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1.
The density of states for bulk and confined fluids have been modeled using a recently proposed gamma distribution (Krishnan, S. H.; Ayappa, K. G. J. Chem. Phys. 2004, 121, 3197). The gamma distribution results in a closed form analytical expression for the velocity autocorrelation function and the relaxation time of the fluid. The two parameters of the gamma distribution are related analytically to the second and fourth frequency moments of the fluid using short time expansions. The predictions by the proposed gamma model are compared with the velocity autocorrelation functions obtained using the theory of instantaneous normal modes (INMs) and from molecular dynamics simulations. The model is applied to a bulk soft sphere liquid and fluids confined in a spherical cavity and slit-shaped pores. The gamma model is able to capture the resulting changes in relaxation time due to changes in density and temperature extremely well for both the bulk liquid and confined inhomogeneous fluid situations. In all cases, the predictions by the gamma model are superior to those obtained from the INM theory. In the case of the fluid confined in a slit pore, the loadings were obtained from a grand canonical Monte Carlo simulation where the pore is equilibrated with a bulk fluid. This is similar to a confinement situation in a surface force apparatus. The predicted relaxation times vs pore widths from the gamma model are seen to accurately capture the oscillations due to formation and disruption of layers within the slit pore.  相似文献   

2.
The interplay between the structural relaxation and the rheological response of a simple amorphous system {a 80:20 binary Lennard-Jones mixture [W. Kob and H. C. Andersen, Phys. Rev. Lett. 73, 1376 (1994)]} is studied via molecular dynamics simulations. In the quiescent state, the model is well known for its sluggish dynamics and a two step relaxation of correlation functions at low temperatures. An ideal glass transition temperature of Tc=0.435 has been identified in the previous studies via the analysis of the system's dynamics in the framework of the mode coupling theory of the glass transition [W. Kob and H. C. Andersen, Phys. Rev. E 51, 4626 (1995)]. In the present work, we focus on the question whether a signature of this ideal glass transition can also be found in the case where the system's dynamics is driven by a shear motion. Indeed, the following distinction in the structural relaxation is found: In the supercooled state, the structural relaxation is dominated by the shear at relatively high shear rates gamma, whereas at sufficiently low gamma the (shear-independent) equilibrium relaxation is recovered. In contrast to this, the structural relaxation of a glass is always driven by shear. This distinct behavior of the correlation functions is also reflected in the rheological response. In the supercooled state, the shear viscosity eta decreases with increasing shear rate (shear thinning) at high shear rates, but then converges toward a constant as the gamma is decreased below a (temperature-dependent) threshold value. Below Tc, on the other hand, the shear viscosity grows as eta proportional, etax 1/gamma, suggesting a divergence at gamma=0. Thus, within the accessible observation time window, a transition toward a nonergodic state seems to occur in the driven glass as the driving force approaches zero. As to the flow curves (stress versus shear rate), a plateau forms at low shear rates in the glassy phase. A consequence of this stress plateau for Poiseuille-type flows is demonstrated.  相似文献   

3.
Molecular dynamics simulations were used to study the conformational dynamics of a bead-spring model polymer in an explicit solvent under good solvent conditions. The dynamics of the polymer chain were investigated using an analysis of the time autocorrelation functions of the Rouse coordinates of the polymer chain. We have investigated the variation of the correlation functions with polymer chain length N, solvent density rho, and system size. The measured initial decay rates gamma(p) of the correlation functions were compared with the predictions from a theory of polymer dynamics which uses the Oseen tensor to describe hydrodynamic interactions between monomers. Over the range of chain lengths considered (N = 30-60 monomers), the predicted scaling of gamma(p) proportional to N(-3nu) was observed at high rho, where nu is the polymer scaling exponent. The predicted gamma(p) are generally higher than the measured values. This discrepancy increases with decreasing rho, as a result in the breakdown in the conditions required for the Oseen approximation. The agreement between theory and simulation at high rho improves considerably if the theoretical expression for gamma(p) is modified to avoid sum-to-integral approximations, and if the values of (R(p)2), which are used in the theory, are taken directly from the simulation rather than being calculated using approximate scaling relations. The observed finite-size scaling of gamma(p) is not quantitatively consistent with the theoretical predictions.  相似文献   

