Kinetic Quantities Research Articles

Mobilities and diffusivities for bcc Nb–W, Nb–Ta, Zr–Mo and Zr–Hf alloys

CALPHAD kinetic has evolved to maturity where the atomic mobilities can be combined with thermodynamic descriptions to retrieve kinetic quantities for nucleation and subsequent growth/coarsening. In order to assist computational design of refractory alloys that are indispensable for nuclear applications, the atomic mobilities and the related kinetic implications for bcc Nb–W, Nb–Ta, Zr–Mo and Zr–Hf alloys are studied in this work, based on the CALPHAD framework and the DICTRA software. The self-diffusion coefficients, impurity diffusion coefficients, tracer diffusion coefficients and interdiffusion coefficients for such binary systems are critically explored, the results of which are beneficial to facilitate alloy design and product development for the nuclear industry.

A mixed formulation of mortar-based contact with friction

A classical three-field mixed variational formulation of frictionless contact is extended to the frictional regime. The construction of the variational framework with respect to a curvilinear coordinate system naturally induces projected mortar counterparts of tangential kinetic and kinematic quantities while automatically satisfying incremental objectivity of the associated discrete penalty-regularized mortar constraints. Mixed contact variables that contribute to the boundary value problem are then obtained through unconstrained, lumped or constrained recovery approaches, complemented by Uzawa augmentations. Patch tests and surface locking studies are presented together with local and global quality monitors of the contact interactions in two- and three-dimensional settings at the infinitesimal and finite deformation regimes.

Density Functional Theoretical Study on the Substituent Effect in Aryl Halide Oxidative Additions to a Rh Pincer Complex

were performed to determine the Gibbs energy ofthe reaction for C–X oxidative addition to fragment 1, andcompare the relative stability of the initial adduct andoxidative addition product. In addition, the Gibbs energy ofactivation of the reactions was calculated. These thermo-dynamic and kinetic quantities are the key parameters fordetermining the preference and reactivity toward chemicalspecies. DFT calculations

Protein folding kinetics and thermodynamics from atomistic simulation

Advances in simulation techniques and computing hardware have created a substantial overlap between the timescales accessible to atomic-level simulations and those on which the fastest-folding proteins fold. Here we demonstrate, using simulations of four variants of the human villin headpiece, how simulations of spontaneous folding and unfolding can provide direct access to thermodynamic and kinetic quantities such as folding rates, free energies, folding enthalpies, heat capacities, Φ-values, and temperature-jump relaxation profiles. The quantitative comparison of simulation results with various forms of experimental data probing different aspects of the folding process can facilitate robust assessment of the accuracy of the calculations while providing a detailed structural interpretation for the experimental observations. In the example studied here, the analysis of folding rates, Φ-values, and folding pathways provides support for the notion that a norleucine double mutant of villin folds five times faster than the wild-type sequence, but following a slightly different pathway. This work showcases how computer simulation has now developed into a mature tool for the quantitative computational study of protein folding and dynamics that can provide a valuable complement to experimental techniques.

A mixed formulation of mortar-based frictionless contact

A class of mortar-based frictionless contact formulations is derived based on a classical three-field mixed variational framework. Within a penalty regularization complemented by Uzawa augmentations, discrete mortar constraints are naturally induced by the variational setting. Major aspects of earlier mortar approaches are obtained through constrained, lumped or unconstrained recovery procedures for the mixed kinematic and kinetic mortar quantities from their projected counterparts. Two- and three-dimensional examples at the infinitesimal and finite deformation regimes highlight the local and global quality of the contact interactions.

Kinetic roughening, global quantities, and fluctuation–dissipation relations

Growth processes and interface fluctuations can be studied through the properties of global quantities. We here discuss a global quantity that not only captures better the roughness of an interface than the widely studied surface width, but that is also directly conjugate to an experimentally accessible parameter, thereby allowing us to study in a consistent way the global response of the system to a global change of external conditions. Exploiting the full analyticity of the linear Edwards–Wilkinson and Mullins–Herring equations, we study in detail various two-time functions related to that quantity. This quantity fulfills the fluctuation–dissipation theorem when considering steady-state equilibrium fluctuations.

