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This paper focuses on phase and aggregation behavior for linear chains composed of blocks of hydrophilic and hydrophobic segments. Phase and conformational transitions of patterned chains are relevant for understanding liquid–liquid separation of biomolecular condensates, which play a prominent role in cellular biophysics and for surfactant and polymer applications. Previous studies of simple models for multiblock chains have shown that, depending on the sequence pattern and chain length, such systems can fall into one of two categories: displaying either phase separation or aggregation into finite-size clusters. The key new result of this paper is that both formation of finite-size aggregates and phase separation can be observed for certain chain architectures at appropriate conditions of temperature and concentration. For such systems, a bulk dense liquid condenses from a dilute phase that already contains multi-chain finite-size aggregates. The computational approach used in this study involves several distinct steps using histogram-reweighting grand canonical Monte Carlo simulations, which are described in some level of detail. [ABSTRACT FROM AUTHOR]

Lyotropic liquid crystal phases (LCPs) are widely studied for diverse applications, including protein crystallization and drug delivery. The structure and properties of LCPs vary widely depending on the composition, concentration, temperature, pH, and pressure. High-throughput structural characterization approaches, such as small-angle x-ray scattering (SAXS), are important to cover meaningfully large compositional spaces. However, high-throughput LCP phase analysis for SAXS data is currently lacking, particularly for patterns of multiphase mixtures. In this paper, we develop semi-automated software for high throughput LCP phase identification from SAXS data. We validate the accuracy and time-savings of this software on a total of 668 SAXS patterns for the LCPs of the amphiphile hexadecyltrimethylammonium bromide (CTAB) in 53 acidic or basic ionic liquid derived solvents, within a temperature range of 25–75 °C. The solvents were derived from stoichiometric ethylammonium nitrate (EAN) or ethanolammonium nitrate (EtAN) by adding water to vary the ionicity, and adding precursor ions of ethylamine, ethanolamine, and nitric acid to vary the pH. The thermal stability ranges and lattice parameters for CTAB-based LCPs obtained from the semi-automated analysis showed equivalent accuracy to manual analysis, the results of which were previously published. A time comparison of 40 CTAB systems demonstrated that the automated phase identification procedure was more than 20 times faster than manual analysis. Moreover, the high throughput identification procedure was also applied to 300 unpublished scattering patterns of sodium dodecyl-sulfate in the same EAN and EtAN based solvents in this study, to construct phase diagrams that exhibit phase transitions from micellar, to hexagonal, cubic, and lamellar LCPs. The accuracy and significantly low analysis time of the high throughput identification procedure validates a new, rapid, unrestricted analytical method for the determination of LCPs. [ABSTRACT FROM AUTHOR]

We obtain the phase diagram of the hard core lattice gas with third nearest neighbor exclusion on the triangular lattice using Monte Carlo simulations that are based on a rejection-free flat histogram algorithm. In a recent paper [Darjani et al., J. Chem. Phys. 151, 104702 (2019)], it was claimed that the lattice gas with third nearest neighbor exclusion undergoes two phase transitions with increasing density with the phase at intermediate densities exhibiting hexatic order with continuously varying exponents. Although a hexatic phase is expected when the exclusion range is large, it has not been seen earlier in hard core lattice gases with short range exclusion. In this paper, by numerically determining the entropies for all densities, we show that there is only a single phase transition in the system between a low-density fluid phase and a high density ordered sublattice phase and that a hexatic phase is absent. The transition is shown to be first order in nature, and the critical parameters are determined accurately. [ABSTRACT FROM AUTHOR]

The ability of biomolecules to exert forces on their surroundings or resist compression from the environment is essential in a variety of biologically relevant contexts. For filaments in the low-temperature limit and under a constant compressive force, Euler buckling theory predicts a sudden transition from a compressed state to a bent state in these slender rods. In this paper, we use a mean-field theory to show that if a semiflexible chain is compressed at a finite temperature with a fixed end-to-end distance (permitting fluctuations in the compressive forces), it exhibits a continuous phase transition to a buckled state at a critical level of compression. We determine a quantitatively accurate prediction of the transverse position distribution function of the midpoint of the chain that indicates this transition. We find that the mean compressive forces are non-monotonic as the extension of the filament varies, consistent with the observation that strongly buckled filaments are less able to bear an external load. We also find that for the fixed extension (isometric) ensemble, the buckling transition does not coincide with the local minimum of the mean force (in contrast to Euler buckling). We also show that the theory is highly sensitive to fluctuations in length in two dimensions and the buckling transition can still be accurately recovered by accounting for those fluctuations. These predictions may be useful in understanding the behavior of filamentous biomolecules compressed by fluctuating forces, relevant in a variety of biological contexts. [ABSTRACT FROM AUTHOR]

