Project description:Understanding the local chemical ordering propensity in random solid solutions, and tailoring its strength, can guide the design and discovery of complex, paradigm-shifting multicomponent alloys. First, we present a simple thermodynamic framework, based solely on binary enthalpies of mixing, to select optimal alloying elements to control the nature and extent of chemical ordering in high-entropy alloys (HEAs). Next, we couple high-resolution electron microscopy, atom probe tomography, hybrid Monte-Carlo, special quasirandom structures, and density functional theory calculations to demonstrate how controlled additions of Al and Ti and subsequent annealing drive chemical ordering in nearly random equiatomic face-centered cubic CoFeNi solid solution. We establish that short-range ordered domains, the precursors of long-range ordered precipitates, inform mechanical properties. Specifically, a progressively increasing local order boosts the tensile yield strengths of the parent CoFeNi alloy by a factor of four while also substantially improving ductility, which breaks the so-called strength-ductility paradox. Finally, we validate the generality of our approach by predicting and demonstrating that controlled additions of Al, which has large negative enthalpies of mixing with the constituent elements of another nearly random body-centered cubic refractory NbTaTi HEA, also introduces chemical ordering and enhances mechanical properties.
Project description:BackgroundThe dynamics of biochemical reaction systems are constrained by the fundamental laws of thermodynamics, which impose well-defined relationships among the reaction rate constants characterizing these systems. Constructing biochemical reaction systems from experimental observations often leads to parameter values that do not satisfy the necessary thermodynamic constraints. This can result in models that are not physically realizable and may lead to inaccurate, or even erroneous, descriptions of cellular function.ResultsWe introduce a thermodynamically consistent model calibration (TCMC) method that can be effectively used to provide thermodynamically feasible values for the parameters of an open biochemical reaction system. The proposed method formulates the model calibration problem as a constrained optimization problem that takes thermodynamic constraints (and, if desired, additional non-thermodynamic constraints) into account. By calculating thermodynamically feasible values for the kinetic parameters of a well-known model of the EGF/ERK signaling cascade, we demonstrate the qualitative and quantitative significance of imposing thermodynamic constraints on these parameters and the effectiveness of our method for accomplishing this important task. MATLAB software, using the Systems Biology Toolbox 2.1, can be accessed from http://www.cis.jhu.edu/~goutsias/CSS lab/software.html. An SBML file containing the thermodynamically feasible EGF/ERK signaling cascade model can be found in the BioModels database.ConclusionsTCMC is a simple and flexible method for obtaining physically plausible values for the kinetic parameters of open biochemical reaction systems. It can be effectively used to recalculate a thermodynamically consistent set of parameter values for existing thermodynamically infeasible biochemical reaction models of cellular function as well as to estimate thermodynamically feasible values for the parameters of new models. Furthermore, TCMC can provide dimensionality reduction, better estimation performance, and lower computational complexity, and can help to alleviate the problem of data overfitting.
Project description:Accurate models of electrochemical kinetics at electrode-electrolyte interfaces are crucial to understanding the high-rate behavior of energy storage devices. Phase transformation of electrodes is typically treated under equilibrium thermodynamic conditions, while realistic operation is at finite rates. Analyzing phase transformations under nonequilibrium conditions requires integrating nonlinear electrochemical kinetic models with thermodynamic models. This had only previously been demonstrated for Butler-Volmer kinetics, where it can be done analytically. In this work, we develop a software package capable of the efficient numerical inversion of rate relationships for general kinetic models. We demonstrate building nonequilibrium phase maps, including for models such as Marcus-Hush-Chidsey that require computation of an integral, and also discuss the impact of a variety of assumptions and model parameters, particularly on high-rate phase behavior. Even for a fixed set of parameters, the magnitude of the critical current can vary by more than a factor of 2 among kinetic models.
Project description:Progress in experimental techniques at nanoscale makes measurements of noise in molecular junctions possible. These data are important source of information not accessible through average flux measurements. The emergence of optoelectronics, the recently shown possibility of strong light-matter couplings, and developments in the field of quantum thermodynamics are making measurements of transport statistics even more important. Theoretical methods for noise evaluation in first principles simulations can be roughly divided into approaches for weak intra-system interactions, and those treating strong interactions for systems weakly coupled to baths. We argue that due to structure of its diagrammatic expansion, and the use of many-body states as a basis of its formulation, the recently introduced nonequilibrium diagrammatic technique for Hubbard Green functions is a relatively inexpensive method suitable for evaluation of noise characteristics in first principles simulations over a wide range of parameters. We illustrate viability of the approach by simulations of noise and noise spectrum within generic models for non-, weakly and strongly interacting systems. Results of the simulations are compared to exact data (where available) and to simulations performed within approaches best suited for each of the three parameter regimes.
