Hopping Dynamics Research Articles

Cytosine Methylation Enhances DNA Condensation Revealed by Equilibrium Measurements Using Magnetic Tweezers.

CpG methylation of DNA is common in mammalian cells. In sperm, the DNA has the highest level of CpG methylation and is condensed into toroidal structures. How CpG methylation affects DNA structures and interactions is important to understand its biological roles but is largely unknown. Using an RNA-DNA-RNA structure, we observed the equilibrium hopping dynamics between the condensed and extended states of DNA in the presence of polyamines or polylysine peptide as a reduced model of histone tails. Combing with the measured DNA elasticities, we report that CpG methylation of each cytosine nucleotide substantially increases DNA-DNA attraction by up to 0.2 kBT. For the DNA with 57% GC content, the relative increase caused by CpG methylation is up to 32% for the spermine-induced DNA-DNA attraction and up to 9% for the polylysine-induced DNA-DNA attraction. These findings help us to evaluate the energetic contributions of CpG methylation in sperm development and chromatin regulation.

Revealing Ultrafast Population Transfer between Nearly Degenerate Electronic States.

The response of a molecule to photoexcitation is governed by the coupling of its electronic states. However, if the energetic spacing between the electronically excited states at the Franck–Condon window becomes sufficiently small, it is infeasible to selectively excite and monitor individual states with conventional time-resolved spectroscopy, preventing insight into the energy transfer and relaxation dynamics of the molecule. Here, we demonstrate how the combination of time-resolved spectroscopy and extensive surface hopping dynamics simulations with a global fit approach on individually excited ensembles overcomes this limitation and resolves the dynamics in the n3p Rydberg states in acetone. Photoelectron transients of the three closely spaced states n3px, n3py, and n3pz are used to validate the theoretical results, which in turn allow retrieving a comprehensive kinetic model describing the mutual interactions of these states for the first time.

Vibronic structure and predissociation dynamics of 2-methoxythiophenol (S1): The effect of intramolecular hydrogen bonding on nonadiabatic dynamics.

Vibronic spectroscopy and the S-H bond predissociation dynamics of 2-methoxythiophenol (2-MTP) in the S1 (ππ*) state have been investigated for the first time. Resonant two-photon ionization and slow-electron velocity map imaging (SEVI) spectroscopies have revealed that the S1-S0 transition of 2-MTP is accompanied with the planar to the pseudoplanar structural change along the out-of-plane ring distortion and the tilt of the methoxy moiety. The S1 vibronic bands up to their internal energy of ∼1000 cm-1 are assigned from the SEVI spectra taken via various S1 vibronic intermediate states with the aid of ab initio calculations. Intriguingly, Fermi resonances have been identified for some vibronic bands. The S-H bond breakage of 2-MTP occurs via tunneling through an adiabatic barrier under the S1/S2 conical intersection seam, and it is followed by the bifurcation into either the adiabatic or nonadiabatic channel at the S0/S2 conical intersection where the diabatic S2 state (πσ*) is unbound with respect to the S-H bond elongation coordinate, giving the excited (Ã) or ground (X̃) state of the 2-methoxythiophenoxy radical, respectively. Surprisingly, the nonadiabatic transition probability at the S0/S2 conical intersection, estimated from the velocity map ion images of the nascent D fragment from 2-MTP-d1 (2-CH3O-C6H4SD) at the S1 zero-point energy level, is found to be exceptionally high to give the X̃/Ã product branching ratio of 2.03 ± 0.20, which is much higher than the value of ∼0.8 estimated for the bare thiophenol at the S1 origin. It even increases to 2.33 ± 0.17 at the ν45 2 mode (101 cm-1) before it rapidly decays to 0.69 ± 0.05 at the S1 internal energy of about 2200 cm-1. This suggests that the strong intramolecular hydrogen bonding of S⋯D⋯OCH3 in 2-MTP at least in the low S1 internal energy region should play a significant role in localizing the reactive flux onto the conical intersection seam. The minimum energy pathway calculations (second-order coupled-cluster resolution of the identity or time-dependent-density functional theory) of the adiabatic S1 state suggest that the intimate dynamic interplay between the S-H bond cleavage and intramolecular hydrogen bonding could be crucial in the nonadiabatic surface hopping dynamics taking place at the conical intersection.

