Assessment of interatomic potentials for atomistic analysis of static and dynamic properties of screw dislocations in W

Screw dislocations in bcc metals display non-planar cores at zero temperature which result in high lattice friction and thermally activated strain rate behavior. In bcc W, electronic structure molecular statics calculations reveal a compact, non-degenerate core with an associated Peierls stress between 1.7 and 2.8 GPa. However, a full picture of the dynamic behavior of dislocations can only be gained by using more efficient atomistic simulations based on semiempirical interatomic potentials. In this paper we assess the suitability of five different potentials in terms of static properties relevant to screw dislocations in pure W. As well, we perform molecular dynamics simulations of stress-assisted glide using all five potentials to study the dynamic behavior of screw dislocations under shear stress. Dislocations are seen to display thermally-activated motion in most of the applied stress range, with a gradual transition to a viscous damping regime at high stresses. We find that one potential predicts a core transformation from compact to dissociated at finite temperature that affects the energetics of kink-pair production and impacts the mechanism of motion. We conclude that a modified embedded-atom potential achieves the best compromise in terms of static and dynamic screw dislocation properties, although at an expense of about ten-fold compared to central potentials

Ultra-Fast Semi-Empirical Quantum Chemistry for High-Throughput Computational Campaigns with Sparrow

Semi-empirical quantum chemical approaches are known to compromise accuracy for feasibility of calculations on huge molecules. However, the need for ultrafast calculations in interactive quantum mechanical studies, high-throughput virtual screening, and for data-driven machine learning has shifted the emphasis towards calculation runtimes recently. This comes with new constraints for the software implementation as many fast calculations would suffer from a large overhead of manual setup and other procedures that are comparatively fast when studying a single molecular structure, but which become prohibitively slow for high-throughput demands. In this work, we discuss the effect of various well-established semi-empirical approximations on calculation speed and relate this to data transfer rates from the raw-data source computer to the results visualization front end. For the former, we consider desktop computers, local high performance computing, as well as remote cloud services in order to elucidate the effect on interactive calculations, for web and cloud interfaces in local applications, and in world-wide interactive virtual sessions. The models discussed in this work have been implemented into our open-source software SCINE Sparrow.Comment: 39 pages, 4 figures, 4 table

Analytic many-body potential for GaAs(001) homoepitaxy: Bulk and surface properties

We employ atomic-scale simulation methods to investigate bulk and surface properties of an analytic Tersoff- Abell type potential for describing interatomic interactions in GaAs. The potential is a modified form of that proposed by Albe and colleagues [Phys. Rev. B 66, 035205 (2002)] in which the cut-off parameters for the As-As interaction have been shortened.With this modification, many bulk properties predicted by the potential for solid GaAs are the same as those in the original potential, but properties of the GaAs(001) surface better match results from first-principles calculations with density-functional theory (DFT). We tested the ability of the potential to reproduce the phonon dispersion and heat capacity of bulk solid GaAs by comparing it to experiment and the overall agreement is good. In the modified potential, the GaAs(001) β2(2 × 4) reconstruction is favored under As-rich growth conditions in agreement with DFT calculations. Additionally, the binding energies and diffusion barriers for a Ga adatom on the β2(2 × 4) reconstruction generally match results from DFT calculations. These studies indicate that the potential is suitable for investigating aspects of GaAs(001) homoepitaxy

Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters

Modern semiempirical methods are of sufficient accuracy when used in the modeling of molecules of the same type as used as reference data in the parameterization. Outside that subset, however, there is an abundance of evidence that these methods are of very limited utility. In an attempt to expand the range of applicability, a new method called PM7 has been developed. PM7 was parameterized using experimental and high-level ab initio reference data, augmented by a new type of reference data intended to better define the structure of parameter space. The resulting method was tested by modeling crystal structures and heats of formation of solids. Two changes were made to the set of approximations: a modification was made to improve the description of noncovalent interactions, and two minor errors in the NDDO formalism were rectified. Average unsigned errors (AUEs) in geometry and ΔH(f) for PM7 were reduced relative to PM6; for simple gas-phase organic systems, the AUE in bond lengths decreased by about 5 % and the AUE in ΔH(f) decreased by about 10 %; for organic solids, the AUE in ΔH(f) dropped by 60 % and the reduction was 33.3 % for geometries. A two-step process (PM7-TS) for calculating the heights of activation barriers has been developed. Using PM7-TS, the AUE in the barrier heights for simple organic reactions was decreased from values of 12.6 kcal/mol(-1) in PM6 and 10.8 kcal/mol(-1) in PM7 to 3.8 kcal/mol(-1). The origins of the errors in NDDO methods have been examined, and were found to be attributable to inadequate and inaccurate reference data. This conclusion provides insight into how these methods can be improved. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00894-012-1667-x) contains supplementary material, which is available to authorized users