The rocksalt structure of ZnO has a very promising bandgap for optoelectronic applications. Unfortunately, this high-pressure phase is unstable under ambient conditions. This paper presents experimental results for rocksalt-type ZnO/MgO superlattices and theoretical considerations of the critical thickness of MgxZn1−xO layers. The correlations between the layer/spacer thickness ratio, elastic strain, chemical composition, and critical thickness are analyzed. The Matthews and Blakeslee model is revisited to find analytic conditions for the critical layer thickness resulting in phase transition. Our analysis shows that due to the decrease in misfit stresses below some critical limit, the growth of multiple quantum wells composed of rocksalt ZnO layers and MgO spacers is possible only for very large layer/spacer thickness ratios. [ABSTRACT FROM AUTHOR]

Vapor-phase ammonia, NH3(g), and hydrochloric acid, HCl(g), undergo a series of complex reactions, including nucleation and growth, to form solid ammonium chloride, NH4Cl(s). The counterdiffusional experiment, whereby HCl(g) and NH3(g) diffuse from opposite ends of a tube and react to form spatiotemporally complex patterns, has a rich history of study. In this paper, we combine experimental data, molecular simulations, and analysis and simulations of a partial differential equation model to address the questions of where the first unobserved vapor product NH4Cl(g) and visually observable precipitate NH4Cl(s) form and how these positions depend on experimental parameters. These analyses yield a consistent picture which involves a moving reaction front as well as previously unobserved heterogeneous nucleation, wall nucleation, and homogeneous nucleation. The experiments combined with modeling allow for an estimate of the heterogeneous and homogeneous nucleation thresholds for the vapor-to-solid phase transition. The results, synthesized with the literature on this vapor-to-particle reaction, inform a discussion of the details of the reaction mechanism, including the role of water, which concludes the paper. [ABSTRACT FROM AUTHOR]

General transformation expressions of the second-order non-adiabatic Hamiltonian of the atomic nuclei, including the kinetic-energy correction terms, are derived upon the change from laboratory-fixed Cartesian coordinates to general curvilinear coordinate systems commonly used in rovibrational computations. The kinetic-energy or so-called "mass-correction" tensor elements are computed with the stochastic variational method and floating explicitly correlated Gaussian functions for the H 2 + molecular ion in its ground electronic state. {Further numerical applications for the 4 He 2 + molecular ion are presented in the forthcoming paper, Paper II [E. Mátyus, J. Chem. Phys. 149, 194112 (2018)]}. The general, curvilinear non-adiabatic kinetic energy operator expressions are used in the examples, and non-adiabatic rovibrational energies and corrections are determined by solving the rovibrational Schrödinger equation including the diagonal Born–Oppenheimer as well as the mass-tensor corrections. [ABSTRACT FROM AUTHOR]

It has been recently shown that the Tao–Mo (TM) [J. Tao and Y. Mo, Phys. Rev. Lett. 117, 073001 (2016)] semilocal exchange–correlation energy functional suffers from the order-of-limit problem, which affects the functional performance in phase transition pressures [Furness et al., J. Chem. Phys. 152, 244112 (2020)]. The root of the order-of-limit problem of the TM functional is inherent within the interpolation function, which acts as a switch between the compact density and the slowly varying density. This paper proposes a different switch function that avoids the order-of-limit problem and correctly interpolates the compact density and the slowly varying fourth-order density correction. By circumventing the order-of-limit problem, the proposed form enhances the applicability of the original TM functional on the diverse nature of solid-state properties. Our conclusion is ensured by examining the functional in predicting properties related to general-purpose solids, quantum chemistry, and phase transition pressure. Besides, we discuss the connection between the order-of-limit problem, phase transition pressure, and bandgap of solids. [ABSTRACT FROM AUTHOR]

Chemical reaction networks offer a natural nonlinear generalization of linear Markov jump processes on a finite state-space. In this paper, we analyze the dynamical large deviations of such models, starting from their microscopic version, the chemical master equation. By taking a large-volume limit, we show that those systems can be described by a path integral formalism over a Lagrangian functional of concentrations and chemical fluxes. This Lagrangian is dual to a Hamiltonian, whose trajectories correspond to the most likely evolution of the system given its boundary conditions. The same can be done for a system biased on time-averaged concentrations and currents, yielding a biased Hamiltonian whose trajectories are optimal paths conditioned on those observables. The appropriate boundary conditions turn out to be mixed so that, in the long time limit, those trajectories converge to well-defined attractors. We are then able to identify the largest value that the Hamiltonian takes over those attractors with the scaled cumulant generating function of our observables, providing a nonlinear equivalent to the well-known Donsker-Varadhan formula for jump processes. On that basis, we prove that chemical reaction networks that are deterministically multistable generically undergo first-order dynamical phase transitions in the vicinity of zero bias. We illustrate that fact through a simple bistable model called the Schlögl model, as well as multistable and unstable generalizations of it, and we make a few surprising observations regarding the stability of deterministic fixed points and the breaking of ergodicity in the large-volume limit. [ABSTRACT FROM AUTHOR]

