Search results for "IONS"

Origin of Enzymatic Kinetic Isotope Effects in Human Purine Nucleoside Phosphorylase

2017

Here we report a study of the effect of heavy isotope labeling on the reaction catalyzed by human purine nucleoside phosphorylase (hPNP) to elucidate the origin of its catalytic effect and of the enzymatic kinetic isotope effect (EKIE). Using quantum mechanical and molecular mechanical (QM/MM) molecular dynamics (MD) simulations, we study the mechanism of the hPNP enzyme and the dynamic effects by means of the calculation of the recrossing transmission coefficient. A free energy surface (FES), as a function of both a chemical and an environmental coordinate, is obtained to show the role of the environment on the chemical reaction. Analysis of reactive and nonreactive trajectories allows us …

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…

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…

High Gradient Performance of an S-Band Backward Traveling Wave Accelerating Structure for Medical Hadron Therapy Accelerators

2018

The high-gradient performance of an accelerating structure prototype for a medical proton linac is presented. The structure was designed and built using technology developed by the CLIC collaboration and the target application is the TULIP (Turning Linac for Proton therapy) proposal developed by the TERA foundation. The special feature of this design is to produce gradient of more than 50 MV /m in low-β accelerating structures (v/c=0.38). The structure was tested in an S-band test stand at CERN. During the tests, the structure reached over above 60 MV/m at 1.2 μs pulse length and breakdown rate of about 5x10⁻⁶ bpp. The results presented include ultimate performance, long term behaviour and …

Les enjeux de la sécurité des objets connectés et applications de santé

2016

International audience; The challenges of security of connected objects and health applicationsThe market for connected objects and health applications is booming and is expected to be several billion euros in revenue in the coming years. Their development will have a similar impact to what we experienced with the development of internet earlier this century but even more it should disrupt the organization of our health system, profoundly change the management of care and revolutionize prevention, but it could also call into question medical confidentiality and protection of personal data. This article analyses the societal implications of OCS, the need for a dual medical and ethical evalua…

Iminium Catalysis (n → π*)

2016

Towards Atomically Precise Supported Catalysts from Monolayer‐Protected Clusters: The Critical Role of the Support

2020

Abstract Controlling the size and uniformity of metal clusters with atomic precision is essential for fine‐tuning their catalytic properties, however for clusters deposited on supports, such control is challenging. Here, by combining X‐ray absorption spectroscopy and density functional theory calculations, it is shown that supports play a crucial role in the evolution of monolayer‐protected clusters into catalysts. Based on the acidic nature of the support, cluster‐support interactions lead either to fragmentation of the cluster into isolated Au–ligand species or ligand‐free metallic Au0 clusters. On Lewis acidic supports that bind metals strongly, the latter transformation occurs while pre…