Slow dynamics of the high density Gaussian core model

We numerically study crystal nucleation and glassy slow dynamics of the one-component Gaussian core model (GCM) at high densities. The nucleation rate at a fixed supercooling is found to decrease as the density increases. At very high densities, the nucleation is not observed at all in the time window accessed by long molecular dynamics (MD) simulation. Concomitantly, the system exhibits typical slow dynamics of the supercooled fluids near the glass transition point. We compare the simulation results of the supercooled GCM with the predictions of mode-coupling theory (MCT) and find that the agreement between them is better than any other model glassformers studied numerically in the past. Furthermore, we find that a violation of the Stokes-Einstein relation is weaker and the non-Gaussian parameter is smaller than canonical glassformers. Analysis of the probability distribution of the particle displacement clearly reveals that the hopping effect is strongly suppressed in the high density GCM. We conclude from these observations that the GCM is more amenable to the mean-field picture of the glass transition than other models. This is attributed to the long-ranged nature of the interaction potential of the GCM in the high density regime. Finally, the intermediate scattering function at small wavevectors is found to decay much faster than its self part, indicating that dynamics of the large-scale density fluctuations decouples with the shorter-ranged caging motion.     

Ergodicity breaking and conformational hysteresis in the dynamics of a polymer tethered at a surface stagnation point

We study the dynamics of long chain polymer molecules tethered to a plane wall and subjected to a stagnation point flow. Using a combination of theory and numerical techniques, including Brownian dynamics (BD), we demonstrate that a chain conformation hysteresis exists even for freely draining (FD) chains. Hydrodynamic interactions (HI) between the polymer and the wall are included in the BD simulations. We find qualitative agreement between the FD and HI simulations, with both exhibiting simultaneous coiled and stretched states for a wide range of fixed flow strengths. The range of state coexistence is understood by considering an equivalent projected equilibrium problem of a two state reaction. Using this formalism, we construct Kramers rate theory (from the inverse mean first passage time for a Markov process) for the hopping transition from coil to stretch and stretch to coil. The activation energy for this rate is found to scale proportionally to chain length or Kuhn step number. Thus, in the limit of infinite chain size the hopping rates at a fixed value of the suitably defined Deborah number approach zero and the states are "frozen." We present the results that demonstrate this "ergodicity breaking."     

Communication: Standard surface hopping predicts incorrect scaling for Marcus' golden-rule rate: the decoherence problem cannot be ignored

We evaluate the accuracy of Tully's surface hopping algorithm for the spin-boson model for the case of a small diabatic coupling parameter (V). We calculate the transition rates between diabatic surfaces, and we compare our results to the expected Marcus rates. We show that standard surface hopping yields an incorrect scaling with diabatic coupling (linear in V), which we demonstrate is due to an incorrect treatment of decoherence. By modifying standard surface hopping to include decoherence events, we recover the correct scaling (~V(2)).     

Semiclassical treatment of thermally activated electron transfer in the inverted region under the fast dielectric relaxation

The previously formulated semiclassical theory (Zhao, Liang, and Nakamura, J. Phys. Chem. A 2006, 110, 8204) is used to study electron transfer in the Marcus inverted case by considering multidimensional potential energy surfaces of donor and acceptor. The Zhu-Nakamura formulas of nonadiabatic transition in the case of Landau-Zener type are incorporated into the approach. The theory properly takes into account the nonadiabatic transition coupled with the nuclear tunneling and can cover the whole range from weak to strong coupling regime uniformly under the assumption of fast solvent relaxation. The numerical calculations are performed for the 12-dimensional model of shifted harmonic oscillators and demonstrate that the reaction rate with respect to the electronic coupling shows a maximum, confirming the adiabatic suppression in the strong coupling limit. The adiabatic suppression is dramatically reduced by the effect of nuclear tunneling compared to the case that the Landau-Zener formula is used. The possible extension and applications to the case of the slow solvent dynamics are discussed.     