Velocity-dependent friction enhances tribomechanical differences between monolayer and multilayer graphene

The influence of sliding speed in the nanoscale friction forces between a silicon tip and monolayer and multilayer graphene were investigated with the use of an atomic force microscope. We found that the friction forces increase linearly with the logarithm of the sliding speed in a highly layer-dependent way. The increase in friction forces with velocity is amplified at the monolayer. The amplification of the friction forces with velocity results from the introduction of additional corrugation in the interaction potential driven by the tip movement. This effect can be interpreted as a manifestation of local thermally induced surface corrugations in nanoscale influencing the hopping dynamics of the atoms at the contact. These experimental observations were explained by modeling the friction forces with the thermally activated Prandtl-Tomlinson model. The model allowed determination of the interaction potential between tip and graphene, critical forces, and attempt frequencies of slip events. The latter was observed to be dominated by the effective contact stiffness and independent of the number of layers.

Microscopic dynamics of electron hopping in a semiconductor quantum well probed by spin-dependent photon echoes

Spin-dependent photon echoes in combination with pump-probe Kerr rotation are used to study the microscopic electron spin transport in a CdTe/(Cd,Mg)Te quantum well in the hopping regime. We demonstrate that independent of the particular spin relaxation mechanism, hopping of resident electrons leads to a shortening of the photon echo decay time, while the transverse spin relaxation time evaluated from pump-probe transients increases due to motional narrowing of spin dynamics in the fluctuating effective magnetic field of the lattice nuclei.

Solid-State 17O NMR Study of Carboxylic Acid Dimers: Simultaneously Accessing Spectral Properties of Low- and High-Energy Tautomers.

We report a solid-state 17O NMR study of several crystalline carboxylic acids. We found that, while each of these compounds forms discrete hydrogen-bonded dimers in the crystal lattice, their solid-state 17O magic-angle spinning (MAS) NMR spectra display quite different features and different temperature dependencies. We showed that experimentally observed 17O NMR spectral behaviors can be explained as being due to thermal averaging between the two tautomers that are produced as a result of concerted double-hydrogen hopping dynamics within each dimer. In general, the two tautomers have different energies due to intramolecular interactions and crystal packing. From an analysis of variable-temperature 17O MAS NMR spectra, energy asymmetry between the two tautomers was experimentally determined for each of the carboxylic acid compounds studied. The same data analysis also offers an opportunity to simultaneously assess 17O NMR parameters in both low- and high-energy tautomers. We concluded that the periodic plane-wave density functional theory (DFT) calculations can produce reliable 17O NMR parameters (chemical shift and quadrupolar coupling tensors) for both tautomers. The same periodic DFT calculations have also produced reasonable energy asymmetry values for the studied carboxylic acid dimers. We have also observed substantial H/D isotope shifts in solid-state 17O NMR.

Deciphering the Mechanism of Aggregation-Induced Emission of a Quinazolinone Derivative Displaying Excited-State Intramolecular Proton-Transfer Properties: A QM, QM/MM, and MD Study.

A combination of excited-state intramolecular proton transfer (ESIPT) and aggregation-induced emission (AIE) has opened new opportunities to develop color-tunable luminescent materials with high quantum yield. Understanding the emission mechanism of these luminophores is essential for the molecular design and construction of a functional system. Herein, we report QM (MS-CASPT2//TD-DFT, MS-CASPT2//CASSCF) and ONIOM (QM/MM) studies on the fluorescence quenching and AIE mechanisms of 2-(2-hydroxy-phenyl)-4(3H)-quinazolinone with typical characteristics of AIE and ESIPT as an example. The computational results indicate that in the tetrahydrofuran solution, once being excited to the S1 state, the molecule tends to undergo an ultrafast, barrierless ESIPT from enol to keto tautomer and then accesses a S1/S0 conical intersection in the vicinity of a C═C bond twisted intramolecular charge-transfer (TICT) intermediate, leading to a nonradiative decay from the excited to ground state. Hence, the TICT-induced nonadiabatic transition, which has been further confirmed by the on-the-fly trajectory surface hopping dynamics simulations, accounts for the fluorescence quenching in solution. In contrast, in the solid state, the nonradiative relaxation pathway via the C═C bond rotation is suppressed due to environmental hindrance, leaving the ESIPT-induced enol-keto tautomerization as the only excited-decay channel, thus the fluorescence is observably enhanced in the crystal.

