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The presence of gradient softer outer layers, commonly observed in biological systems (such as cartilage and ocular tissues), as well as synthetic crosslinked hydrogels, profoundly influences their interactions with opposing surfaces. Our prior research demonstrated that gradient-stiffness hydrogel layers, characterized by increasing elasticity with depth, control contact mechanics, particularly in proximity to the layer thickness. We postulate that the distribution of polymers within these gradient layers imparts extraordinary stretch and adhesion characteristics due to network adaptability and stress-induced reorganization. To investigate this phenomenon, we utilized Atomic Force Microscopy nanoindentation to assess the depth-dependent adhesion behavior of polyacrylamide hydrogels with varying gradient layer thicknesses. Two gradient layer thicknesses were achieved by employing different molding materials: glass and polyoxymethylene (POM). Glass-molded hydrogels exhibited a thinner gradient layer alongside a stiffer bulk layer compared to their POM-molded counterparts. In indentation experiments, the POM-molded hydrogel had larger adhesion compared to glass-molded hydrogel. We find that indenting within the gradient layer engenders increased load-unload hysteresis due to heightened fluid transport in the sparse outer polymer network. Consequently, this led to augmented adhesion and work of separation at shallow depths. We suggest that the prominent stretching capability of the sparse outer polymer network during probe retraction contributes to enhanced adhesion. The Maugis–Dugdale adhesive model only fits well to indentations on the thin layer or indentations which engage significantly with the bulk. These results facilitate a comprehensive characterization of adhesion mechanics in gradient-stiffness hydrogels, which could foster their application across emerging contexts in health science and environmental domains. [ABSTRACT FROM AUTHOR]

Polymer crystallization is a long-standing interesting problem both in fundamental polymer physics and in polymer manufacturing. Fundamentally, the connectivity of the macromolecules provides a unique feature for the study of nucleation and growth of crystals in contrast to the crystallization of smaller molecules. In addition, understanding the crystallization in polymers is industrially important due to the necessity of its control to achieve mechanically durable plastic materials. Molecular dynamics simulations offer a suitable way of studying this phenomenon due to their capability to probe the small time and length scales that are characteristic of nucleation. In this paper, we use a long alkane chain model to study nucleation and the growth of polyethylene crystals both within bulk and nano-droplets whose diameters range from about 6 to 11 nm. It is found that the droplets approach being more spherical during the nucleation whereas they deviate from this shape during the growth regime. Strikingly, a mean first passage time analysis indicates that the nucleation rate per unit volume decreases as the droplet size is increased. Finally, visual inspection of the simulation snapshots suggests that nuclei majorly emerged from the surface of the droplets. [ABSTRACT FROM AUTHOR]

The time evolution in open quantum systems, such as a molecular aggregate in contact with a thermal bath, still poses a complex and challenging problem. The influence of the thermal noise can be treated using a plethora of schemes, several of which decompose the corresponding correlation functions in terms of weighted sums of exponential functions. One such scheme is based on the hierarchical equations of motion (HEOM), which is built using only certain forms of bath correlation functions. In the case where the environment is described by a complex spectral density or is at a very low temperature, approaches utilizing the exponential decomposition become very inefficient. Here, we utilize an alternative decomposition scheme for the bath correlation function based on Chebyshev polynomials and Bessel functions to derive a HEOM approach up to an arbitrary order in the environmental coupling. These hierarchical equations are similar in structure to the popular exponential HEOM scheme, but are formulated using the derivatives of the Bessel functions. The proposed scheme is tested up to the fourth order in perturbation theory for a two-level system and compared to benchmark calculations for the case of zero-temperature quantum Ohmic and super-Ohmic noise. Furthermore, the benefits and shortcomings of the present Chebyshev-based hierarchical equations are discussed. [ABSTRACT FROM AUTHOR]

In quantum transport across molecular junctions, time-dependent effects arise mainly due to interactions with external perturbations such as pulsed laser fields or fluctuating environments. While the calculation of the charge dynamics in such an open quantum system is a complex problem, it is highly relevant for engineering nanoscale devices. Several theoretical approaches to this problem including some based on quantum master equations, hierarchical schemes, or non-equilibrium Green's functions (NEGFs) rely on assuming a molecule-lead coupling composed of Lorentzian functions and a decomposition of the Fermi function. The underlying assumptions in this strategy lead to limitations in the functional form of the molecule-lead coupling and to an inefficiency at low temperatures. To overcome these restrictions, a Chebyshev expansion is applied to derive a set of coupled ordinary differential equations within the NEGF formalism. The numerical efficiency of this approach is independent of temperature and band structure of the electrodes. Moreover, since the scheme deals with a single particle basis set, it is possible to replace all auxiliary matrices present in the equations by vectors. Test setups for this new scheme include molecular junctions under the influence of strong time-dependent perturbations leading, for example, to coherent destruction of tunneling. [ABSTRACT FROM AUTHOR]

