter Szabó ◽  
Magnus Gustafsson
Keyword(s):  
Direct Method ◽  
Md Simulations ◽  
Gas Mixture ◽  
Induced Absorption

scholarly journals Contribution from dimers to the collision-induced absorption spectra in an Ar–Kr gas mixture

2019 ◽  
Vol 1289 ◽  
pp. 012021
Author(s):  
Wissam Fakhardji ◽  
M.S.A. El-Kader ◽  
Anastasios Haskopoulos ◽  
George Maroulis ◽  
Magnus Gustafsson
Keyword(s):  
Absorption Spectra ◽  
Gas Mixture ◽  
Induced Absorption

Molecular dynamics calculations of collision-induced absorption in a gas mixture of neon and krypton

2020 ◽  
Vol 152 (23) ◽  
pp. 234302
Author(s):  
Wissam Fakhardji ◽  
Péter Szabó ◽  
M. S. A. El-Kader ◽  
Magnus Gustafsson
Keyword(s):  
Molecular Dynamics ◽  
Gas Mixture ◽  
Induced Absorption ◽  
Molecular Dynamics Calculations

scholarly journals Testing the Limitations of MD-based Local Electric Fields Using the Vibrational Stark Effect in Solution: Penicillin G as a Test Case

2021 ◽  
Author(s):  
Jacek Kozuch ◽  
Samuel Schneider ◽  
Chu Zheng ◽  
Zhe Ji ◽  
Richard T Bradshaw ◽  
...  
Keyword(s):  
Electric Fields ◽  
Active Sites ◽  
Stark Effect ◽  
Force Fields ◽  
Direct Method ◽  
Md Simulations ◽  
Penicillin G ◽  
Conformational Sampling ◽  
Test Case ◽  
Water Models

<div>Non-covalent interactions underlie nearly all molecular processes in the condensed phase from solvation to</div><div>catalysis. Their quantification within a physically consistent framework remains challenging. Experimental vibrational Stark effect (VSE)-based solvatochromism can be combined with molecular dynamics (MD) simulations to quantify the electrostatic forces in solute-solvent interactions for small rigid molecules and, by extension, when these solutes bind in enzyme active sites. While generalizing this approach towards more complex (bio)molecules, such as the conformationally flexible and charged penicillin G (PenG), we were surprised to observe inconsistencies in MD-based electric fields. Combining synthesis, VSE spectroscopy, and computational methods, we provide an intimate view on the origins of these discrepancies. We observe that the electrics fields are correlated to conformation-dependent effects of the flexible PenG side-chain, including both local solvation structure and solute conformational sampling in MD. Additionally, we identified that MD-based electric fields are consistently overestimated in 3-point water models in the vicinity of charged groups; this cannot be entirely ameliorated using polarizable force fields (AMOEBA) or advanced water models. This work demonstrates the value of the VSE as a direct method for experiment-guided refinements of MD force fields and establishes a general reductionist approach to calibrating vibrational probes for complex (bio)molecules.</div>

scholarly journals Testing the Limitations of MD-based Local Electric Fields Using the Vibrational Stark Effect in Solution: Penicillin G as a Test Case

2021 ◽  
Author(s):  
Jacek Kozuch ◽  
Samuel Schneider ◽  
Chu Zheng ◽  
Zhe Ji ◽  
Richard T Bradshaw ◽  
...  
Keyword(s):  
Electric Fields ◽  
Active Sites ◽  
Stark Effect ◽  
Force Fields ◽  
Direct Method ◽  
Md Simulations ◽  
Penicillin G ◽  
Conformational Sampling ◽  
Test Case ◽  
Water Models

<div>Non-covalent interactions underlie nearly all molecular processes in the condensed phase from solvation to</div><div>catalysis. Their quantification within a physically consistent framework remains challenging. Experimental vibrational Stark effect (VSE)-based solvatochromism can be combined with molecular dynamics (MD) simulations to quantify the electrostatic forces in solute-solvent interactions for small rigid molecules and, by extension, when these solutes bind in enzyme active sites. While generalizing this approach towards more complex (bio)molecules, such as the conformationally flexible and charged penicillin G (PenG), we were surprised to observe inconsistencies in MD-based electric fields. Combining synthesis, VSE spectroscopy, and computational methods, we provide an intimate view on the origins of these discrepancies. We observe that the electrics fields are correlated to conformation-dependent effects of the flexible PenG side-chain, including both local solvation structure and solute conformational sampling in MD. Additionally, we identified that MD-based electric fields are consistently overestimated in 3-point water models in the vicinity of charged groups; this cannot be entirely ameliorated using polarizable force fields (AMOEBA) or advanced water models. This work demonstrates the value of the VSE as a direct method for experiment-guided refinements of MD force fields and establishes a general reductionist approach to calibrating vibrational probes for complex (bio)molecules.</div>

Thermal Conductivity and Natural Cooling Rate of Excimer-Laser Annealed SI: A Molecular Dynamics Study

2006 ◽  
Vol 910 ◽  
Author(s):  
Byoung-Min Lee ◽  
Baek Seok Seong ◽  
Hong Koo Baik ◽  
Shinji Munetoh ◽  
Teruaki Motooka
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Cooling Rate ◽  
Size Effects ◽  
Direct Method ◽  
Finite Size ◽  
Md Simulations ◽  
Heat Current ◽  
Finite Size Effects ◽  
The Relationship

AbstractTo investigate the relationship between the thermal conductivity and the cooling rate, we have performed molecular-dynamics (MD) simulations based on a combination of the Langevin and Newton equations to deal with a heat transfer from l-Si to c-Si. The thermal conductivity of c-Si was measured by the direct method. In order to deal with finite-size effects, different cell sizes perpendicular to the direction of the heat current were used. The values of the thermal conductivity of 58 W/mK and 35.7 W/mK in the Tersoff potential were obtained at 1000 K and 1500 K, respectively. A MD cell with a length of 488.75 ¡Ê in the direction of a heat flow was used for estimating the natural cooling rate. The initial c/l interface systems were obtained by setting the temperatures of the MD cell at 1000 K and 1500 K, respectively, for Z <= 35 ¡Ê and 3800 K for Z > 35 ¡Ê. During the natural cooling processes, the temperature of the bottom 10 ¡Ê of the MD cell was controlled. The cooling rates of 7.4 × 1011 K/sec for 1000 K and 5.9 × 1011 K/sec for 1500 K were obtained, respectively.