A homogenization method for thermomechanical continua using extensive physical quantities

This article proposes a continuum thermomechanical homogenization method inspired by the Irving–Kirkwood procedure relating the atomistic equations of motion to the balance laws of continuum mechanics. This method yields expressions for the macroscopic stress and heat flux in terms of microscopic kinematic and kinetic quantities. The resulting equation for macroscopic stress affords a rational comparison with the widely used Hill–Mandel stress-deformation condition, while the one for heat flux reduces, under certain assumptions, to a Hill–Mandel-like condition involving heat flux and the gradient of temperature.

Atomic mobilities, diffusivities and their kinetic implications for U–[formula omitted] ([formula omitted], Nb and Mo) bcc alloys

Based on various kinds of diffusivities as well as the thermodynamic descriptions within the CALPHAD framework, the atomic mobilities of U, Ti, Nb and Mo are explored in this work with the DICTRA software. The mobility end-members are evaluated from the impurity diffusivities as well as the extrapolated interdiffusivities, while the interaction parameters for atomic mobilities are determined from the tracer diffusivities, the intrinsic diffusivities and the interdiffusivities. The reliability of such purely kinetic quantities is carefully verified by the comparison between the calculated and experimentally measured quantities, including the concentration profiles in Ti/U diffusion couples. This work is established to provide fundamental information for U-based alloy design when the kinetics of microstructure evolution is of prime concern.

Plate with decentralised velocity feedback loops: Power absorption and kinetic energy considerations

This paper is focused on the vibration effects produced by an array of decentralised velocity feedback loops that are evenly distributed over a rectangular thin plate to minimise its flexural response. The velocity feedback loops are formed by collocated ideal velocity sensor and point force actuator pairs, which are unconditionally stable and produce ‘sky-hook’ damping on the plate. The study compares how the overall flexural vibration of the plate and the local absorption of vibration power by the feedback loops vary with the control gains. The analysis is carried out both considering a typical frequency-domain formulation based on kinetic energy and structural power physical quantities, which is normally used to study vibration and noise problems, and a time-domain formulation also based on kinetic energy and structural power, which is usually implemented to investigate control problems. The time-domain formulation shows to be much more computationally efficient and robust with reference to truncation errors. Thus it has been used to perform a parametric study to assess if, and under which conditions, the minimum of the kinetic energy and the maximum of the absorbed power cost functions match with reference to: (a) the number of feedback control loops, (b) the structural damping in the plate, (c) the mutual distance of a pair of control loops and (d) the mutual gains implemented in a pair of feedback loops.

124I-PET/CT images of differentiated thyroid cancer patients

SummaryFor an adequate therapy planning and staging of patients with differentiated thyroid cancer (DTC), the correct assignment of thyroid remnants (TRs) and lymph node metastases (LMs) is important. Patients, method: We retrospectively analyzed whether kinetic quantities can help improving LM assignment using serial 124I-PET/CT data. 127 patients with a total of 317 lesions (TR: n = 265; LM: n = 52) received pre-therapy 124I-PET/CT lesion dosimetry using images 24 h and > 96 h after 124I administration. For each lesion, maximum activity concentration (MAC) at 24 h and effective half-life (EHL) were determined. Moreover, the product of MAC and EHL was also investigated as a quantity and is referred to CAQ (cumulated activity proportional quantity). In addition, differences between endogenous and exogenous thyroid-stimulating hormone (TSH) stimulation and between papillary (PTC) and follicular thyroid cancer (FTC) were investigated. Results, conclusion: The median MAC, EHL, and CAQ values in TR were significantly higher than in LM but a clinically relevant cut-off value could not be determined because of high overlapping regions. No significant differences for the three quantities were found for the mode of TSH stimulations, but a significant difference for MAC and CAQ between PTC and FTC.