The stretching of plasma membranes of cells and lipid bilayers of vesicles affects the physical properties of the membrane as well as the functions of proteins/peptides in the membranes. Here, we examined the effect of membrane tension on the rate constant of the transbilayer movement (kFF) of fluorescent probe-labeled lipids using a new method. Specifically, we recently reported [Hasan et al., Langmuir 34, 3349 (2018)] the development of a technique that employs giant unilamellar vesicles (GUVs) with asymmetric lipid compositions in two monolayers. In the present work, we found that the kFF greatly increased with tension without leakage of water-soluble fluorescent probes from the GUV lumen (i.e., without the formation of pores in the GUV membrane). We discussed the plausible mechanisms for the effect of tension on the transbilayer movement of lipids. As one of the mechanisms, we hypothesized that the transbilayer movement of lipids occurs through the lateral diffusion of lipids in the walls of hydrophilic pre-pores. [ABSTRACT FROM AUTHOR]

Irradiation by laser pulses and a fluctuating surrounding liquid environment can, for example, lead to time-dependent effects in the transport through molecular junctions. From the theoretical point of view, time-dependent theories of quantum transport are still challenging. In one of these existing transport theories, the energy-dependent coupling between molecule and leads is decomposed into Lorentzian functions. This trick has successfully been combined with quantum master approaches, hierarchical formalisms, and non-equilibrium Green's functions. The drawback of this approach is, however, its serious limitation to certain forms of the molecule-lead coupling and to higher temperatures. Tian and Chen [J. Chem. Phys. 137, 204114 (2012)] recently employed a Chebychev expansion to circumvent some of these latter problems. Here, we report on a similar approach also based on the Chebychev expansion but leading to a different set of coupled differential equations using the fact that a derivative of a zeroth-order Bessel function can again be given in terms of Bessel functions. Test calculations show the excellent numerical accuracy and stability of the presented formalism. The time span for which this Chebychev expansion scheme is valid without any restrictions on the form of the spectral density or temperature can be determined a priori. [ABSTRACT FROM AUTHOR]

We report our study of a silica-water interface using reactive molecular dynamics. This first-of-its-kind simulation achieves length and time scales required to investigate the detailed chemistry of the system. Our molecular dynamics approach is based on the ReaxFF force field of van Duin et al. [J. Phys. Chem. A 107, 3803 (2003)]. The specific ReaxFF implementation (SERIALREAX) and force fields are first validated on structural properties of pure silica and water systems. Chemical reactions between reactive water and dangling bonds on a freshly cut silica surface are analyzed by studying changing chemical composition at the interface. In our simulations, reactions involving silanol groups reach chemical equilibrium in ∼250 ps. It is observed that water molecules penetrate a silica film through a proton-transfer process we call “hydrogen hopping,” which is similar to the Grotthuss mechanism. In this process, hydrogen atoms pass through the film by associating and dissociating with oxygen atoms within bulk silica, as opposed to diffusion of intact water molecules. The effective diffusion constant for this process, taken to be that of hydrogen atoms within silica, is calculated to be 1.68×10-6 cm2/s. Polarization of water molecules in proximity of the silica surface is also observed. The subsequent alignment of dipoles leads to an electric potential difference of ∼10.5 V between the silica slab and water. [ABSTRACT FROM AUTHOR]

Employing frequency-dependent dielectric susceptibility we characterize the aging in two supercooled liquids, sorbitol and xylitol, below their calorimetric glass transition temperatures. In addition to the alpha relaxation that tracks the structural dynamics, the susceptibility of both liquids possesses a secondary Johari-Goldstein relaxation at higher frequencies. Following a quench through the glass transition, the susceptibility slowly approaches the equilibrium behavior. For both liquids, the magnitude of the Johari-Goldstein relaxation displays a dependence on the time since the quench, or aging time, that is quantitatively very similar to the age dependence of the alpha peak frequency. The Johari-Goldstein relaxation time remains constant during aging for sorbitol while it decreases slightly with age for xylitol. Hence, one cannot sensibly assign a fictive temperature to the Johari-Goldstein relaxation. This behavior contrasts with that of liquids lacking distinct Johari-Goldstein peaks for which the excess wing of the alpha peak tracks the main part of the peak during aging, enabling the assignment of a single fictive temperature to the entire spectrum. The aging behavior of the Johari-Goldstein relaxation time further calls into question the possibility that the relaxation time possesses stronger temperature dependence in equilibrium than is observed in the out-of-equilibrium state below the glass transition. [ABSTRACT FROM AUTHOR]