4.
NMR chemical shielding anisotropy (CSA) relaxation is an important tool in the study of dynamical processes in proteins and nucleic acids in solution. Herein, we investigate how dynamical variations in local geometry affect the chemical shielding anisotropy relaxation of the carbonyl carbon nucleus, using the following protocol: 1) Using density functional theory, the carbonyl (13)C' CSA is computed for 103 conformations of the model peptide group N-methylacetamide (NMA). 2) The variations in computed (13)C' CSA parameters are fitted against quadratic hypersurfaces containing cross terms between the variables. 3) The predictive quality of the CSA hypersurfaces is validated by comparing the predicted and de novo calculated (13)C' CSAs for 20 molecular dynamics snapshots. 4) The CSA fluctuations and their autocorrelation and cross correlation functions due to bond-length and bond-angle distortions are predicted for a chemistry Harvard molecular mechanics (CHARMM) molecular dynamics trajectory of Ca(2+)-saturated calmodulin and GB3 from the hypersurfaces, as well as for a molecular dynamics (MD) simulation of an NMA trimer using a quantum mechanically correct forcefield. We find that the fluctuations can be represented by a 0.93 scaling factor of the CSA tensor for both R(1) and R(2) relaxations for residues in helix, coil, and sheet alike. This result is important, as it establishes that (13)C' relaxation is a valid tool for measurement of interesting dynamical events in proteins.  相似文献   

5.
We propose a model for the short-time dynamics of fluids confined in slit-shaped pores. The model has been developed from the observation that the real lobe of the instantaneous normal mode density of states (INM DOS) closely follows a gamma distribution. By proposing that the density of states of the confined fluid can be represented by a gamma distribution, the resulting velocity autocorrelation function (VACF) is constructed such that it is accurate upto the fourth frequency moment. The proposed model results in an analytical expression for the VACF and relaxation times. The VACFs obtained from the model have been compared with the VACFs obtained from molecular dynamic simulations and INM analysis for fluids confined in slit-shaped pores over a wide range of confinement and temperatures. The model is seen to capture the short-time behavior of the VACF extremely accurately and in this region is superior to the predictions of the VACF obtained from the real lobe of the INM DOS. Although the model predicts a zero self-diffusivity, the predicted relaxation times are in better agreement with the molecular dynamics results when compared with those obtained from the INM theory.  相似文献   

6.
Rotational diffusion in liquid acetonitrile, dimethylsulphoxide (DMSO), water, and methanol is studied with molecular dynamics simulations. The effects of hydrogen bonding and local dipole-dipole correlations (Kirkwood g-factor) on the relationship between the single molecule and collective relaxation are examined. The first rank single molecule dipole moment autocorrelation functions (ACFs) are constructed in the molecule-fixed coordinate frame and the principal components of rotation diffusion tensor are reported. Higher rank orientational ACFs are computed. These ACFs, as a rule, are strongly nonexponential (at least not single exponential) at longer times and the decomposition of these functions into a series of single exponentials results in broad distributions of relaxation times, with the broadening being particularly prominent in the case of higher rank ACFs. The rank dependence of characteristic times calculated as weighted averages over the relaxation time distributions does not follow the pattern of small angle (Debye) diffusion model for all liquids studied in this work except methanol. In contradiction, the same rank dependence computed by direct integration of ACFs leads to good agreement with the Debye diffusion model in the case of acetonitrile, DMSO, and water (but not methanol). The linear-angular momentum cross correlation functions are also computed and the effect of rototranslational coupling on reorientaional relaxation at longer times (>1.0?ps) is found to be small.  相似文献   

7.
In this work,all-atom molecular dynamics simulations were employed to study the influence of the side alkyl chain on glass transition behavior of several carbazole trimers(CT) in a temperature range from 423 to 183 K.The glass transition temperatures were obtained from the break in the slope of the volume-temperature curves and found to agree with the experimental values.The short time dynamics of four CT molecules were probed by usingvelocity autocorrelation functions and mean-square displacements.The current studies showed that the dynamics of CT systems can be easily interpreted through the cage effect.Furthermore,the investigation of the torsional autocorrelation function and P_(2-state)/P_(3-state) functions showed that the rotational barriers of side chains can slow down the conformational relaxation and lead to stronger temperature dependence of conformational relaxation.The relaxation time,characteristic time of P_(2-state)(t) and P_(3-state)(t) functions were all found to have Arrhenius-type temperature dependence.  相似文献   