Geometric Specification of Dynamics: Learning to Visually Perceive Kinetic Quantities from Static Images

In a single experiment, perceivers viewed computer-generated hammer-like objects and estimated a kinetic property. Each hammer comprised a cylinder of some diameter and height, attached to a handle-a second cylinder of fixed diameter and variable length. On 5 blocks of trials, three groups of perceivers reported a property reflecting mass, torque, or moment of inertia. Blocks 2-4 were training blocks on which numerical feedback was given. On blocks 6 and 7, perceivers were asked to report the kinetic properties not reported on blocks 1-5. We were interested in how geometrical object properties affected the perception of kinetic properties, and how that perception changed with experience. To determine how geometrical object properties informed reports of kinetics, a continuous information space of head diameter and height, and handle length was created, and perceivers' loci within that space were determined. Perceivers began at various distances from the optimum for the to-be-reported property and were closer to the optimum after training. On blocks 6 and 7, performance did not reflect transfer from training on another property. The results were interpreted in the context of the theory of direct learning.

Magnetic reconstruction of nonaxisymmetric quasi-single-helicity configurations in the Madison Symmetric Torus

Quasi-single-helicity (QSH) states, characterized by a magnetic spectrum dominated by the innermost resonant tearing mode, are common to all the reversed field pinch (RFP) experiments. The internal magnetic field structure produced by the dominant mode is investigated for the QSH observed in the Madison Symmetric Torus (MST) RFP in discharges with zero toroidal magnetic field at the plasma boundary. The reconstruction is based on an MHD model coupled to edge measurements of the magnetic field. The model discards pressure, which has little effect on the equilibrium magnetic profile of present RFP plasmas, but adopts a realistic toroidal geometry. The technique is the adaptation to the MST configuration of a procedure already applied in RFX-mod, but a more general radial profile for the current density is needed for an adequate reconstruction of the MST case. The emerging features are similar to those found in RFX-mod. The helical flux surfaces of the dominant mode provide, with a good degree of reliability, a basis for mapping kinetic quantities such as electron density and soft-x-ray emissivity.

Ambulatory measurement of ankle kinetics for clinical applications

This study aimed to design and validate the measurement of ankle kinetics (force, moment, and power) during consecutive gait cycles and in the field using an ambulatory system. An ambulatory system consisting of plantar pressure insole and inertial sensors (3D gyroscopes and 3D accelerometers) on foot and shank was used. To test this system, 12 patients and 10 healthy elderly subjects wore shoes embedding this system and walked many times across a gait lab including a force-plate surrounded by seven cameras considered as the reference system. Then, the participants walked two 50-meter trials where only the ambulatory system was used. Ankle force components and sagittal moment of ankle measured by ambulatory system showed correlation coefficient ( R) and normalized RMS error (NRMSE) of more than 0.94 and less than 13% in comparison with the references system for both patients and healthy subjects. Transverse moment of ankle and ankle power showed R>0.85 and NRMSE<23%. These parameters also showed high repeatability (CMC>0.7). In contrast, the ankle coronal moment of ankle demonstrated high error and lower repeatability. Except for ankle coronal moment, the kinetic features obtained by the ambulatory system could distinguish the patients with ankle osteoarthritis from healthy subjects when measured in 50-meter trials. The proposed ambulatory system can be easily accessible in most clinics and could assess main ankle kinetics quantities with acceptable error and repeatability for clinical evaluations. This system is therefore suggested for field measurement in clinical applications.

Virtual Quantification of Protein Stability Using Applied Kinetic and Thermodynamic Parameters

Protein stability, the most important aspect of molecular dynamics and simulations, requires sophisticated instrumentations of molecular biology to analyze its kinetic and thermodynamic background. Sequence- and structure-based programs on protein stability exist which relies only on single point mutations and sequence optimality. The energy distribution conferred by each hydrophobic amino acid in the protein essentially paves way for understanding its stability. To the best of our knowledge, Protein Stability is a first program of its kind, developed to explore the energy requirement of each amino acid in the protein sequence derived from various applied kinetic and thermodynamic quantities. The algorithm is strongly dependent both on kinetic quantities such as atomic solvation energies and solvent accessible surface area and thermodynamic quantities viz. enthalpy, entropy, heat capacity, etc. The hydrophobicity pattern of protein was considered as the important component of protein stabilization.