Luminescence and power-gated spectral holeburning studies have been performed on Eu-doped MgS nanoparticles. These particles are atomically tailored to produce and control the relative concentration of Eu2+ and Eu3+, which is necessary for power-gated holeburning. The spectral holes are permanent at low temperatures. Optical studies show that the electron-phonon coupling is stronger in nanoparticles than in thin films or microparticles of the same material. This is the reason for inherently broader spectral holes in nanoparticles as compared to microparticle or thin-film samples. Temperature broadening of spectral holes in nanoparticles follows a T2.4 behavior, a faster rate than thin films or microparticles. This behavior can be attributed to the glassy nature of the particles produced. [ABSTRACT FROM AUTHOR]

We report the development and testing of new integrated cyberinfrastructure for performing free energy simulations with generalized hybrid quantum mechanical/molecular mechanical (QM/MM) and machine learning potentials (MLPs) in Amber. The Sander molecular dynamics program has been extended to leverage fast, density-functional tight-binding models implemented in the DFTB+ and xTB packages, and an interface to the DeePMD-kit software enables the use of MLPs. The software is integrated through application program interfaces that circumvent the need to perform "system calls" and enable the incorporation of long-range Ewald electrostatics into the external software's self-consistent field procedure. The infrastructure provides access to QM/MM models that may serve as the foundation for QM/MM–ΔMLP potentials, which supplement the semiempirical QM/MM model with a MLP correction trained to reproduce ab initio QM/MM energies and forces. Efficient optimization of minimum free energy pathways is enabled through a new surface-accelerated finite-temperature string method implemented in the FE-ToolKit package. Furthermore, we interfaced Sander with the i-PI software by implementing the socket communication protocol used in the i-PI client–server model. The new interface with i-PI allows for the treatment of nuclear quantum effects with semiempirical QM/MM–ΔMLP models. The modular interoperable software is demonstrated on proton transfer reactions in guanine-thymine mispairs in a B-form deoxyribonucleic acid helix. The current work represents a considerable advance in the development of modular software for performing free energy simulations of chemical reactions that are important in a wide range of applications. [ABSTRACT FROM AUTHOR]

Nonlinear optical properties of the linear polyenes C4H6 through C30H32 are calculated at frequencies below the first resonance using ab initio time-dependent Hartree–Fock theory. The results are used to determine accurate values for the infinite polymer, polyacetylene, by means of a new extrapolation method. Dispersion coefficients describing the low frequency behavior are obtained for the largest oligomer. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Linear and nonlinear static electronic polarizabilities of the σ-conjugated polymer trans-polysilane (t-PSi) are obtained at the Hartree–Fock level by extrapolation of ab initio calculations on the oligomers H3Si–(SiH2)N–SiH3 (N odd). For the longitudinal components, in particular, a 6–31 G basis is shown to yield accurate values if the chains are long enough. No computational advantage is found in using effective core potentials. Chain lengths through N=13 are sufficient to give limiting infinite chain polarizabilities with relatively small uncertainty. The calculated longitudinal linear polarizability per SiH unit is about the same as the corresponding property in the prototype π-conjugated polymers polyacetylene (PA) and polydiacetylene (PDA), but the longitudinal second hyperpolarizability is significantly less in the σ-conjugated polymer. In t-PSi the conjugation length is about half that in either PA or PDA. Frequency-dependent vibrational distortion contributions are estimated in the doubly harmonic approximation and turn out to be important in trisilane and pentasilane even at optical frequencies. An analysis is developed which sheds light on the expected behavior for increasing chain lengths. Reasonable agreement with experiment is obtained for both the electronic and vibrational longitudinal second hyperpolarizabilities. [ABSTRACT FROM AUTHOR]

The spin distribution of the neutral soliton in trans-polyacetylene is controversial, as evidenced by the markedly different interpretations given by the various active experimental groups to their ENDOR measurements of proton hyperfine coupling (hfc) constants. To help resolve the discrepancies, ab initio electronic structure calculations were carried out for proton and carbon-13 hfc on the series of model polyene radicals C5H7,C9H11,...,C21H23 and the most important characteristics of the spin distribution were extrapolated to the long chain limit. Here σ spin polarization was treated through single excitation configuration interaction, both with respect to Hartree–Fock and to multiconfiguration reference spaces that include the most significant effects of π electron correlation. Particular attention was paid to basis set requirements necessary for proper treatment of hfc. It turns out that the ab initio hfc does not agree with that obtained by any of the major experimental groups. In particular, the calculated width of the bell-shaped distribution for the central and other even proton sites is much narrower than all experimental reports, and the anisotropic coupling calculated for the central proton along the fibril axis is much larger. Several assumptions commonly made in analyzing the ENDOR spectra are shown not to be quantitatively justifiable, but their improvement is unlikely to resolve the large discrepancies we have found between theory and current experimental interpretations. Thus, it appears likely that the experimental spectra are significantly influenced by environmental effects and cannot be adequately modeled by an isolated long chain polyene radical as heretofore assumed. [ABSTRACT FROM AUTHOR]