Photophysics of BODIPY-Based Photosensitizer for Photodynamic Therapy: Surface Hopping and Classical Molecular Dynamics.

Halogenated BODIPY derivatives are emerging as important candidates for photodynamic therapy of cancer cells due to their high triplet quantum yield. We probed fundamental photophysical properties and interactions with biological environments of such photosensitizers. To this end, we employed static TD-DFT quantum chemical calculations as well as TD-DFT surface hopping molecular dynamics on potential energy surfaces resulting from the eigenstates of the total electronic Hamiltonian including the spin-orbit (SO) coupling. Matrix elements of an effective one-electron spin-orbit Hamiltonian between singlet and triplet configuration interaction singles (CIS) auxiliary wave functions are calculated using a new code capable of dealing with singlets and both restricted and unrestricted triplets built up from up to three different and independent sets of (singlet, alpha, and beta) molecular orbitals. The interaction with a biological environment was addressed by using classical molecular dynamics (MD) in a scheme that implicitly accounts for electronically excited states. For the surface hopping trajectories, an accelerated MD approach was used, in which the SO couplings are scaled up, to make the calculations computationally feasible, and the lifetimes are extrapolated back to unscaled SO couplings. The lifetime of the first excited singlet state estimated by semiclassical surface hopping simulations is 139 ± 75 ps. Classical MD demonstrates that halogenated BODIPY in the ground state, in contrast to the unsubstituted one, is stable in the headgroup region of minimalistic cell membrane models, and while in the triplet state, the molecule relocates to the membrane interior ready for further steps of photodynamic therapy.

Uphill migration in coupled driven particle systems

In particle systems subject to a nonuniform drive, particle migration is observed from the driven to the non-driven region and vice-versa, depending on details of the hopping dynamics, leading to apparent violations of Fick’s law and of steady-state thermodynamics. We propose and discuss a very basic model in the framework of independent random walkers on a pair of rings, one of which features biased hopping rates, in which this phenomenon is observed and fully explained.

Loschmidt Echo and Fidelity Decay Near an Exceptional Point

AbstractNon‐Hermitian classical and open quantum systems near an exceptional point (EP) are known to undergo strong deviations in their dynamical behavior under small perturbations or slow cycling of parameters as compared to Hermitian systems. Such a strong sensitivity is at the heart of many interesting phenomena and applications, such as the asymmetric breakdown of the adiabatic theorem, enhanced sensing, non‐Hermitian dynamical quantum phase transitions, and photonic catastrophe. Like for Hermitian systems, the sensitivity to perturbations on the dynamical evolution can be captured by Loschmidt echo and fidelity after imperfect time reversal or quench dynamics. Here, a rather counterintuitive phenomenon in certain non‐Hermitian systems near an EP is disclosed, namely the deceleration (rather than acceleration) of the fidelity decay and improved Loschmidt echo as compared to their Hermitian counterparts, despite large (non‐perturbative) deformation of the energy spectrum introduced by the perturbations. This behavior is illustrated by considering the fidelity decay and Loschmidt echo for the single‐particle hopping dynamics on a tight‐binding lattice under an imaginary gauge field.

Ultrafast Photoinduced Dynamics of 1,3-Cyclohexadiene Using XMS-CASPT2 Surface Hopping.

A full-dimensional simulation of the photodissociation of 1,3-cyclohexadiene in the manifold of three electronic states was performed via nonadiabatic surface hopping dynamics using extended multistate complete active space second-order perturbation (XMS-CASPT2) electronic structure theory with fully analytic nonadiabatic couplings. With the 47 ± 8% product quantum yield calculated from the 136 trajectories, generally 400 fs-long, and an estimated excited lifetime of 89 ± 9 fs, our calculations provide a detailed description of the nonadiabatic deactivation mechanism, showing the existence of an extended conical intersection seam along the reaction coordinate. The nature of the preferred reaction pathways on the ground state is discussed and extensive comparison to the previously published full dimensional dynamics calculations is provided.