Density Functional Theoretical Study on the Oxidative Additions of Silyl Halides to the Rh Pincer Complex

The oxidative addition reactions of C–X bonds in alkyl halides or aryl halides to transition-metal complexes are one of the fundamental reactions in organometallic chemistry. However, the reaction involving silicon receives less attention. Recently oxidative addition reactions involving silicon-halide bonds to a rhodium complex were reported. (PNP)Rh fragment 1 (where PNP is the bis(o-diisopropylphosphinophenyl)amide “pincer” ligand), generated from (PNP)Rh(SPr2), reacts with silyl halides compounds to undergo a silicon-halogen oxidative addition reaction. The fragment 1 has been considered to be convenient for the comparative studies because it is compatible with many reactions which provide several kinetic and thermodynamic parameters of the reactions. In this study the density functional theoretical (DFT) studies were conducted in order to determine the Gibbs free energy of reaction for the Si–X oxidative addition to 1 and hence to compare the relative stability between the initial adduct and the oxidative addition product. These kinetic and thermodynamic quantities are the key parameters for elucidating the reactivity and the preference toward the chemical species. B3LYP/LACVP** level calculations were chosen because the level of theory was successfully applied to the oxidative addition/reductive elimination reactions involving organometallic pincer complexes. First we examined the dependence of the reactivity and the thermodynamics of the reaction on the halide species. Figure 1 shows the Gibbs free energy diagrams for the reaction between 1 and SiMe3X, where X = Cl, Br, or I. The Gibbs activation energy, ΔG, were 10.8 kcal/mol for Cl, 8.7 kcal/ mol for Br, and 7.8 kcal/mol for I in the gas phase at 298 K. In addition the Gibbs free energy of reaction, ΔGreaction, were –9.1 kcal/mol for Cl, –17.6 kcal/mol for Br, and –20.9 kcal/ mol for I, indicating higher stability of the oxidative addition reaction products over the reactants. The reactivities of silyl halides toward (PNP)Rh fragments are potentially related to the bond dissociation enthalpies of the Si–X bond in the SiMe3X molecule. For instance weaker bonds in heavier silyl halides are less inert to the Rh fragment. Furthermore the thermodynamics of the reaction is

ChemInform Abstract: Uncovering Molecular Processes in Crystal Nucleation and Growth by Using Molecular Simulation

AbstractReview: 120 refs.

The direct observation of secondary radical chain chemistry in the heterogeneous reaction of chlorine atoms with submicron squalane droplets

The reaction of Cl atoms, in the presence of Cl(2) and O(2), with sub-micron squalane particles is used as a model system to explore how surface hydrogen abstraction reactions initiate chain reactions that rapidly transform the chemical composition of an organic particle. The heterogeneous reaction is measured in a photochemical flow tube reactor in which chlorine atoms are produced by the photolysis of Cl(2) at 365 nm. By monitoring the heterogeneous reaction, using a vacuum ultraviolet photoionization aerosol mass spectrometer, the effective reactive uptake coefficient and the distributions of both oxygenated and chlorinated reaction products are measured and found to depend sensitively upon O(2), Cl(2), and Cl concentrations in the flow reactor. In the absence of O(2), the effective reactive uptake coefficient monotonically increases with Cl(2) concentration to a value of ∼3, clearly indicating the presence of secondary chain chemistry occurring in the condensed phase. The effective uptake coefficient decreases with increasing O(2) approaching a diffusion corrected value of 0.65 ± 0.07, when 20% of the total nitrogen flow rate in the reactor is replaced with O(2). Using a kinetic model it is found that the amount of secondary chemistry and the product distributions in the aerosol phase are controlled by the competitive reaction rates of O(2) and Cl(2) with alkyl radicals. The role that a heterogeneous pathway might play in the reaction of alkyl radicals with O(2) and Cl(2) is investigated within a reasonable range of reaction parameters. These results show, more generally, that for heterogeneous reactions involving secondary chain chemistry, time and radical concentration are not interchangeable kinetic quantities, but rather the observed reaction rate and product formation chemistry depends sensitively upon the concentrations and time evolution of radical initiators and those species that propagate or terminate free radical chain reactions.