A simple method is presented for calculating approximate static and dynamic vibrational hyperpolarizabilities. It involves determining electrical properties in the presence of a static field with and without geometry optimization. This method is readily applicable to all tensor components of a general polyatomic molecule. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We present a sub-picosecond resolved investigation of the structural solvent reorganization and geminate recombination dynamics following 400 nm two-photon excitation and photodetachment of a valence p electron from the aqueous atomic solute, I−(aq). The measurements utilized time-resolved X-ray Absorption Near Edge Structure (TR-XANES) spectroscopy and X-ray Solution Scattering (TR-XSS) at the Linac Coherent Light Source x-ray free electron laser in a laser pump/x-ray probe experiment. The XANES measurements around the L1-edge of the generated nascent iodine atoms (I0) yield an average electron ejection distance from the iodine parent of 7.4 ± 1.5 Å with an excitation yield of about 1/3 of the 0.1M NaI aqueous solution. The kinetic traces of the XANES measurement are in agreement with a purely diffusion-driven geminate iodine–electron recombination model without the need for a long-lived (I0:e−) contact pair. Nonequilibrium classical molecular dynamics simulations indicate a delayed response of the caging H2O solvent shell and this is supported by the structural analysis of the XSS data: We identify a two-step process exhibiting a 0.1 ps delayed solvent shell reorganization time within the tight H-bond network and a 0.3 ps time constant for the mean iodine–oxygen distance changes. The results indicate that most of the reorganization can be explained classically by a transition from a hydrophilic cavity with a well-ordered first solvation shell (hydrogens pointing toward I−) to an expanded cavity around I0 with a more random orientation of the H2O molecules in a broadened first solvation shell. [ABSTRACT FROM AUTHOR]

Optical excitation and emission spectra are reported for the Cs2NaErCl6 system under variable-temperature (8.5–298 K) conditions. Detailed line assignments are made for the 4I15/2←4S3/2 and 4I15/2←4F9/2 high-resolution emission spectra, and all five crystal-field levels split out of the 4I15/2 ground multiplet are located. These results combined with our previously reported absorption results provide the locations of 35 crystal-field levels spanning 11 multiplets of the Er3+ ion in Cs2NaErCl6. Energy level calculations based on a nine-parameter 4f-electron Hamiltonian operating within the 4f11 configuration of Er3+ give results in good agreement with experiment. Excitation spectra for 4I15/2←4S3/2 emission are reported at several temperatures over the 340–540 nm spectral region. Emission spectra excited by near-ultraviolet radiation (centered at 383 nm) are reported over the 405–725 nm spectral region for sample temperatures ranging from 8.5 to 298 K. All but one of the seven multiplet-to-multiplet emission bands observed in this region decrease in intensity as the sample temperature is increased. The 4I13/2←4G11/2 emission exhibits an increase in intensity with increasing temperature. [ABSTRACT FROM AUTHOR]

Publisher's Note: "Tracking structural solvent reorganization and recombination dynamics following e- photoabstraction from aqueous I- with femtosecond x-ray spectroscopy and scattering" [J. Chem. Phys. The footnote indicators are correct as they appear. This article was originally published online on 8 December 2022 with an error in the author footnote indicators for authors Jochen Rittman and Christian Bressler. [Extracted from the article]

Compressibility characterizes three interconnecting properties of a protein: dynamics, structure, and function. The compressibility values for the electron-carrying protein cytochrome c and for other proteins, as well, available in the literature vary considerably. Here, we apply two synchrotron-based techniques––nuclear resonance vibrational spectroscopy and inelastic x-ray scattering––to measure the adiabatic compressibility of this protein. This is the first report of the compressibility of any material measured with this method. Unlike the methods previously used, this novel approach probes the protein globally, at ambient pressure, does not require the separation of protein and solvent contributions to the total compressibility, and uses samples that contain the heme iron, as in the native state. We show, by comparing our results with molecular dynamics predictions, that the compressibility is almost independent of temperature. We discuss potential applications of this method to other materials beyond proteins. [ABSTRACT FROM AUTHOR]

Ab initio restricted Hartree–Fock 6-31G calculations are reported for the static longitudinal hyperpolarizability of the linear polyenes C4H6 through C44H46. Using a new extrapolation technique the infinite chain value in polyacetylene is determined with an accuracy similar to that achieved for small molecules. This is the first in a series of articles leading to a comprehensive ab initio treatment for the nonlinear optical properties of conjugated polymers. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]