Numerical simulations of the controlled motion of a hopping asteroid lander on the regolith surface

Previous missions have revealed that small Solar system bodies are topographically diverse, which raises an immense challenge to a lander that aims to perform scientific measurements at different locations on the surface of the target. In recent years, hopping mechanism has attracted considerable attention due to its adaptability to the granular regolith and the low-gravity environment. However, the hopping dynamics related to granular materials remains to be explored, which will contribute not only to future space missions but also to the understanding of the dynamical behaviour of granular systems under low gravity. In this paper, we studied the hopping locomotion of a cuboid lander on the regolith surface of an asteroid. Numerical simulations are performed based on the soft-sphere discrete element method. We systematically explored the effects of the controlled parameter and physical properties of the regolith particles. The results show that the hopping outcomes (velocity, angle, and morphology of the cavity left in the regolith) are strongly dependent on these parameters. The high resistance improves the robustness of granular force networks, therefore the lander hops farther in gravel-like media than less frictional media. When the cohesion between regolith particles is included, the cavity left after the hop becomes a mild indentation, differing from the non-cohesive cases, that give distinct crater-like cavities.

Interlayer hopping dynamics of bilayer water confined between graphene sheets

Abstract The ubiquitous existence of water confined in nano-capillaries is key to fundamental biological and technological applications. Using molecular dynamics simulations, we analyzed the hopping-like interlayer relocation dynamics of bilayer water confined between two parallel graphene sheets. In contrary to the common scheme that relocation is driven by density fluctuations, analysis of the transition path ensemble revealed that interlayer hopping is induced by local hydrogen bond configuration fluctuations coupled with activated consecutive transient angular reorientations. Our results consolidated the anisotropic nature of water relocation under strong ordering, which provided a mechanistic insight into the relaxation behavior at glass-forming water’s fragile-to-strong crossover.

The effect of boundaries and impurity on a system with non-local hop dynamics

We study a one-dimensional lattice model of particles which interact with each other via hard-core repulsion, and which can make long hops in addition to the usual nearest neighbour hopping dynamics. The parameter p gives the probability for long hops and the p = 0 limit leads to the well studied totally asymmetric simple exclusion process (TASEP). The first part of this study describes the combined effect of open boundaries and long hops on the steady state of the system. Apart from the usual low density (LD), high density (HD) and maximum current (MC) phases, the introduction of a finite p leads to a new possibility-an empty road (ER) phase with particles clearing out faster than they enter. The variation in the phase diagram with p is interesting, with the LD and MC phases vanishing at large values of p while the ER and HD phases divide the parameter space into 1/2. In the second part of this study, we look at the combined effect of long hops and static/dynamic impurities. The boundaries are taken to be periodic for simplicity. We see that the system with a static impurity and with 0 < p < 1 shows a phase transition from a shock phase characterised by finite densities on either side of the shock (HD–LD phase) to a phase where the density on one side of the shock is zero (HD-ER phase). We also study the effect of a dynamic impurity, introduced via a slow particle. Here, the system undergoes a phase transition from a homogeneous phase to a shock phase depending on the density, the speed of the particle, as well as the probability p. The shock phase dominates the phase diagram at large values of p. All our studies involve numerical simulations which are supported by mean field theory arguments. The mean field approximation works well qualitatively and correctly identifies the possible phases, while the quantitative agreement with numerics varies, depending on parameter values.

Configuration interaction singles with spin-orbit coupling: Constructing spin-adiabatic states and their analytical nuclear gradients.

For future use in modeling photoexcited dynamics and intersystem crossing, we calculate spin-adiabatic states and their analytical nuclear gradients within configuration interaction singles theory. These energies and forces should be immediately useful for surface hopping dynamics, which are natural within an adiabatic framework. The resulting code has been implemented within the Q-Chem software and preliminary results suggest that the additional cost of including spin-orbit coupling within the singles-singles block is not large.