Universal QM/MM Approaches for General Nanoscale Applications

Hybrid quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address chemical phenomena in complex molecular environments. However, they are tedious to construct and they usually require significant manual preprocessing and expertise. As a result, these models may not be easily transferable to new application areas and the many parameters are not easy to adjust to reference data that are typically scarce. Therefore, it has been difficult to devise automated procedures of controllable accuracy, which makes such type of modelling far from being standardized or of black-box type. Although diverse best-practice protocols have been set up for the construction of individual components of a QM/MM model (e.g., the MM potential, the type of embedding, the choice of the QM region), no automated procedures are available for all steps of the QM/MM model construction. Here, we review the state of the art of QM/MM modeling with a focus on automation. We elaborate on the MM model parametrization, on atom-economical physically-motivated QM region selection, and on embedding schemes that incorporate mutual polarization as critical components of the QM/MM model. In view of the broad scope of the field, we mostly restrict the discussion to methodologies that build de novo models based on first-principles data, on uncertainty quantification, and on error mitigation with a high potential for automation. Ultimately, it is desirable to be able to set up reliable QM/MM models in a fast and efficient automated way without being constrained by some specific chemical or technical limitations.Comment: 54 pages, 3 figures, 1 tabl

THE DESIGN OF A POINT OF CARE FET BIOSENSOR TO DETECT AND SCREEN COVID-19

This work proposes and demonstrates a biosensor with reduced Graphene Oxide (rGO) based Field Effect Transistor (FET) for rapid and selective detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The main objective of this thesis is to detect the SARS-CoV-2 spike protein antigen on spot selectively and rapidly. The rGO channel is coated with the spike protein antibodies to achieve selectivity. Moreover, the biosensing performance and specificity are governed by decorating the sensor’s channel with Metal Nanoparticles (MNPs) such as, copper, and silver. The designed sensor successfully detects the SARS-CoV-2 spike protein and shows singular electrical behavior for detection. The rGO-FET biosensor electronic transport characteristics such as transmission spectrum, electronic current, and transfer curves are studied by using semiempirical modeling combined with a nonequilibrium Green’s function. The transmission spectrum, I-V and transfer curves are investigated to spot the performance alteration caused by detecting the target molecule. The sensor is also tested against another virus, namely Rabies virus, and showed no detection reaction towards it. The introduced sensor is 8.2 nm long and 6.1 nm wide which makes it a perfect candidate for easy handling and transporting. RGO FET-based biosensor is developed and tested to take the advantage of the unique electronic properties of the rGO channel and offer a quick, rapid, easy, and accurate detection method for SARS-CoV-2 virus. The semiempirical study, along with the simulations results are in agreement with the previous literature studies and provide an excellent pathway for practical fabrication

Improved time-resolved measurements of inorganic ions in particulate matter by PILS-IC integrated with a sample pre-concentration system

A particle-into-liquid sampler coupled with ion chromatograph (PILS-IC) for the on-line measurement of inorganic ions has been modified by the insertion of two ion-exchange pre-concentration cartridges that enrich the sample during the period of the IC analysis. The limits of detection of the modified instrument were 10-15 times lower and the time coverage 24 times higher (from 2 to 48 min per hour) than those of the original PILS-IC setup. The instrumental performance in terms of recovery and break-through volume from the cartridges was satisfactory. The modified PILS-IC was operated in comparison with a diffusion denuder line and with a high-resolution time-of-flight aerosol mass spectrometer (HR-TOF-AMS) during a short intensive measurement period organized in the framework of the European Monitoring and Evaluation Programme (EMEP), a co-operative program for monitoring and evaluation of the long-range transmission of the air pollutants in Europe. The instrument showed a quantitative response in agreement with the results of the diffusion lines, and an ability to trace fine concentration variations not so different from the performance of the much more complex HR-TOF-AMS. From the time patterns of the ion concentrations measured by the modified PILS-IC, it was possible to obtain useful information about the variations in the air quality and in the strength of the particulate matter sourc