Solid-state nudged elastic band (SSNEB) methods can be used for finding solid-solid transition paths when solids are subjected to external stress fields. However, previous SSNEB methods may lead to inaccurate barriers and deviated reaction paths for transitions under stress and finite deformation due to an inaccurate evaluation of the external work contributions in enthalpies. In this paper, a finite deformation nudged elastic band (FD-NEB) method is formulated for finding transition paths of solids under finite deformation. Applications of FD-NEB to a phase transition of silicon from the diamond phase to the β-tin phase under uniaxial compression are presented. The results are compared with those from the generalized solid-state nudged elastic band method. [ABSTRACT FROM AUTHOR]

This paper determines the thermodynamic phase diagram of the EXP system of particles interacting by the purely repulsive exponential pair potential. The solid phase is face-centered cubic (fcc) at low densities and pressures. At higher densities and pressures, the solid phase is body-centered cubic (bcc) with a re-entrant liquid phase at the highest pressures simulated. The investigation first identifies the phase diagram at zero temperature at which the following four crystal structures are considered: fcc, bcc, hexagonal close packed, and cubic diamond. There is a T = 0 phase transition at pressure 2.651 × 10−3 with the thermodynamically stable structure being fcc below and bcc above this pressure. The densities of the two crystal structures at the phase transition are 1.7469 × 10−2 (fcc) and 1.7471 × 10−2 (bcc). At finite temperatures, the fcc–bcc, fcc-liquid, and bcc-liquid coexistence lines are determined by numerical integration of the Clausius–Clapeyron equation and validated by interface-pinning simulations at selected state points. The bcc-fcc phase transition is a weak first-order transition. The liquid-fcc–bcc triple point, which is determined by the interface-pinning method, has temperature 5.9 × 10−5 and pressure 2.5 × 10−6; the triple-point densities are 1.556 × 10−3 (liquid), 1.583 × 10−3 (bcc), and 1.587 × 10−3 (fcc). [ABSTRACT FROM AUTHOR]

We demonstrate the utility of an unsupervised machine learning tool for the detection of phase transitions in off-lattice systems. We focus on the application of principal component analysis (PCA) to detect the freezing transitions of two-dimensional hard-disk and three-dimensional hard-sphere systems as well as liquid-gas phase separation in a patchy colloid model. As we demonstrate, PCA autonomously discovers order-parameter-like quantities that report on phase transitions, mitigating the need for a priori construction or identification of a suitable order parameter—thus streamlining the routine analysis of phase behavior. In a companion paper, we further develop the method established here to explore the detection of phase transitions in various model systems controlled by compositional demixing, liquid crystalline ordering, and non-equilibrium active forces. [ABSTRACT FROM AUTHOR]

The solid-solid and melting transitions that occur in Lennard-Jones LJn clusters have been both fascinating and challenging for the computational physics community over the last several decades. A number of attempts to extend these studies to the quantum case have also been made. Particularly interesting is the exploration of the parallel between the thermally induced and quantum-induced transitions. Yet, both numerically accurate and systematic studies of the latter are still lacking. In this paper, we apply the diffusion Monte Carlo method to the especially difficult case of LJ38. Starting with the truncated octahedral global minimum configuration, as the de Boer quantum delocalization parameterΛincreases, the system undergoes two consecutive solid-solid transitions, switching to anti-Mackay configurations. At sufficiently large values of Λ, the cluster is completely "melted" which is manifested by delocalization of the ground statewavefunction over a very large number of minima that represent several structural motifs. [ABSTRACT FROM AUTHOR]

The purpose of this paper is to investigate several analytical methods of solving first passage (FP) problem for the Rouse model, a simplest model of a polymer chain. We show that this problem has to be treated as a multi-dimensional Kramers' problem, which presents rich and unexpected behavior. We first perform direct and forward-flux sampling (FFS) simulations and measure the mean first-passage time t(z) for the free end to reach a certain distance z away from the origin. The results show that the mean FP time is getting faster if the Rouse chain is represented by more beads. Two scaling regimes of t(z) are observed, with transition between them varying as a function of chain length. We use these simulation results to test two theoretical approaches. One is a well known asymptotic theory valid in the limit of zero temperature. We show that this limit corresponds to fully extended chain when each chain segment is stretched, which is not particularly realistic. A new theory based on the well known Freidlin-Wentzell theory is proposed, where dynamics is projected onto the minimal action path. The new theory predicts both scaling regimes correctly, but fails to get the correct numerical prefactor in the first regime. Combining our theory with the FFS simulations leads us to a simple analytical expression valid for all extensions and chain lengths. One of the applications of polymer FP problem occurs in the context of branched polymer rheology. In this paper, we consider the arm-retraction mechanism in the tube model, which maps exactly on the model we have solved. The results are compared to the Milner-McLeish theory without constraint release, which is found to overestimate FP time by a factor of 10 or more. [ABSTRACT FROM AUTHOR]