Self‐Organized Helical Equilibria in the RFX‐Mod Reversed Field Pinch

AbstractWith operation at high plasma current (Ip ∼ 1.5 MA), the plasma in the RFX‐mod reversed field pinch self‐organises in a 3D helical state with almost conserved flux surfaces featuring strong electron temperature barriers. Up to now the equilibrium of such states was obtained by a perturbative solution of the Newcomb equation in toroidal geometry. This allowed for the mapping of the electron temperature, density and SXR emissivity profiles on helical flux surfaces thus proving the correlation between kinetic plasma quantities and the underlying helical magnetic topology.In order to obtain a full 3D equilibrium reconstruction, the magnetic topology of a SHAx state has been also reconstructed with the VMEC code adapted for the RFP using experimental profiles as input data. Previous results for the axisymmetric case were used as benchmark. It is found that helical equilibria are characterised by a particular q profile with a region of zero magnetic shear as this has been found to be a key ingredient to trigger internal transport barriers (© 2010 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Markov dynamic models for long-timescale protein motion.

Molecular dynamics (MD) simulation is a well-established method for studying protein motion at the atomic scale. However, it is computationally intensive and generates massive amounts of data. One way of addressing the dual challenges of computation efficiency and data analysis is to construct simplified models of long-timescale protein motion from MD simulation data. In this direction, we propose to use Markov models with hidden states, in which the Markovian states represent potentially overlapping probabilistic distributions over protein conformations. We also propose a principled criterion for evaluating the quality of a model by its ability to predict long-timescale protein motions. Our method was tested on 2D synthetic energy landscapes and two extensively studied peptides, alanine dipeptide and the villin headpiece subdomain (HP-35 NleNle). One interesting finding is that although a widely accepted model of alanine dipeptide contains six states, a simpler model with only three states is equally good for predicting long-timescale motions. We also used the constructed Markov models to estimate important kinetic and dynamic quantities for protein folding, in particular, mean first-passage time. The results are consistent with available experimental measurements.Contact: chiangts@comp.nus.edu.sg

Coupled Electron/Proton Transfer Studies of Benzoquinone-Modified Monolayers

The electrochemical reduction of benzoquinone involves a coupled transfer of protons and electrons. Theoretical treatments of proton-coupled electron transfer (PCET) indicate that both thermodynamic (apparent formal potential) and kinetic (apparent standard heterogeneous rate constants) quantities should be highly pH-dependent. Although there are several reports of quinone-derivatized self-assembled monolayers (SAMs) in the literature, no systematic studies on the pH dependence of the PCET kinetics have been reported. In this work, we outline a method to produce SAM-aminobenzoquinone monolayers starting from diluted monolayers of an amine-terminated SAM. The electroactive monolayer behaves as a nearly ideal Nernstian system (no interactions between redox centers). In neutral to weakly acidic electrolytes, the aminobenzoquinone can be reduced in a kinetically slow, two-electron, two-proton (2e2H) process, but in lower pH solutions, the observed reaction is consistent with an overall 2e3H transfer. Kinetic measurements have been made using techniques that do not rely on the assumption of a potential-independent apparent transfer coefficient. The apparent standard rate constants range from 0.1 to 0.01 s−1, which is roughly an order of magnitude faster than previous reports for comparable systems. Plots of log(ks,app) versus pH are distorted variants of the expected W plots predicted from the theory of 2e2H PCET. These deviations may be caused by surface pKa effects and/or additional reaction pathways arising from the third proton transfer.