Semiclassical initial value representation study of internal conversion rates

Internal conversion is an inherently quantum mechanical process. To date, "on the fly" computation of internal conversion rates is limited to harmonic approximations, which would seem to be especially unsuitable, given that the typical transition to the ground electronic state occurs at energies which are far from the harmonic limit. It is thus of interest to study the applicability of the semiclassial initial value representation (SCIVR) approach which is in principle amenable to on the fly studies even with "many" degrees of freedom. In this paper we study the applicability of the Herman-Kluk (HK) SCIVR to a model system with two coupled and anharmonic degrees of freedom. We find that (a) the HK SCIVR is a good approximation to the exact quantum dynamics; (b) computation of the first order correction to the HK-SCIVR approximation corroborates the accuracy; (c) by studying a large parameter range, we find that the harmonic approximation is mostly unsatisfactory; and (d) for the specific model used, the coupling between the modes was found to be relatively unimportant. These results imply that the HK-SCIVR methodology is a good candidate for on the fly studies of internal conversion processes of "large" molecules.     

Calculating the hopping times of confined fluids: two hard disks in a box

The dynamical transition between the anomalous single file diffusion of highly confined fluids and bulk normal diffusion can be described by a phenomenological model involving a particle hopping time tau(hop). We suggest a theoretical formalism that will be useful for the calculation of tau(hop) for a variety of systems and test it using a simple model consisting of two hard disks confined to a rectangular box with hard walls. In the case where the particles are moving diffusively, we find the hopping time diverges as a power law in the threshold region with an exponent of -(3/2). Under conditions where the particles move inertially, transition state theory predicts a power law behavior with an exponent of -2. Molecular dynamics simulations confirm the transition state theory result for inertial dynamics, while Brownian dynamics simulations suggest the scaling exponent is highly sensitive to the details of the algorithm.     

Ab Initio Nonadiabatic Dynamics of Semiconductor Materials via Surface Hopping Method

Photoinduced carrier dynamic processes are without doubt the main driving force responsible for the efficient performance of semiconductor nanomaterials in applications like photoconversion and photonics. Nevertheless, establishing theoretical insights into these processes is computationally challenging owing to the multiple factors involved in the processes, namely reaction rate, material surface area, material composition etc. Modelling of photoinduced carrier dynamic processes can be performed via nonadiabatic molecular dynamics (NA-MD) methods, which are methods specifically designed to solve the time-dependent Schrodinger equation with the inclusion of nonadiabatic couplings. Among NA-MD methods, surface hopping methods have been proven to be a mighty tool to mimic the competitive nonadiabatic processes in semiconductor nanomaterials, a worth noticing feature is its exceptional balance between accuracy and computational cost. Consequently, surface hopping is the method of choice for modelling ultrafast dynamics and more complex phenomena like charge separation in Janus transition metal dichalcogenides-based van der Waals heterojunction materials. Covering latest stateof-the-art numerical simulations along with experimental results in the field, this review aims to provide a basic understanding of the tight relation between semiconductor nanomaterials and the proper simulation of their properties via surface hopping methods. Special stress is put on emerging state-ot-the-art techniques. By highlighting the challenge imposed by new materials, we depict emerging creative approaches, including high-level electronic structure methods and NA-MD methods to model nonadiabatic systems with high complexity.     

Condensed-phase relaxation of multilevel quantum systems. I. An exactly solvable model

An analytically solvable model of multilevel condensed-phase quantum dynamics relevant to vibrational relaxation and electron transfer is presented. Exact solutions are derived for the reduced system density matrix dynamics of a degenerate N-level quantum system characterized by nearest-neighbor hopping and off-diagonal coupling (which is linear in the bath coordinates) to a harmonic oscillator bath. We demonstrate that for N> 2 the long-time steady-state system site occupation probabilities are not the same for all sites; that is, they are distributed in a non-Boltzmann manner, which depends on the initial conditions and the number of levels in the system. Although the system-bath Hamiltonian considered here is restricted in form, the availability of an exact solution enables us to study the model in all regions of an extensive parameter space.     