8.
The dynamics and mechanism of proton exchange in phosphonic acid‐functionalized polymers were studied using poly(vinyl‐phosphonic acid) (PVPA) as a model system along with quantum chemical calculations and Born–Oppenheimer molecular dynamics (BOMD) simulations at the B3LYP/TZVP level as model calculations. This theoretical study began with searching for the smallest, most active polymer segments and their intermediate conformations which could be involved in the local proton‐exchange process. The B3LYP/TZVP results confirmed that a low local dielectric environment and excess proton conditions are required to generate the intermediate conformations, and the shapes of the potential energy curves of the proton exchange between the two phosphonic acid functional groups are sensitive to the local conformational changes. In contrast, a high local dielectric environment increases the energy barriers, thereby preventing the proton from returning to the original functional group. Based on the static results, a mechanism for the proton exchange between the two functional groups involving fluctuations in the local dielectric environment and a local conformational change was proposed. The BOMD results confirmed the proposed mechanism by showing that the activation energies for the proton exchange in the hydrogen bond between two immobilized phosphonic acid moieties, obtained from the exponential relaxation behaviors of the envelopes of the velocity autocorrelation functions and the 1H Nuclear Magnetic Resonance (NMR) line‐shape analyses, are too low to be the rate‐determining process. Instead, coupled librational motion in the backbone which leads to the interconversion between the two intermediate conformations possesses higher activation energy, and therefore represents one of the most important rate‐determining processes. These findings suggested that the rate of the proton exchange in the model phosphonic acid‐functionalized polymer is determined by the polymer mobility which, in this case, is the large‐amplitude librational motion of the vinyl backbone. © 2015 Wiley Periodicals, Inc.  相似文献   

9.
The density of states of rare gas atoms confined in carbon nanotubes is analyzed using a recently proposed model based on gamma distributions [Krishnan and Ayappa, J. Chem. Phys., 124 144503 (2006)]. The inputs into the model are the 2nd and 4th frequency moments that are obtained from molecular dynamics simulations. The predicted density of states, velocity autocorrelation functions and self-diffusivities are compared with those obtained from molecular dynamics simulations, for different nanotube loadings and temperatures. All results are reported for argon confined in a (16,16) carbon nanotube. The model predictions are extremely accurate at intermediate reduced densities of rhosigma(3) = 0.3, 0.4, where the majority of the self-diffusivity predictions lie within 10% of the simulation results. Since the frequency moments can be also obtained from Monte Carlo simulations, the study suggests an alternate route to the system dynamics of strongly confined fluids.  相似文献   

10.
The dielectric relaxation properties are considered for polymer networks built from polar macromolecules with the dipole moment directed along the end-to-end chain vector. The viscoeleastic cubic model of a regular network is used. The fixed average volume of a polymer network is ensured by the effective internal pressure. The dynamic models of polymer networks with external and interchain friction are studied. Two cases are considered: (1) polar chains cross-linked in a network at their ends, and (2) a densely cross-linked network with many network junctions per polar chain. The expressions for the autocorrelation functions of the total dipole moment of a network, which determine the dielectric susceptibility, are calculated. The relaxation spectrum of the autocorrelation function consists of two regions: the high-frequency relaxation spectrum of a chain fragment between two neighbouring junctions (intrachain relaxation spectrum) and the lowfrequency interchain relaxation spectrum. The interchain relaxation spectrum is determined by cooperative motions of chains which form a network. The characteristic time of this spectrum for networks of type (1) is the relaxation time of a chain between junctions τmin. For networks of type (2) a second time scale τ1 exists, which corresponds to motions inside the volume occupied by a single long polar chain included in a network. It leads to different time behaviour of the autocorrelation functions for both network models. The existence of only interchain friction in the network model leads to a cut-off of the relaxation spectrum at the time τmax depending on the volume of viscous interchain interactions.  相似文献   