Nature employs lipids to construct nanostructured membranes that self-assemble in an aqueous environment to separate the cell interior from the exterior environment. Membrane composition changes among species and according to environmental conditions, which allows organisms to occupy a wide variety of different habitats. Lipid bilayers are phase-change materials that exhibit strong thermotropic and lyotropic phase behavior in an aqueous environment, which may also cause thermal rectification. Among different types of lipids, archaeal lipids are of great interest due to their ability to withstand extreme conditions. In this paper, nonequilibrium molecular dynamics simulations were employed to study the nanostructures and thermal properties of different archaeols and to investigate thermal rectification effects in asymmetric archaeal membranes. In particular, we are interested in understanding the role of bridged phytanyl chains and cyclopentane groups in controlling the phase transition temperature and heat flow across the membrane. Our results indicate that the bridged phytanyl chains decrease the molecular packing of lipids, whereas the existence of cyclopentane rings on the tail groups increases the molecular packing by enhancing the interactions between isoprenoid chains. We found that macrocyclic archaeols have the highest thermal conductivity, whereas macrocyclic archaeols with two cyclopentane rings have the lowest. The effect of the temperature on the variation of thermal conductivity was found to be progressive. Our results further indicate that small thermal rectification effects occur in asymmetric archaeol bilayer membranes at around 25 K temperature gradient. The calculated thermal rectification factor was around 0.09 which is in the range of rectification factor obtained experimentally for nanostructures such as carbon nanotubes (0.07). Such phenomena may be of biological significance and could also be optimized for use in various engineering applications. [ABSTRACT FROM AUTHOR]

This paper is broadly concerned with the dynamics of a polymer confined to a rectangular slit of width D and deformed by a planar elongational flow of strength ẏ. It is interested, more specifically, in the nature of the coil-stretch transition that such polymers undergo when the flow strength ẏ is varied, and in the degree to which this transition is affected by the presence of restrictive boundaries. These issues are explored within the framework of a finitely extensible Rouse model that includes pre-averaged surface-mediated hydrodynamic interactions. Calculations of the chain's steady-state fractional extension x using this model suggest that different modes of relaxation (which are characterized by an integer p) exert different levels of control on the coil-stretch transition. In particular, the location of the transition (as identified from the graph of x versus the Weissenberg number Wi, a dimensionless parameter defined by the product of ẏ and the time constant τp of a relaxation mode p) is found to vary with the choice of τp. In particular, when τ1 is used in the definition of Wi, the x vs. Wi data for different D lie on a single curve, but when τ3 is used instead (with τ3 > τ1) the corresponding data lie on distinct curves. These findings are in close qualitative agreement with a number of experimental results on confinement effects on DNA stretching in electric fields. Similar D-dependent trends are seen in our calculated force vs. Wi data, but force vs. x data are essentially D-independent and lie on a single curve. [ABSTRACT FROM AUTHOR]

The laser induced fluorescence (LIF) spectrum of the à ²Δ - X ²Π transition was obtained for SiCN generated by laser ablation under supersonic free jet expansion. The vibrational structures of the dispersed fluorescence (DF) spectra from single vibronic levels (SVL's) were analyzed with consideration of the Renner-Teller (R-T) interaction. Analysis of the pure bending (ν2) structure by a perturbation approach including R-T, anharmonicity, spin-orbit (SO), and Herzberg-Teller (H-T) interactions indicated considerably different spin splitting for the μ and ? levels of the X ²Π state of SiCN, in contrast to identical spin splitting for general species derived from the perturbation approach, where μ and ? specify the lower and upper levels, respectively, separated by R-T. Further analysis of the vibrational structure including R-T, anharmonicity, SO, H-T, Fermi, and Sears interactions was carried out via a direct diagonalization procedure, where Sears resonance is a second-order interaction combined from SO and H-T interactions with ΔK = ±1, Δ∑ = ±1, and ΔP = 0, and where P is a quantum number, P = K + ∑. The later numerical analysis reproduced the observed structure, not only the pure ν2 structure but also the combination structure of the ν2 and the Si-CN stretching (ν3) modes. As an example, the analysis demonstrates Sears resonance between vibronic levels, (01¹0) ? ∑(+) and (0200) μ Π½, with ΔK = ±1 and ΔP = 0. On the basis of coefficients of their eigen vectors derived from the numerical analysis, it is interpreted as an almost one-to-one mixing between the two levels. The mixing coefficients of the two vibronic levels agree with those obtained from computational studies. The numerical analysis also indicates that some of the vibronic levels show chaotic characteristics in view of the two-dimensional harmonic oscillator (2D-HO) basis which is used as the basis function in the present numerical analysis; i.e., the eigen vectors for some of the observed levels have several components of the basis, and we have not been able to give precise vibronic assignments for the levels, but just vibronically labeled, referring the largest component in their vectors. (To emphasize this situation, we do not use the word "assignment," but prefer to use "label" as the meaning of just "label," but not "assign," throughout this paper.) The latter shows that the vibronic labels of the levels are meaningless, and the P quantum number and the order of their eigen states in the P matrix block derived in the numerical analysis only characterize the vibronic levels. Comparing the constants obtained for all of the interactions with those of species showing Sears resonance and studied previously, it is found that none of them are strong, but are moderate. It is thus concluded that the chaotic appearance is not derived by any strong interaction, but is induced by complex and accidental proximities of the vibronic levels caused by the moderate interactions. [ABSTRACT FROM AUTHOR]