Predicting the Most Stable Aptamer/Target Molecule Complex Configuration Using a Stochastic-Tunnelling Basin-Hopping Discrete Molecular Dynamics Method: A Novel Global Minimum Search Method for a Biomolecule Complex

This study proposed a novel global minimum search method for predicting the most stable biomolecule complex, which combines the strengths of three global minimum search methods (stochastic tunnelling, basin hopping, and discrete molecular dynamics) to efficiently improve the spatial domain search ability of the stochastic tunnelling–basin hopping (STUN–BH) method from our previous study. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as a benchmark target molecule for the EpCAM aptamer EpA (AptEpA). For the most stable AptEpA/EpCAM complex predicted by our new method, the AptEpA was attached to the entangling loop fragments of the two EpCAM molecules with the most AptEpA residues. After the AptEpA/EpCAM complex had equilibrated with the water environment through a molecular dynamics simulation at 300 K for 10 ns, stable hydrogen bonds formed between the bases of AptEpA and EpCAM residues of the secondary structures, which included the alpha helix and beta sheet becoming less stable in the water environment. Those hydrogen bonds formed between the bases of AptEpA and EpCAM loop fragment residues remained stable in the water environment.

Treatment of Nonadiabatic Dynamics by On-The-Fly Trajectory Surface Hopping Dynamics

Treatment of Nonadiabatic Dynamics by On-The-Fly Trajectory Surface Hopping Dynamics

Highly efficient surface hopping dynamics using a linear vibronic coupling model.

We report an implementation of the linear vibronic coupling (LVC) model within the surface hopping dynamics approach and present utilities for parameterizing this model in a blackbox fashion. This results in an extremely efficient method to obtain qualitative and even semi-quantitative information about the photodynamical behavior of a molecule, and provides a new route toward benchmarking the results of surface hopping computations. The merits and applicability of the method are demonstrated in a number of applications. First, the method is applied to the SO2 molecule showing that it is possible to compute its absorption spectrum beyond the Condon approximation, and that all the main features and timescales of previous on-the-fly dynamics simulations of intersystem crossing are reproduced while reducing the computational effort by three orders of magnitude. The dynamics results are benchmarked against exact wavepacket propagations on the same LVC potentials and against a variation of the electronic structure level. Four additional test cases are presented to exemplify the broader applicability of the model. The photodynamics of the isomeric adenine and 2-aminopurine molecules are studied and it is shown that the LVC model correctly predicts ultrafast decay in the former and an extended excited-state lifetime in the latter. Futhermore, the method correctly predicts ultrafast intersystem crossing in the modified nucleobase 2-thiocytosine and its absence in 5-azacytosine while it fails to describe the ultrafast internal conversion to the ground state in the latter.

Asymptotic behavior and aging of a low temperature cascading 2-GREM dynamics at extreme time scales

We derive scaling limit results for the Hierarchical Random Hopping Dynamics for the cascading two-level GREM at low temperature at extreme time scales. It is known that in the cascading regime there are two static critical temperatures. We show that there exists a (narrow) set of fine tuning temperatures; when they lie below the static lowest critical temperature, three distinct dynamical phases emerge below the lowest critical temperature, with three different types of limiting dynamics depending on whether the temperature is (well) above or below, or at a fine tuning temperature, all of which are given in terms of K processes. We also derive scaling limit results for temperatures between the lowest and he highest critical ones, as well as aging results for all the limiting processes mentioned above, by taking a second small time limit.

Computational insight into excited states of the ring-opening radicals from the pyrolysis of furan biofuels.

The low-lying valence excited states and Rydberg states of the radical species from the ring-opening reactions in pyrolysis of furan biofuels have been determined by extensive density functional theory and sophisticated wave function theory calculations. The radicals 1-C4 H5 O-2, 2-furylCH2 , and 4-C6 H7 O with the delocalized π-type single electron are predicted to be most stable among the reactive species here for furan, 2-methyfuran, and 2,5-dimethylfuran, respectively. Predicted vertical transition energies by TD-CAM-B3LYP show good agreement with those by CASPT2. Some among the electronic excitations to low-lying states can take place in the visible light region, and they may be involved in the combustion process. Further surface hopping dynamics simulations on the excited states of the most stable ring-opening radical 1-C4 H5 O-2 of furan as an example reveal that 89.9% sampling trajectories at the initial excited state of 22 A"(π1 π*2 ) decay to the 12 A'(n1 π*2 ) state within an average of 384 fs, and then 81.2% trajectories at the 12 A' state go to the ground state within an average of 114 fs. At the end of the simulation for 1000 fs, 18.8% trajectories still stay on the excited states of 22 A" and 12 A', suggesting that the reactive radicals in the ground state are mainly responsible for the combustion chemistry of furan biofuels. © 2018 Wiley Periodicals, Inc.