Sensitivity of femtosecond quantum dynamics and control with respect to non-adiabatic couplings: Model simulations for the cis–trans isomerization of the dideuterated methaniminium cation

We investigate the non-radiative decay in the photo-isomerization of the dideuterated methaniminium cation HDN⁺CDH by means of quantum dynamical simulations of the laser driven torsion. For the present model, the torsional dynamics is nearly adiabatic, but this is shown to be extremely sensitive to the large non-adiabatic coupling elements close to the conical intersection as well as to the apparently small values in the other domains. Neglecting those small couplings artificially changes the nearly adiabatic dynamics into diabatic dynamics. The non-adiabatic coupling terms are calculated ab initio with a test of accuracy which is based on the strict adiabaticity of pure rotational motions. Moreover, we present a novel mechanism for the enhancement of the laser-induced isomerization which may be interpreted as coherent control of competing pump–dump and two interfering non-radiative decay processes.     

Mixed quantum-classical equilibrium: Surface hopping

We re-examine the analysis of the equilibrium limits of the fewest switches surface hopping algorithm for mixed quantum-classical dynamics. In contrast with previously reported results, we show that surface hopping does not, in general, exactly yield Boltzmann equilibrium, but that in practice the observed deviations are quite small. We also demonstrate that surface hopping does approach the exact equilibrium distribution in both the limits of small adiabatic splitting and/or strong nonadiabatic coupling. We verify these analytical results with numerical simulations for a simple two-level quantum system connected to a bath of classical particles.     

Effects of Configurational Fluctuation on Electronic Coupling for Charge Transfer Dynamics

We advance a theory for the effects of bridge configurational fluctuations on the electronic coupling for electron transfer reactions in donor-bridge-acceptor systems. The theory of radiationless transitions was applied for activationless electron transfer, where the nuclear Franck–Condon constraints are minimized, with the initial vibronic state interacting directly with the final vibronic manifold, without the need for thermal activation. Invoking the assumption of energy-independent coupling, the time-dependent initial state population probability was analyzed in terms of a cumulant expansion. Two limiting situations were distinguished, i.e. the fast configurational fluctuation limit, where the electron transfer rate is given in terms of the configurational average of me squared electronic coupling, and the slow configurational fluctuation limit, where the dynamics is determined by a configurational averaging over a static distribution of electron transfer probability densities. The correlation times for configurational fluctuations of the electronic coupling will be obtained from the analysis of molecular dynamics, in conjunction with quantum mechanical calculations of the electronic coupling, to establish the appropriate limit for electron transfer dynamics.     

Energy transfer in the nanostar: the role of coulombic coupling and dynamics

We present a theoretical investigation of energy transfer in the phenylene ethynelene dendrimer known as the nanostar. Data from extensive molecular dynamics simulations are used to model the dynamical effects caused by torsional motion of the phenyl groups. We compare rate constants for energy transfer between the two-ring chromophore and the three-ring chromophore obtained via the F?rster model, the ideal dipole approximation (IDA), and the transition density cube (TDC) method, which has as its limit an exact representation of the Coulombic coupling. We find that the rate constants obtained with the TDC are extremely sensitive to the phenyl group rotation, whereas the constants computed with the F?rster model and the IDA are not. The implications of these results for the interpretation of recent pump-probe experiments on the nanostar are discussed in detail. Finally, we predict the temperature dependence of the rate constant for energy transfer.     

Bias annealing: a method for obtaining transition paths de novo

Computational studies of dynamics in complex systems require means for generating reactive trajectories with minimum knowledge about the processes of interest. Here, we introduce a method for generating transition paths when an existing one is not already available. Starting from biased paths obtained from steered molecular dynamics, we use a Monte Carlo procedure in the space of whole trajectories to shift gradually to sampling an ensemble of unbiased paths. Application to basin-to-basin hopping in a two-dimensional model system and nucleotide-flipping by a DNA repair protein demonstrates that the method can efficiently yield unbiased reactive trajectories even when the initial steered dynamics differ significantly. The relation of the method to others and the physical basis for its success are discussed.     

Charge transport in DNA via thermally induced hopping.