When a CHD3 molecule is pumped to the C-H stretching-excited state by absorbing a linearly polarized infrared (IR) photon via the R(0) branch of the v1 = 1 ← 0 transition, the rotational angular momentum j of the prepared state |jK = |10 preferentially lies in a plane perpendicular to the IR polarization axis εIR. By way of contrast, when the Q(1) branch is used, the state of |jK = |1 ± 1 is prepared with j aligned along the direction of εIR. Reported here is a detailed study of the title reaction by actively controlling the collision geometries under these two IR-excitation schemes at collision energy Ec = 8.6 kcal mol−1, using a crossed molecular beam, product imaging approach. We found that under the R(0) excitation, the polarization-dependent differential cross sections for the HCl(v = 0) + CD3(00) channel can largely be understood by invoking dual reaction mechanisms. The forward-scattered products are most likely mediated by a time-delayed resonance mechanism--as the formation of the HCl(v = 1) + CD3(00) channel, whereas the backward/sideways scattered products are governed by a direct abstraction mechanism. Compared to the previous results at lower Ec of 3.8 kcal mol−1, the sighting of opening-up the attack angle at the transition state of the direct pathway is proposed. Results under the Q(1) excitation are, however, perplexing and bear no obvious correlation to the corresponding ones for the R(0) excitation, defying simple intuitive interpretation. Possible reasons are put forward, which call for theoretical investigations for deeper insights. The results on the alternative isotope channel, DCl + CHD2, will be reported in the following paper. [ABSTRACT FROM AUTHOR]

A complete set of four polarization-dependent differential cross sections in the reactions of Cl + aligned-CHD3(v1 = 1, |jK) → DCl(v = 0) + CHD2(v1 = 1) is reported here for two different, rotationally polarized states with j = 1: specifically the |jK = |10 state prepared via the R(0) excitation and the |1 ± 1 state via Q(1). In stark contrast to the complicated situation of the HCl(v) + CD3(v = 0) channel reported in Paper-I, the stereo-requirement of this isotopic channel for both polarized reactants appears quite straightforward and consistent with a direct rebound mechanism. The extent of steric effects is moderate and relatively smaller than the alternative H-atom abstraction channel. All major findings reported here can qualitatively be understood by first noting that the present reaction invokes abstracting a D-atom, which is the spectator in the IR-excitation process. Next, it is recognized that the directional properties of two polarized states of CHD3(v1 = 1, |jK) should manifest primarily in the IR-excited C-H bond, leaving secondary imprints in the unexcited CD3-moiety. The stereo-specificity of the DCl + CHD2 product channel is further reduced by the fact that the abstraction can occur with any one of the three spatially distinct D-atoms. [ABSTRACT FROM AUTHOR]

Restricting the number of attractive physical "bonds" that can form between particles in a fluid suppresses the usual demixing phase transition to very low particle concentrations, allowing for the formation of open, percolated, and homogeneous states, aptly called equilibrium or "empty" gels. Most demonstrations of this concept have directly limited the microscopic particle valence via anisotropic (patchy) attractions; however, an alternative macroscopic valence limitation would be desirable for greater experimental tunability and responsiveness. One possibility, explored in this paper, is to employ primary particles with attractions mediated via a secondary species of linking particles. In such a system, the linker-to-primary particle ratio serves as a macroscopic control parameter for the average microscopic valence. We show that the phase behavior of such a system predicted by Wertheim's first order perturbation theory is consistent with equilibrium gel formation: the primary particle concentrations corresponding to the two-phase demixing transition are significantly suppressed at both low and high linker-to-primary particle ratios. Extensive molecular dynamics simulations validate these theoretical predictions but also reveal the presence of loops of bonded particles, which are neglected in the theory. Such loops cause densification and inhibit percolation, and hence the range of viable empty gel state conditions is somewhat reduced relative to theWertheim theory predictions. [ABSTRACT FROM AUTHOR]