Performance of Localized-Orbital Coupled Cluster Approaches for the Conformational Energies of Longer n-alkane Chains

We report an update and enhancement of the ACONFL (conformer energies of large alkanes [Ehlert, S.; Grimme, S.; Hansen, A. J. Phys. Chem. A 2022, 126, 3521-3535]) dataset. For the ACONF12 (n-dodecane) subset, we report basis set limit canonical CCSD(T) reference data obtained from MP2-F12/cc-pV{T,Q}Z-F12 extrapolation, [CCSD(F12*)-MP2-F12]/aug-cc-pVTZ-F12, and a (T) correction from conventional CCSD(T)/aug-cc-pV{D,T}Z calculations. Then we explored the performance of a variety of single and composite localized-orbital CCSD(T) approximations, ultimately finding an affordable LNO-CCSD(T)-based post-MP2 correction that agrees to 0.008 kcal/mol MAD (mean absolute deviation) with the revised canonical reference data. In tandem with canonical MP2-F12/CBS extrapolation, this was then used to re-evaluate the ACONF16 and ACONF20 subsets for n-hexadecane and n-icosane, respectively. A revised ACONFL set was thus obtained. It was then used to assess the performance of different localized-orbital coupled cluster approaches, such as PNO-LCCSD(T) as implemented in MOLPRO, DLPNO-CCSD (T1) as implemented in ORCA, and LNO-CCSD(T) as implemented in MRCC, at their various accuracy settings. A three-tier LNO-CCSD(T)-based composite scheme disagrees by only 0.02 kcal/mol from the revised ACONFL reference data. When extrapolated to the complete PNO space limit, DLPNO-CCSD(T1, Tight) and a composite method are the best picks among all the localized coupled cluster methods tested for the dodecane conformers. Dispersion-corrected dRPA-based double hybrids perform remarkably well for the ACONFL set. While the revised reference data do not affect any conclusions on the less accurate methods, they may upend orderings for more accurate methods with error statistics on the same order as the difference between reference datasets.Comment: 28 pages, submitte

Simulations of proton transfer processes using reactive force fields

Within this thesis we presented the development of reactive force fields that are ca- pable to describe the dynamics of proton and hydrogen atom transfer processes. The presented implementation in CHARMM overcomes the limitation that bond break- ing and formation cannot be investigated by conventional classical MD simulations. Derived from high-level ab initio calculations this approach combines the accuracy of such calculations with the speed of MD simulations. The high-quality force fields of the prototype systems are comparable to high-level ab initio calculations in terms of structure and energy barriers. The PESs of proton transfer reactions are extremely sensitive with respect to the chemical environment. Nevertheless one is always able to classify the PT under investigation into symmetric and asymmetric PES. We de- veloped a series of parameter sets that are not only able to describe symmetric and asymmetric correctly but also can accommodate to different locations of energetic minima and barriers. The chosen three-dimensional potential energy functions have shown to be quite flexible and transferable in characterizing PT reactions in quite diverse chemical systems. The morphing transformation of MMPT force field param- eter, starting from one of our prototype systems to develop a new force field for a new molecular system which exhibits a similar topology in the PES along the proton reac- tion coordinates, has been shown to be successfully applicable in various examples. Energy scaling has been employed to investigate the effect on the proton transfer os- cillation in NH+ 4 · · ·NH3. New parameters through morphing have been developed for protonated diglyme, as well as for double proton transfer in 2PY2HP and for as- partic acid and water as model system for PT reactions in the active site of bacterial ferredoxin I. We applied the MMPT force field to investigate the vibrational infrared spectra of proton-bound species and explored the relationship of infrared spectra for protonated water dimer and protonated diglyme. The results for protonated water dimer compared well with other high-level calculations. Besides the further system- atic development of the morphing approach one can also employ the force field in combination with Feynman path integral methods. The MMPT force field could be a viable alternative to lower level quantum mechanical methods because the accuracy of the force field is only limited by the initial determination of the underlying PES for the PT of interest