In this contribution we advance and explore the thermally induced hopping (TIH) mechanism for long-range charge transport (CT) in DNA and in large-scale chemical systems. TIH occurs in donor-bridge-acceptor systems, which are characterized by off-resonance donor-bridge interactions (energy gap DeltaE > 0), involving thermally activated donor-bridge charge injection followed by intrabridge charge hopping. We observe a "transition" from superexchange to TIH with increasing the bridge length (i.e., the number N of the bridge constituents), which is manifested by crossing from the exponential N-dependent donor-acceptor CT rate at low N (< N(X)) to a weakly (algebraic) N-dependent CT rate at high N (>N(X)). The "critical" bridge size N(X) is determined by the energy gap, the nearest-neighbor electronic couplings, and the temperature. Experimental evidence for the TIH mechanism was inferred from our analysis of the chemical yields for the distal/proximal guanine (G) triplets in the (GGG)(+)TTXTT(GGG) duplex (X = G, azadine (zA), and adenine (A)) studied by Nakatani, Dohno and Saito [J. Am. Chem. Soc. 2000, 122, 5893]. The TIH sequential model, which involves hole hopping between (GGG) and X, is analyzed in terms of a sequential process in conjunction with parallel reactions of (GGG)(+) with water, and provides a scale of (free) energy gaps (relative to (GGG)(+)) of Delta = 0.21-0.24 eV for X = A, Delta = 0.10-0.14 eV for X = zA, and Delta = 0.05-0.10 eV for X = G. We further investigated the chemical yields for long-range TIH in (G)l(+)Xn(G)l (l = 1-3) duplexes, establishing the energetic constraints (i.e., the donor - bridge base (X) energy gap Delta), the bridge structural constraints (i.e., the intrabridge X-X hopping rates k(m)), and the kinetic constraints (i.e., the rate k(d) for the reaction of with water). Effective TIH is expected to prevail for Delta less than or approximately equal to 0.20 eV with a "fast" water reaction (k(d)/k(m) approximately 10(-3)) and for Delta < 0.30 eV with a "slow" water reaction (k(d)/k(m) approximately 10(-5)). We conclude that (T)n bridges (for which Delta approximately equals 0.6 eV) cannot act in TIH of holes. From an analysis based on the energetics of the electronic coupling matrix elements in G(+)(T-A)n(GGG) duplexes we conclude that the superexchange mechanism is expected to dominate for n = 1-4. For long (A)n bridges (n > or approximately equal to 4) the TIH prevails, provided that the water side reaction is slow, raising the issue of chemical control of TIH through long (A)n bridges in DNA attained by changing the solution composition.     

Theory of gelation, vitrification, and activated barrier hopping in mixtures of hard and sticky spheres

Naive mode coupling theory (NMCT) and the nonlinear stochastic Langevin equation theory of activated dynamics have been generalized to mixtures of spherical particles. Two types of ideal nonergodicity transitions are predicted corresponding to localization of both, or only one, species. The NMCT transition signals a dynamical crossover to activated barrier hopping dynamics. For binary mixtures of equal diameter hard and attractive spheres, a mixture composition sensitive "glass-melting" type of phenomenon is predicted at high total packing fractions and weak attractions. As the total packing fraction decreases, a transition to partial localization occurs corresponding to the coexistence of a tightly localized sticky species in a gel-like state with a fluid of hard spheres. Complex behavior of the localization lengths and shear moduli exist because of the competition between excluded volume caging forces and attraction-induced physical bond formation between sticky particles. Beyond the NMCT transition, a two-dimensional nonequilibrium free energy surface emerges, which quantifies cooperative activated motions. The barrier locations and heights are sensitive to the relative amplitude of the cooperative displacements of the different species.     

Charge hopping in DNA.

