Search results for "computer"
showing 10 items of 30657 documents
Adaptive Finite Temperature String Method in Collective Variables.
2017
Here we present a modified version of the on-the-fly string method for the localization of the minimum free energy path in a space of arbitrary collective variables. In the proposed approach the shape of the biasing potential is controlled by only two force constants, defining the width of the potential along the string and orthogonal to it. The force constants and the distribution of the string nodes are optimized during the simulation, improving the convergence. The optimized parameters can be used for umbrella sampling with a path CV along the converged string as the reaction coordinate. We test the new method with three fundamentally different processes: chloride attack to chloromethane…
Data Reweighting in Metadynamics Simulations.
2020
The data collected along a metadynamics simulation can be used to recover information about the underlying unbiased system by means of a reweighting procedure. Here, we analyze the behavior of several reweighting techniques in terms of the quality of the reconstruction of the underlying unbiased free energy landscape in the early stages of the simulation and propose a simple reweighting scheme that we relate to the other techniques. We then show that the free energy landscape reconstructed from reweighted data can be more accurate than the negative bias potential depending on the reweighting technique, the stage of the simulation, and the adoption of well-tempered or standard metadynamics. …
Introducing Memory in Coarse-Grained Molecular Simulations
2021
[Image: see text] Preserving the correct dynamics at the coarse-grained (CG) level is a pressing problem in the development of systematic CG models in soft matter simulation. Starting from the seminal idea of simple time-scale mapping, there have been many efforts over the years toward establishing a meticulous connection between the CG and fine-grained (FG) dynamics based on fundamental statistical mechanics approaches. One of the most successful attempts in this context has been the development of CG models based on the Mori–Zwanzig (MZ) theory, where the resulting equation of motion has the form of a generalized Langevin equation (GLE) and closely preserves the underlying FG dynamics. In…
Bond Dissociation Energies for Diatomic Molecules Containing 3d Transition Metals: Benchmark Scalar-Relativistic Coupled-Cluster Calculations for 20 …
2017
Benchmark scalar-relativistic coupled-cluster calculations for dissociation energies of the 20 diatomic molecules containing 3d transition metals in the 3dMLBE20 database ( J. Chem. Theory Comput. 2015 , 11 , 2036 ) are reported. Electron correlation and basis set effects are systematically studied. The agreement between theory and experiment is in general satisfactory. For a subset of 16 molecules, the standard deviation between computational and experimental values is 9 kJ/mol with the maximum deviation being 15 kJ/mol. The discrepancies between theory and experiment remain substantial (more than 20 kJ/mol) for VH, CrH, CoH, and FeH. To explore the source of the latter discrepancies, the …
MD Simulation Investigation on the Binding Process of Smoke-Derived Germination Stimulants to Its Receptor
2019
Karrikins (KARs) are a class of smoke-derived seed germination stimulants with great significance in both agriculture and plant biology. By means of direct binding to the receptor protein KAI2, the compounds can initiate the KAR signal transduction pathway, hence triggering germination of the dormant seeds in the soil. In the research, several molecular dynamics (MD) simulation techniques were properly integrated to investigate the binding process of KAR1 to KAI2 and reveal the details of the whole binding event. The calculated binding free energy, -7.00 kcal/mol, is in good agreement with the experimental measurement, -6.83 kcal/mol. The obtained PMF profile indicates the existence of thre…
Monte Carlo Simulations of Au38(SCH3)24 Nanocluster Using Distance-Based Machine Learning Methods
2020
We present an implementation of distance-based machine learning (ML) methods to create a realistic atomistic interaction potential to be used in Monte Carlo simulations of thermal dynamics of thiol...
Ten Facets, One Force Field: The GAL19 Force Field for Water–Noble Metal Interfaces
2020
International audience; Understanding the structure of the water/metal interfaces plays an important role in many areas ranging from surface chemistry to environmental processes. The size, required phase-space sampling, and the slow diffusion of molecules at the water/metal interfaces motivate the development of accurate force fields. We develop and parametrize GAL19, a novel force field, to describe the interaction of water with two facets (111 and 100) of five metals (Pt, Pd, Au, Ag, Cu). To increase transferability compared to its predecessor GAL17, the water–metal interaction is described as a sum of pairwise terms. The interaction energy has three contributions: (i) physisorption is de…
Operational Experience and Performance of the Belle II Pixel Detector
2021
Proceedings of the 29th International Workshop on Vertex Detectors (VERTEX2020), Tsukuba, Japan (Online); Journal of the Physical Society of Japan 34, 010002 (2021). doi:10.7566/JPSCP.34.010002
Neutron imaging and tomography: Applications in food science
2018
International audience; Neutron imaging and tomography allow observing the structure of large objects (from few to hundred centimeters) at a resolution around 100 μm. This non-destructive method is based on the detection of the transmission of a neutron beam through an object in 2D (imaging) or 3D after rotating the sample (tomography). The components of the object attenuate the neutron beam differently, depending on their composition, and produce accurate pictures of objects which give information about their structure. Neutron imaging has been used for quality control purposes in industries (aircraft, motor engineering...), but also find application from materials sciences (fuel cells, li…
Active components for integrated plasmonic circuits
2009
International audience; We present a comprehensive study of highly efficient and compact passive and active components for integrated plasmonic circuit based on dielectric-loaded surface plasmon polariton waveguides.