This paper is the first application of the tensor-train (TT) cross approximation procedure for potential energy surface fitting. In order to reduce the complexity, we combine the TT-approach with another technique recently introduced in the field of numerical analysis: an affine transformation of Cartesian coordinates into the active subspaces where the PES function has the most variability. The numerical experiments for the water molecule and for the nitrous acid molecule confirm the efficiency of this approach. [ABSTRACT FROM AUTHOR]

This paper is devoted to bulk-mediated surface diffusion of a particle which can diffuse both on a flat surface and in the bulk layer above the surface. It is assumed that the particle is on the surface initially (at t = 0) and at time t, while in between it may escape from the surface and come back any number of times. We propose a new approach to the problem, which reduces its solution to that of a two-state problem of the particle transitions between the surface and the bulk layer, focusing on the cumulative residence times spent by the particle in the two states. These times are random variables, the sum of which is equal to the total observation time t. The advantage of the proposed approach is that it allows for a simple exact analytical solution for the double Laplace transform of the conditional probability density of the cumulative residence time spent on the surface by the particle observed for time t. This solution is used to find the Laplace transform of the particle mean square displacement and to analyze the peculiarities of its time behavior over the entire range of time. We also establish a relation between the double Laplace transform of the conditional probability density and the Fourier-Laplace transform of the particle propagator over the surface. The proposed approach treats the cases of both finite and infinite bulk layer thicknesses (where bulk-mediated surface diffusion is normal and anomalous at asymptotically long times, respectively) on equal footing. [ABSTRACT FROM AUTHOR]

The first-order liquid-liquid phase transition in supercooled Si is revisited by long-time first-principle molecular dynamics simulations. As the focus of the present paper, its nature is revealed by analyzing the inherent structures of low-density liquid (LDL) and high-density liquid (HDL). Our results show that it is a transition between a sp³-hybridization LDL and a white-tin-like HDL. This uncovers the origin of the semimetal-metal transition accompanying it and also proves that HDL is the metastable extension of high temperature equilibrium liquid into the supercooled regime. The pressuretemperature diagram of supercooled Si thus can be regarded in some respects as shifted reflection of its crystalline phase diagram. [ABSTRACT FROM AUTHOR]

In this paper, we present an improved method for obtaining unbiased estimates of the free energy difference between two thermodynamic states using the work distribution measured in nonequilibrium driven experiments connecting these states. The method is based on the assumption that any observed work distribution is given by a mixture of Gaussian distributions, whose normal components are identical in either direction of the nonequilibrium process, with weights regulated by the Crooks theorem. Using the prototypical example for the driven unfolding/folding of deca-alanine, we show that the predicted behavior of the forward and reverse work distributions, assuming a combination of only two Gaussian components with Crooks derived weights, explains surprisingly well the striking asymmetry in the observed distributions at fast pulling speeds. The proposed methodology opens the way for a perfectly parallel implementation of Jarzynski-based free energy calculations in complex systems. [ABSTRACT FROM AUTHOR]

This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internal centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions. [ABSTRACT FROM AUTHOR]

The first-order liquid-liquid phase transition in supercooled Si is revisited by long-time first-principle molecular dynamics simulations. As the focus of the present paper, its nature is revealed by analyzing the inherent structures of low-density liquid (LDL) and high-density liquid (HDL). Our results show that it is a transition between a sp³-hybridization LDL and a white-tin-like HDL. This uncovers the origin of the semimetal-metal transition accompanying it and also proves that HDL is the metastable extension of high temperature equilibrium liquid into the supercooled regime. The pressuretemperature diagram of supercooled Si thus can be regarded in some respects as shifted reflection of its crystalline phase diagram. [ABSTRACT FROM AUTHOR]

Oxygen transport is central to many properties of oxides such as stoichiometric changes, phase transformation, and ionic conductivity. In this paper, we report a mechanism for oxygen transport in uranium dioxide (UO2) in which the kinetics is mediated by defect clustering dynamics. In particular, the kinetic Monte Carlo method has been used to investigate the kinetics of oxygen transport in UO2 under the condition of creation and annihilation of oxygen vacancies and interstitials as well as oxygen interstitial clustering, with variable off-stoichiometry and temperature conditions. It is found that in hypo-stoichiometric U O2-x, oxygen transport is well described by the vacancy diffusion mechanism while in hyper-stoichiometric UO2+x, oxygen interstitial cluster diffusion contributes significantly to oxygen transport kinetics, particularly at high temperatures and high off-stoichiometry levels. It is also found that di-interstitial clusters and single interstitials play dominant roles in oxygen diffusion while other larger clusters have negligible contributions. However, the formation, coalescence, and dissociation of these larger clusters indirectly affects the overall oxygen diffusion due to their interactions with mono and di-interstitials, thus providing an explanation of the experimental observation of saturation or even drop of oxygen diffusivity at high off-stoichiometry. [ABSTRACT FROM AUTHOR]