11.
An accurate model for the density of states (DOS) for strongly inhomogeneous and bulk fluids has been proposed based on gamma distributions. The contribution to the density of states from the collective dynamics is modeled as an incomplete gamma distribution and the high frequency region is obtained from the solution of the memory equation using a sech memory kernel. Using only the frequency moments as input, the model parameters for the collective dynamics are obtained by matching moments of the resulting distribution. The model results in an analytical expression for the self-diffusivity of the fluid. We present results for soft sphere fluids confined in slit-shaped pores as well as bulk soft sphere liquids. Comparisons of the DOS, velocity autocorrelation functions, and memory kernels with molecular dynamics simulations reveal that the model predicts features in the DOS over the entire frequency range and is able to capture changes in the DOS as a function of fluid density and temperature. As a result the predicted VACFs, memory kernels, and self-diffusivities are accurately predicted over a wide range of conditions. Since the frequency moments for bulk liquids can be obtained from pair correlation functions, our method provides a direct route from fluid structure to dynamics. For fluids confined in slit-shaped pores, where the frequency moments are obtained from molecular dynamics simulations, the predicted self-diffusivities capture the resulting oscillations due to variations in the solvation pressure, and in the case of smooth walled pores, the predictions are superior to those obtained using kinetic theory.  相似文献   

12.
Molecular dynamics (MD) simulations of liquid tin between its melting point and 1600 °C have been performed in order to interpret and discuss the ionic structure. The interactions between ions are described by a new accurate pair potential built within the pseudopotential formalism and the linear response theory. The calculated structure factor that reflects the main information on the local atomic order in liquids is compared to diffraction measurements. Having some confidence in the ability of this pair potential to give a good representation of the atomic structure, we then focused our attention on the investigation of the atomic transport properties through the MD computations of the velocity autocorrelation function and stress autocorrelation function. Using the Green-Kubo formula (for the first time to our knowledge for liquid tin) we determine the macroscopic transport properties from the corresponding microscopic time autocorrelation functions. The selfdiffusion coefficient and the shear viscosity as functions of temperature are found to be in good agreement with the experimental data.  相似文献   

13.
Discontinuous molecular dynamics simulations are performed on a system containing 32 hard chains of length 192 at a volume fraction of phi = 0.45 to explore the idea that localized entanglements have a significant effect on the dynamics of the individual chains within an entangled polymer melt. Anomalous behavior can still be observed when studying the dynamics of the individual chains, although increased time averaging causes the anomalous relaxation-memory-release behavior that was observed previously in the system to smooth out. First, the individual chain mean squared displacements and apparent diffusion coefficients are calculated, and a wide distribution of diffusive behavior is found. Although the apparent diffusion coefficient curve averaged over all chains displays the predicted long-time diffusive behavior, the curves for the individual chains differ both qualitatively and quantitatively. They display superdiffusive, diffusive, and subdiffusive behavior, with the largest percentage of chains exhibiting superdiffusive behavior and the smallest percentage exhibiting the predicted diffusive behavior. Next, the individual chain end-to-end vector autocorrelation functions and relaxation times are determined, and a wide distribution of stress relaxation behavior is found. The times when the end-to-end vector autocorrelation functions relax completely span almost an order of magnitude in reduced time. For some chains, the end-to-end vector autocorrelation function relaxes smoothly toward zero similar to the system average; however, for other chains the relaxation is slowed greatly, indicating the presence of additional entanglements. Almost half of the chains exhibit the anomalous behavior in the end-to-end vector autocorrelation function. Finally, the dynamic properties are displayed for a single chain exhibiting anomalous relaxation-memory-release behavior, supporting the idea that the relaxation-memory-release behavior is a single-chain property.  相似文献   