An innovative method for exhaust gases toxicity evaluation in the miniature turbojet engine

2017 ◽  
Vol 89 (6) ◽  
pp. 757-763 ◽  
Author(s):  
Bartosz Gawron ◽  
Tomasz Białecki ◽  
Anna Janicka ◽  
Aleksander Górniak ◽  
Maciej Zawiślak
Keyword(s):  
Respiratory System ◽  
Direct Method ◽  
Small Scale ◽  
Gas Mixture ◽  
Toxicity Evaluation ◽  
Content Type ◽  
Exhaust Gases ◽  
Turbojet Engine ◽  
Human Respiratory System

Purpose The purpose of this paper is to present an assessment method of the toxicity emission evaluation during combustion in the miniature turbojet engine. Design/methodology/approach A small-scale turbojet engine was used for the research because measurements on real aircraft turbines are complex and expensive. The experiment was performed in accordance with innovative BAT – CELL Bio – Ambient Cell method which consists of determination of virtual toxic impact of the gas mixture on the living cells; it is therefore a direct method. The most significant innovation of this method is that, during the test, which consists of exposing the cells to the gas mixture, the cells are deprived of culture fluid. Findings The preliminary analysis shows that the method used here allows to determine the virtual impact of the gases on the human respiratory system and skin. It could be useful in defining the arduousness of an airport. The obtained results show that both of exhaust gases represent similar toxicity. Practical implications The new in vitro method allows to determine the virtual impact of the gases on the human respiratory system and skin. Significant potential for further research not only on the miniaturised engines, but also in the case of real objects, as this method does not have to be performed in a laboratory. Originality/value The work presents potential application of the innovatory method for exhaust gases toxicity evaluation in jet engines, which could be useful in defining the arduousness of an airport.

Characterization of frozen hydrated biological specimens by low-loss EELS

1992 ◽  
Vol 50 (2) ◽  
pp. 1572-1573
Author(s):  
Songquan Sun ◽  
Richard D. Leapman
Keyword(s):  
Water Content ◽  
Direct Method ◽  
Internal Standard ◽  
Dry Weight ◽  
Dark Field ◽  
Protein Solutions ◽  
Subcellular Compartment ◽  
Differential Shrinkage ◽  
Electron Energy Loss

Analyses of ultrathin cryosections are generally performed after freeze-drying because the presence of water renders the specimens highly susceptible to radiation damage. The water content of a subcellular compartment is an important quantity that must be known, for example, to convert the dry weight concentrations of ions to the physiologically more relevant molar concentrations. Water content can be determined indirectly from dark-field mass measurements provided that there is no differential shrinkage between compartments and that there exists a suitable internal standard. The potential advantage of a more direct method for measuring water has led us to explore the use of electron energy loss spectroscopy (EELS) for characterizing biological specimens in their frozen hydrated state.We have obtained preliminary EELS measurements from pure amorphous ice and from cryosectioned frozen protein solutions. The specimens were cryotransfered into a VG-HB501 field-emission STEM equipped with a 666 Gatan parallel-detection spectrometer and analyzed at approximately −160 C.

A Simple Real-Space Channelling Theory for Electron Diffraction and HREM

1990 ◽  
Vol 48 (1) ◽  
pp. 64-65
Author(s):  
D. Van Dyck
Keyword(s):  
High Resolution ◽  
Electron Diffraction ◽  
Direct Method ◽  
Real Space ◽  
Zone Axis ◽  
Phase Object ◽  
High Resolution Images ◽  
The Many ◽  
Analytical Expressions ◽  
Electron Wavefunction

The computation of the many beam dynamical electron diffraction amplitudes or high resolution images can only be done numerically by using rather sophisticated computer programs so that the physical insight in the diffraction progress is often lost. Furthermore, it is not likely that in this way the inverse problem can be solved exactly, i.e. to reconstruct the structure of the object from the knowledge of the wavefunction at its exit face, as is needed for a direct method [1]. For this purpose, analytical expressions for the electron wavefunction in real or reciprocal space are much more useful. However, the analytical expressions available at present are relatively poor approximations of the dynamical scattering which are only valid either for thin objects ((weak) phase object approximation, thick phase object approximation, kinematical theory) or when the number of beams is very limited (2 or 3). Both requirements are usually invalid for HREM of crystals. There is a need for an analytical expression of the dynamical electron wavefunction which applies for many beam diffraction in thicker crystals. It is well known that, when a crystal is viewed along a zone axis, i.e. parallel to the atom columns, the high resolution images often show a one-to-one correspondence with the configuration of columns provided the distance between the columns is large enough and the resolution of the instrument is sufficient. This is for instance the case in ordered alloys with a column structure [2,3]. From this, it can be suggested that, for a crystal viewed along a zone axis with sufficient separation between the columns, the wave function at the exit face does mainly depend on the projected structure, i.e. on the type of atom columns. Hence, the classical picture of electrons traversing the crystal as plane-like waves in the directions of the Bragg beams which historically stems from the X-ray diffraction picture, is in fact misleading.

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