Hybrid systems consisting of organic molecules at inorganic semiconductor surfaces are gaining increasing importance as thin film devices for optoelectronics. The efficiency of such devices strongly depends on the collective behavior of the adsorbed molecules. In the present paper, we propose a novel, coarse-grained model addressing the condensed phases of a representative hybrid system, that is, para-sexiphenyl (6P) at zinc-oxide (ZnO). Within our model, intermolecular interactions are represented via a Gay-Berne potential (describing steric and van-der-Waals interactions) combined with the electrostatic potential between two linear quadrupoles. Similarly, the molecule-substrate interactions include a coupling between a linear molecular quadrupole to the electric field generated by the line charges characterizing ZnO(10-10). To validate our approach, we perform equilibrium Monte Carlo simulations, where the lateral positions are fixed to a 2D lattice, while the rotational degrees of freedom are continuous. We use these simulations to investigate orientational ordering in the condensed state. We reproduce various experimentally observed features such as the alignment of individual molecules with the line charges on the surface, the formation of a standing uniaxial phase with a herringbone structure, as well as the formation of a lying nematic phase. [ABSTRACT FROM AUTHOR]

We have updated the isotopically invariant Dunham fit of O2 with newly reported literature transitions to derive (1) the energy levels, partition sums, band-by-band molecular constants, and RKR poten-tials for the X³Σg-, a¹Δg+, and b¹Σg+ states of the six O2 isotopologues: 16O16O, 16O17O, 16O18O, 17O17O, 17O18O, and 18O18O; (2) Franck-Condon factors for their a¹Δg- X³Σg-, b¹Σg+ - X³Σg-, and a¹Δg -- b¹Σg+ band systems. This new spectroscopic parameterization characterizes all known transitions within and between the X³Σg--, a¹Δg, and b¹Σg+ states within experimental uncertainty and can be used for accurate predictions of as yet unmeasured transitions. All of these results are necessary to provide a consistent linelist of all transitions which will be reported in a followup paper. [ABSTRACT FROM AUTHOR]

The theory of optical transitions developed in Barford and Marcus ["Theory of optical transitions in conjugated polymers. I. Ideal systems," J. Chem. Phys. 141, 164101 (2014)] for linear, ordered polymer chains is extended in this paper to model conformationally disordered systems. Our key result is that in the Born-Oppenheimer regime the emission intensities are proportional to S(1)/IPR, where S(1) is the Huang-Rhys parameter for a monomer. IPR is the average inverse participation ratio for the emitting species, i.e., local exciton ground states (LEGSs). Since the spatial coherence of LEGSs determines the spatial extent of chromophores, the significance of this result is that it directly relates experimental observables to chromophore sizes (where IPR is half the mean chromophore size in monomer units). This result is independent of the chromophore shape, because of the Born-Oppenheimer factorization of the many body wavefunction. We verify this prediction by density matrix renormalization group (DMRG) calculations of the Frenkel-Holstein model in the adiabatic limit for both linear, disordered chains and for coiled, ordered chains. We also model optical spectra for poly(p-phenylene) and poly(p-phenylene-vinylene) oligomers and polymers. For oligomers, we solve the fully quantized Frenkel-Holstein model via the DMRG method. For polymers, we use the much simpler method of solving the one-particle Frenkel model and employ the Born-Oppenheimer expressions relating the effective Franck-Condon factor of a chromophore to its inverse participation ratio. We show that increased disorder decreases chromophore sizes and increases the inhomogeneous broadening, but has a non-monotonic effect on transition energies. We also show that as planarizing the polymer chain increases the exciton band width, it causes the chromophore sizes to increase, the transition energies to decrease, and the broadening to decrease. Finally, we show that the absorption spectra are more broadened than the emission spectra and that the broadening of the absorption spectra increases as the chains become more coiled. This is primarily because absorption occurs to both LEGSs and quasi-extended exciton states (QEESs), and QEES acquire increased intensity as chromophores bend, while emission only occurs from LEGSs. [ABSTRACT FROM AUTHOR]

Commensurate-incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs-Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the kryptongraphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton-carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas-solid and solid-solid system. [ABSTRACT FROM AUTHOR]