Project description:Nucleic acid secondary structure plays an important role in nucleic acid-nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have not been systematically investigated. Such thermodynamically unfavorable secondary structures should not be ignored in DNA hybridization kinetics, especially under isothermal conditions. Here, we report that positive ΔG° secondary structures can change the hybridization rate by two-orders of magnitude, despite the fact that their hybridization obeyed second-order reaction kinetics. The temperature dependence of hybridization rates showed non-Arrhenius behavior; thus, their hybridization is considered to be nucleation limited. We derived a model describing how ΔG° positive secondary structures affect hybridization kinetics in stopped-flow experiments with 47 pairs of oligonucleotides. The calculated hybridization rates, which were based on the model, quantitatively agreed with the experimental rate constant.
Project description:Even though many partially ordered ices are known, it remains elusive to understand and categorize them. In this study, we study the ordering from ice V to XIII using calorimetry at ambient pressure and discover that the transition takes place via an intermediate that is thermodynamically stable at 113-120 K. Our isothermal ordering approach allows us to highlight the distinction of this intermediate from ice V and XIII, where there are clear differences both in terms of enthalpy and ordering kinetics. We suggest that the approach developed in the present work can also reveal the nature of partially ordered forms in the hydrogen order-disorder series of other ice phases.
Project description:The kinetics of lithium diisopropylamide (LDA) in tetrahydrofuran under nonequilibrium conditions are reviewed. These conditions correspond to a class of substrates in which the rates of LDA aggregation and solvation events are comparable to the rates at which various fleeting intermediates react with substrate. Substrates displaying these reactivities, by coincidence, happen to be those that react at tractable rates on laboratory time scales at -78 °C. In this strange region of nonlimiting behavior, rate-limiting steps are often poorly defined, sometimes involve deaggregation, and at other times include reaction with substrate. Changes in conditions routinely cause shifts in the rate-limiting steps, and autocatalysis is prevalent and can be acute. The studies are described in three distinct portions: (1) methods and strategies used to deconvolute complex reaction pathways, (2) the resulting conclusions about organolithium reaction mechanisms, and (3) perspectives on the concept of rate limitation reinforced by studies of LDA in tetrahydrofuran at -78 °C under nonequilibrium conditions.
Project description:The interplay between the electronic and lattice degrees of freedom in nonequilibrium states of strongly correlated systems has been debated for decades. Although progress has been made in establishing a hierarchy of electronic interactions with the use of time-resolved techniques, the role of the phonons often remains in dispute, a situation highlighting the need for tools that directly probe the lattice. We present the first combined megaelectron volt ultrafast electron diffraction and time- and angle-resolved photoemission spectroscopy study of optimally doped Bi2Sr2CaCu2O8+?. Quantitative analysis of the lattice and electron subsystems' dynamics provides a unified picture of nonequilibrium electron-phonon interactions in the cuprates beyond the N-temperature model. The work provides new insights on the specific phonon branches involved in the nonequilibrium heat dissipation from the high-energy Cu-O bond stretching "hot" phonons to the lowest-energy acoustic phonons with correlated atomic motion along the <110> crystal directions and their characteristic time scales. It reveals a highly nonthermal phonon population during the first several picoseconds after the photoexcitation. The approach, taking advantage of the distinct nature of electrons and photons as probes, is applicable for studying energy relaxation in other strongly correlated electron systems.
Project description:Disordered hyperuniform structures are an exotic state of matter having vanishing long-wavelength density fluctuations similar to perfect crystals but without long-range order. Although its importance in materials science has been brought to the fore in past decades, the rational design of experimentally realizable disordered strongly hyperuniform microstructures remains challenging. Here we find a new type of nonequilibrium fluid with strong hyperuniformity in two-dimensional systems of chiral active particles, where particles perform independent circular motions of the radius R with the same handedness. This new hyperuniform fluid features a special length scale, i.e., the diameter of the circular trajectory of particles, below which large density fluctuations are observed. By developing a dynamic mean-field theory, we show that the large local density fluctuations can be explained as a motility-induced microphase separation, while the Fickian diffusion at large length scales and local center-of-mass-conserved noises are responsible for the global hyperuniformity.
Project description:The phenomenon of cation ordering is closely related to certain physical properties of complex oxides, which necessitates the search of underlying structure-property relationship at atomic resolution. Here we study the superlattices within reduced calcium titanate single crystal micro-pillars, which are unexpected from the originally proposed atomic model. Bright and dark contrasts at alternating Ti double layers perpendicular to b axis are clearly observed, but show no signs in corresponding image simulations based on the proposed atomic model. The multi-dimensional chemical analyses at atomic resolution reveal periodic lower Ti concentrations at alternating Ti double layers perpendicular to b axis. The following in-situ heating experiment shows no phase transition at the reported T c and temperature independence of the superlattices. The dimerization of the Ti-Ti bonds at neighboring double rutile-type chains within Ti puckered sheets are directly observed, which is found to be not disturbed by the cation ordering at alternating Ti double layers. The characterization of cation ordering of complex oxides from chemical and structural point of view at atomic resolution, and its reaction to temperature variations are important for further understanding their basic physical properties and exploiting potential applications.