The efficiency of charge migration through stacked Watson-Crick base pairs is analyzed for coherent hole motion interrupted by localization on guanine (G) bases. Our analysis rests on recent experiments, which demonstrate the competition of hole hopping transitions between nearest neighbor G bases and a chemical reaction of the cation G(+) with water. In addition, it has been assumed that the presence of units with several adjacent stacked G bases on the same strand leads to the additional vibronic relaxation process (G(+)G...G) --> (GG...G)(+). The latter may also compete with the hole transfer from (G(+)G...G) to a single G site, depending on the relative positions of energy levels for G(+) and (G(+)G...G). A hopping model is proposed to take the competition of these three rate steps into account. It is shown that the model includes two important limits. One corresponds to the situation where the charge relaxation inside a multiple guanine unit is faster than hopping. In this case hopping is terminated by several adjacent G bases located on the same strand, as has been observed for the GGG triple. In the opposite, slow relaxation limit the GG...G unit allows a hole to migrate further in accord with experiments on strand cleavage exploiting GG pairs. We demonstrate that for base pair sequences with only the GGG triple, the fast relaxation limit of our model yields practically the same sequence- and distance dependencies as measurements, without invoking adjustable parameters. For sequences with a certain number of repeating adenine:thymine pairs between neighboring G bases, our analysis predicts that the hole transfer efficiency varies in inverse proportion to the sequence length for short sequences, with change to slow exponential decay for longer sequences. Calculations performed within the slow relaxation limit enable us to specify parameters that provide a reasonable fit of our numerical results to the hole migration efficiency deduced from experiments with sequences containing GG pairs. The relation of the results obtained to other theoretical and experimental studies of charge transfer in DNA is discussed. We propose experiments to gain a deeper insight into complicated kinetics of charge-transfer hopping in DNA.     

Influence of pressure on the slow and fast fractional relaxation dynamics in lysozyme: a simulation study

The article reports on a molecular dynamics simulation study of the influence of moderate, nondenaturing pressure on the slow and fast internal relaxation dynamics of lysozyme. The model parameters of the fractional Ornstein-Uhlenbeck process are used to quantify the changes. We find that the nonexponential character for diffusive motions on time scales above 10 ps is enhanced and that the diffusion processes are slowed down. The diffusive motions on the subpicosecond time scale appear, in contrast, accelerated, whereas the nonexponential character is not altered by pressure. We attribute these findings to the different natures of slow and fast relaxation processes, which are characterized by structural rearrangements and collisions, respectively. The analyses are facilitated by the use of spatially resolved relaxation rate spectra.     

Dilatometric and calorimetric studies of the effect of staphylococcus aureus delta-lysin on the phospholipid phase transition

The interaction of the protein -lysin from Staphylococcus aureus with model membrane of dipalmitol-sn-glycero-3-phosphocholine has been studied by the method of temperature scanning densitometry and high precision differential scanning calorimetry. The studies were performed in the range of low relative protein concentrations (between 10^–4 and 3×10^–2 moles -lysin per mole phospholipid) in order to observe those effects which may be relevant to the high efficiency of membranolysis. -lysin was found to have strong effects on the main transition as well as on the pretransition, i.e., significant reduction of the transition volume and transition enthalpy and complete abolition of the pretransition. The temperature of the main transition was nearly unaffected in this concentration range. These effects can be interpreted as long-range structural changes in the lipid bilayers caused by the protein and are discussed in terms of a cooperative cluster model. The results are in many respects qualitatively similar to those observed earlier with the bee venom protein melittin.Presented at the sixth Italian meeting on Calorimetry and Thermal Analysis (AICAT) held in Naples, December 4–7, 1984     

Role of Temperature in Controlling Performance of Photorefractive Organic Glasses

We present a detailed temperature‐dependence study of dielectric, birefringent, conductive, and photorefractive (PR) properties of high‐performance low‐molecular weight organic glasses that contain 2‐dicyanomethylene‐3‐cyano‐2,5‐dihydrofuran (DCDHF) derivatives. DCDHF organic glasses sensitized with C₆₀ exhibit high two‐beam coupling gain coefficients in the red‐wavelength region. However, in the best performing DCDHF glasses at room temperature the PR dynamics are limited by slow molecular reorientation in the electric field. While orientational and, therefore, PR speed can be significantly improved by increasing the temperature above the glass‐transition temperature of the material, the steady‐state performance may worsen. Comprehensive study of the temperature dependence of various processes, which contribute to the PR effect in DCDHF glasses, clarifies the limiting factors and allows for optimization of the overall PR performance.