The purpose of this paper is to introduce a quasiparticle-based multi-reference coupled-cluster (MRCC) approach. The quasiparticles are introduced via a unitary transformation which allows us to represent a complete active space reference function and other elements of an orthonormal multi-reference (MR) basis in a determinant-like form. The quasiparticle creation and annihilation operators satisfy the fermion anti-commutation relations. On the basis of these quasiparticles, a generalization of the normal-ordered operator products for the MR case can be introduced as an alternative to the approach of Mukherjee and Kutzelnigg [Recent Prog. Many-Body Theor. 4, 127 (1995); J. Chem. Phys. 107, 432 (1997)]. Based on the new normal ordering any quasiparticle-based theory can be formulated using the well-known diagram techniques. Beyond the general quasiparticle framework we also present a possible realization of the unitary transformation. The suggested transformation has an exponential form where the parameters, holding exclusively active indices, are defined in a form similar to the wave operator of the unitary coupled-cluster approach. The definition of our quasiparticle-based MRCC approach strictly follows the form of the single-reference coupled-cluster method and retains several of its beneficial properties. Test results for small systems are presented using a pilot implementation of the new approach and compared to those obtained by other MR methods. [ABSTRACT FROM AUTHOR]

Franck-Condon vibrational overlap integrals for the Ã1Au—X̃1Σg+> transition in acetylene have been calculated in full dimension in the harmonic normal mode basis. The calculation uses the method of generating functions first developed for polyatomic Franck-Condon factors by Sharp and Rosenstock [J. Chem. Phys. 41(11), 3453-3463 (1964)], and previously applied to acetylene by Watson [J. Mol. Spectrosc. 207(2), 276-284 (2001)] in a reduced-dimension calculation. Because the transition involves a large change in the equilibrium geometry of the electronic states, two different types of corrections to the coordinate transformation are considered to first order: corrections for axis-switching between the Cartesian molecular frames and corrections for the curvilinear nature of the normal modes at large amplitude. The angular factor in the wavefunction for the out-of-plane component of the trans bending mode, v"4, is treated as a rotation, which results in an Eckart constraint on the polar coordinates of the bending modes. To simplify the calculation, the other degenerate bending mode, v"5, is integrated in the Cartesian basis and later transformed to the constrained polar coordinate basis, restoring the conventional v and l quantum numbers. An updated Ã-state harmonic force field obtained recently in the R. W. Field research group is evaluated. The results for transitions involving the gerade vibrational modes are in qualitative agreement with experiment. Calculated results for transitions involving ungerade modes are presented in Paper II of this series [G. B. Park, J. H. Baraban, and R. W. Field, "Full dimensional Franck-Condon factors for the acetylene Ã1Au—X̃1Σg+ transition. II. Vibrational overlap factors for levels involving excitation in ungerade modes," J. Chem. Phys. 141, 134305 (2014)]. [ABSTRACT FROM AUTHOR]

Although the volume transition of the polyelectrolyte gel has been studied for decades, less study on the finite size effects of the mobile ions has been conducted. In the present paper, Tanaka's classical theory of polyelectrolyte gel is extended to the cases of mobile ions of finite volume. In the salt free limit, the theoretical results show that the discontinuous volume transition of the polyelectrolyte gel will become a continuous one for counterionic size larger than a critical value. When a significant amount of salt is added, the critical value for the volume transition increases as a result of electrostatic screening. An increase in salt concentration can also make the polyelectrolyte gel in poor solvent collapse. Poorer solvent is needed to trigger the salt-induced collapse in polyelectrolyte gel with larger mobile ions than that with smaller ones. The effects of ionic size on the critical points and phase diagram of the volume transition are also discussed. The theoretical results suggest that the swelling behavior of polyelectrolyte gel might be tuned with salt of different volumes. [ABSTRACT FROM AUTHOR]

The flow-induced coil-stretch transition of high molecular weight polymers has generally been held to be of first order. But evidence of significant slowing down in the rate at which the polymers relax to equilibrium in the vicinity of the transition suggests that the thermodynamic character of the transition may be less clear-cut. The above slowing down effect is actually characteristic of a second-order transition, and it points to the existence of a broad spectrum of conformational states in the transition region, analogous to the existence of fluctuations of all length scales at a critical point. In this paper, using a path integral approach based on a free-draining finitely extensible chain model, we calculate various polymer properties as a function of elongational flow as a way of exploring different statistical mechanical details of the coil-stretch transition. These properties include the molecular weight dependence of the flow-extension curve of the polymer, the distribution of its steady-state end-to-end distances, and the characteristic relaxation time τR of these distances. Among other findings, our calculations indicate that the coil-stretch transition is discontinuous in the N → ∞ limit, that the effective free energy of the chain is unimodal at all values of the flow, becoming broad and flat in the immediate vicinity of the transition, and that the ratio of τR to the Rouse relaxation time increases abruptly at the transition before eventually reaching a plateau value at large flow strengths. These aspects of the coil-stretch transition place it among a larger class of unconventional nominally first-order single chain transitions that include the adsorption transition of surface-tethered polymers and the escape transition of compressed polymers. [ABSTRACT FROM AUTHOR]