14.
Extensive computer simulation was performed using the bond‐fluctuation model and cellular‐automaton (CA)‐based simulation technique to probe the equilibrium structure and dynamical behavior of comb‐branched polymers in which the flexible side chains of a given length are placed regularly along the backbone and the number of branches increases linearly with total molecular weight. By applying very efficient CA algorithm – the “lattice molecular dynamics” (LMD) method – we have been able to study the properties of sufficiently large structures (up to 5880 monomeric units). Depending on the length of main and side chains as well as on interbranch spacing, we have calculated mean chain dimensions, local fractal dimensionalities, particle scattering functions, time autocorrelation functions, etc. The following main conclusions may be drawn from the results presented in our study: (i) The critical exponent, governing the mean size of the main chain, remains unchanged from its value known for a 3d self‐avoiding walk (SAW). On the other hand, two‐dimensional branched macromolecules with one‐sided branches are effectively in a collapsed state even under conditions of a good solvent, forming specific helical superstructures. (ii) Comparison of the simulated data with the predictions of the scaling model indicates that the latter is valid in describing the mean dimensions of the backbone as a function of side‐chain length and interbranch spacing. (iii) The excluded volume interaction between side chains dramatically slows down the relaxation of the backbone chain.  相似文献   

15.
The theory of molecular mobility and relaxation spectra is developed for rodlike particles embedded in a polymer network with allowance for the involvement of the particles in collective network dynamics through topological entanglements with network fragments. A regular cubic coarse-grained network model is used, where the motion of junctions describes the mobility of large fragments (domains) of the initial network with a size equal to the distance between adjacent rodlike particles. The involvement of the rods in collective network dynamics is taken into account by introducing an effective quasi-elastic potential acting between the rods and junctions of the coarse-grained network and preventing long-distance diffusion of the embedded particles. The viscoelastic parameters of the coarse-grained (“renormalized”) network are functions of the viscoelastic characteristics of the initial network. The relaxation time spectra are calculated as well as the frequency dependences of the dielectric loss factor of the embedded particles that possess a permanent dipole moment directed along the major axis of each rod. Depending on the ratio between the viscoelastic characteristics of the rods and the network, the frequency dependence of the dielectric loss factor may have two maxima. The high-frequency maximum corresponds to local orientational movements of particles at fixed junctions of the coarse-grained network, which correspond to the position of the domain centers in the initial network. The low-frequency maximum corresponds to movements of particles involved in large-scale dynamics of network fragments. The dependence of the dielectric loss factor on the ratio between the viscoelastic parameters of the rods and the network is studied.  相似文献   

16.
A core/shell model has often been used to describe water confined to the interior of reverse micelles. The validity of this model for water encapsulated in AOT/isooctane reverse micelles ranging in diameter from 1.7 to 28 nm (w0 = 2-60) and bulk water is investigated using four experimental observables: the hydroxyl stretch absorption spectra, vibrational population relaxation times, orientational relaxation rates, and spectral diffusion dynamics. The time dependent observables are measured with ultrafast infrared spectrally resolved pump-probe and vibrational echo spectroscopies. Major progressive changes appear in all observables as the system moves from bulk water to the smallest water nanopool, w0 = 2. The dynamics are readily distinguishable for reverse micelle sizes smaller than 7 nm in diameter (w0 = 20) compared to the response of bulk water. The results also demonstrate that the size dependent absorption spectra and population relaxation times can be quantitatively predicted using a core-shell model in which the properties of the core (interior of the nanopool) are taken to be those of bulk water and the properties of the shell (water associated with the headgroups) are taken to be those of w0 = 2. A weighted sum of the core and shell components reproduces the size dependent spectra and the nonexponential population relaxation dynamics. However, the same model does not reproduce the spectral diffusion and the orientational relaxation experiments. It is proposed that, when hydrogen bond structural rearrangement is involved (orientational relaxation and spectral diffusion), dynamical coupling between the shell and the core cause the water nanopool to display more homogeneous dynamics. Therefore, the absorption spectra and vibrational lifetime decays can discern different hydrogen bonding environments whereas orientational and spectral diffusion correlation functions predict that the dynamics are size dependent but not as strongly spatially dependent within a reverse micelle.  相似文献   

