Search results for "Molecular dynamics"
showing 10 items of 1075 documents
Modeling self-sustaining waves of exothermic dissolution in nanometric Ni-Al multilayers
2016
Abstract The self-sustained propagating reaction occurring in nanometric metallic multilayers was studied by means of molecular dynamics (MD) and numerical modeling. We focused on the phenomenon of the exothermic dissolution of one metallic reactant into the less refractory one, such as Ni into liquid Al. The exothermic character is directly related to a negative enthalpy of mixing. An analytical model based on the diffusion-limited dissolution [1] coupled with heat transfer was derived to account for the main aspects of the process. Together, several microscopic simulations were carried out. The first series were set up to obtain all the parameters governing the process, including the heat…
Explosive crystallization in amorphous CuTi thin films: a molecular dynamics study
2019
Abstract Molecular dynamic simulation was used to study mechanism of self-propagating waves of explosive crystallization (devitrification) in the CuTi metallic glass. Processes in thin rectangular samples composed of one to two million atoms were simulated and compared with experimental data. It was shown that the nucleation of primary crystalline clusters occurs homogeneously due to spontaneous fluctuations of atomic structure; the clusters not
Molecular dynamics simulations of nanometric metallic multilayers: Reactivity of the Ni-Al system
2011
The reactivity of a layered Ni-Al-Ni system is studied by means of molecular dynamics simulations, using an embedded-atom method type potential. The system, made of an fcc-Al layer embedded in fcc-Ni, is initially thermalized at the fixed temperature of 600 K. The early interdiffusion of Ni and Al at interfaces is followed by the massive diffusion of Ni in the Al layer and by the spontaneous phase formation of $B2$-NiAl. The solid-state reaction is associated with a rapid system heating, which further enhances the diffusion processes. For longer times, the system may partly lose some its $B2$-NiAl microstructure in favor of the formation of $L{1}_{2}$-${\mathrm{Ni}}_{3}\mathrm{Al}$. This st…
Variable-charge method applied to study coupled grain boundary migration in the presence of oxygen
2009
International audience; One of the important differences between simulation and experiments in grain boundary (GB)-dominated metallic structures is the lack of impurities such as oxygen in computational samples. A modified variable-charge method [Elsener A, Politano O, Derlet PM, Van Swygenhoven H. Modell Simul Mater Sci Eng 2008;16:025006] based on the Streitz and Mintmire approach [Streitz FH, Mintmire JW. Phys Rev B 1994;50:11996] is used to study coupled GB motion in an Al bicrystal with a [1 1 2] symmetrical tilt GB in the presence of substitutional O, and compared with the stick–slip process identified by Cahn and Mishin [Cahn JW, Mishin Y, Suzuki A. Acta Mater 2006;54:4953]. It is found…
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 …
Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness.
2017
We present a detailed study of the parameter dependence of force probe molecular dynamics (FPMD) simulations. Using a well studied calix[4]arene catenane dimer as a model system, we systematically vary the pulling velocity and the stiffness of the applied external potential. This allows us to investigate how the results of pulling simulations operating in the constant velocity mode (force-ramp mode) depend on the details of the simulation setup. The system studied has the further advantage of showing reversible rebinding meaning that we can monitor the opening and the rebinding transition. Many models designed to extract kinetic information from rupture force distributions work in the limit…
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…
Effect of molecular Stokes shift on polariton dynamics
2021
When the enhanced electromagnetic field of a confined light mode interacts with photoactive molecules, the system can be driven into the regime of strong coupling, where new hybrid light-matter states, polaritons, are formed. Polaritons, manifested by the Rabi split in the dispersion, have shown potential for controlling the chemistry of the coupled molecules. Here, we show by angle-resolved steady-state experiments accompanied by multi-scale molecular dynamics simulations that the molecular Stokes shift plays a significant role in the relaxation of polaritons formed by organic molecules embedded in a polymer matrix within metallic Fabry-Pérot cavities. Our results suggest that in the case …
Heavy enzymes and the rational redesign of protein catalysts
2019
Abstract An unsolved mystery in biology concerns the link between enzyme catalysis and protein motions. Comparison between isotopically labelled “heavy” dihydrofolate reductases and their natural‐abundance counterparts has suggested that the coupling of protein motions to the chemistry of the catalysed reaction is minimised in the case of hydride transfer. In alcohol dehydrogenases, unnatural, bulky substrates that induce additional electrostatic rearrangements of the active site enhance coupled motions. This finding could provide a new route to engineering enzymes with altered substrate specificity, because amino acid residues responsible for dynamic coupling with a given substrate present…
Determining Factors for the Unfolding Pathway of Peptides, Peptoids, and Peptidic Foldamers.
2016
We present a study of the mechanical unfolding pathway of five different oligomers (α-peptide, β-peptide, δ-aromatic-peptides, α/γ-peptides, and β-peptoids), adopting stable helix conformations. Using force-probe molecular dynamics, we identify the determining structural factors for the unfolding pathways and reveal the interplay between the hydrogen bond strength and the backbone rigidity in the stabilization of their helix conformations. On the basis of their behavior, we classify the oligomers in four groups and deduce a set of rules for the prediction of the unfolding pathways of small foldamers.