17.
The intramolecular relaxation dynamics of semiflexible dendrimers in dilute solutions are theoretically investigated in the framework of optimized Rouse-Zimm formalism. Semiflexibility is implemented by modeling topological restrictions on the bond directions and orientations of the respective bond-vectors. Based on our recently developed approach for semiflexible dendrimers [A. Kumar and P. Biswas, Macromolecules 43, 7378 (2010)], the mechanical and dielectric relaxation moduli are studied as functions of local flexibility parameters and branching topology. It is rather interesting to observe that semiflexibility affects the local modes of G'(ω) and Δε'(ω), which have lower relaxation rate with increasing bond restrictions, while the collective modes with small relaxation rate remain almost constant. The relaxation dynamics of the flexible dendrimer is similar to that of the semiflexible dendrimer with unrestricted bond orientations (Φ = 0) and is flanked by the compressed (Φ = 30°) and expanded (Φ = 150°) conformations, respectively. The effect of semiflexibility is typically reflected in the intermediate frequency regime. The expanded conformations of semiflexible dendrimers display a power-law behavior in the intermediate frequency regime for both loss and storage modulus resembling fractal structures, while the compressed and unrestricted bond orientation conformations exhibit an approximately logarithmic dependence. The power-law exponent is found to be similar to the flexible dendrimers with excluded volume interactions. Thus, by tuning Φ, a spectrum of dynamic relaxation pattern is obtained spanning a broad range of conformations from a power-law fractal network to a non-fractal one. In certain limits, this highly generalized model captures the characteristics of flexible dendrimers and also resembles La Ferla's model semiflexible dendrimers. The influence of hydrodynamic interactions reduces the dynamical range and the width of the intermediate domain by decreasing the smaller relaxation rates and increasing the higher relaxation rates correspondingly.  相似文献   

18.
The 397.9 nm, 416.0 nm and 435.7 nm resonance Raman spectra were acquired for meso-tetrakis(4-carboxyphenyl)porphyrin (TCPP) in tetrahydrofuran solution, and the Raman effect of relaxation dynamics was analyzed according to Herzberg-Teller (vibronic coupling) contributions. Density functional calculations were done to help the elucidation of the Soret (B(x) and B(y)-band) electronic transitions and the corresponding photo relaxation dynamics of TCPP. The spectra indicate that the Franck-Condon region photo relaxation dynamics upon S(0) → S(4) electronic transition are predominantly along the totally symmetric C(m)-ph stretch and Porphin ring breath stretch, and simultaneously along the asymmetric ν(C(m)-Phenyl) + δ(N-H) and ν(C(α)-C(m)-C(α))(as) + def (pyr) vibrational relaxation processes. The excited state structural dynamics of TCPP determined from the resonance Raman spectra show that the internal conversion between the B(y) and B(x) electronic states occurs in tens of femtoseconds, and the electronic relaxation dynamics were firstly interpreted taking into account the time-dependent wave packet theory and Herzberg-Teller (vibronic coupling) contributions.  相似文献   

19.
The bond fluctuation model on a square lattice with a bond-length dependent potential exhibits in simulations of slow cooling a kinetic glass transition where the system falls out of equilibrium. Extending previous work, the relaxation functions of gyration radius and end-to-end distance, and the bond autocorrelation function of the polymers are presented and related to the time-dependent displacements of inner monomeric units and center of gravity of the whole chains, respectively. Over a wide temperature range the data can be collapsed on master curves satisfying the time-temperature superposition principle for Rouse dynamics.  相似文献   

20.
Using normal mode transformation obtained in Part 1 of this series[1], the exact analytical expressions for the mean‐square displacements of junctions and non‐junction beads, the autocorrelation functions of the end‐to‐end chain vectors between neighboring junctions, and those of subchain vectors of a two‐dimensional regular network consisting of "bead and spring" Rouse chains are obtained. Contributions of intra‐ and interchain relaxation processes to the local dynamic characteristics considered are compared. The time behavior of dynamic quantities obtained is estimated for different scales of motions. The possibility of describing long‐time relaxation of a two‐dimensional network by a simplified coarse‐grained network model is demonstrated. It is shown that the local relaxation properties of a two‐dimensional polymer network (as well as a three‐dimensional network) on scales smaller than the average distance between cross‐links are very close to those of a single Rouse chain. The large‐scale collective relaxation of the polymer networks having a two‐dimensional connectivity differs considerably from that of the three‐dimensional networks.  相似文献   

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