Contact Kinetics in Fractal Macromolecules.

We consider the kinetics of first contact between two monomers of the same macromolecule. Relying on a fractal description of the macromolecule, we develop an analytical method to compute the mean first contact time for various molecular sizes. In our theoretical description, the non-Markovian feature of monomer motion, arising from the interactions with the other monomers, is captured by accounting for the nonequilibrium conformations of the macromolecule at the very instant of first contact. This analysis reveals a simple scaling relation for the mean first contact time between two monomers, which involves only their equilibrium distance and the spectral dimension of the macromolecule, independently of its microscopic details. Our theoretical predictions are in excellent agreement with numerical stochastic simulations.

Slow encounters of particle pairs in branched structures.

On infinite homogeneous structures, two random walkers meet with certainty if and only if the structure is recurrent; i.e., a single random walker returns to its starting point with probability 1. However, on general inhomogeneous structures this property does not hold, and, although a single random walker will certainly return to its starting point, two moving particles may never meet. This striking property has been shown to hold, for instance, on infinite combs. Due to the huge variety of natural phenomena which can be modeled in terms of encounters between two (or more) particles diffusing in comblike structures, it is fundamental to investigate if and, if so, to what extent similar effects may take place in finite structures. By means of numerical simulations we provide evidence that, indeed, even on finite structures, the topological inhomogeneity can qualitatively affect the two-particle problem. In particular, the mean encounter time can be polynomially larger than the time expected from the related one-particle problem.

Transport properties of continuous-time quantum walks on Sierpinski fractals.

We model quantum transport, described by continuous-time quantum walks (CTQWs), on deterministic Sierpinski fractals, differentiating between Sierpinski gaskets and Sierpinski carpets, along with their dual structures. The transport efficiencies are defined in terms of the exact and the average return probabilities, as well as by the mean survival probability when absorbing traps are present. In the case of gaskets, localization can be identified already for small networks (generations). For carpets, our numerical results indicate a trend towards localization, but only for relatively large structures. The comparison of gaskets and carpets further implies that, distinct from the corresponding classical continuous-time random walk, the spectral dimension does not fully determine the evolution of the CTQW.

Gaussian semiflexible rings under angular and dihedral restrictions.

Semiflexible polymer rings whose bonds obey both angular and dihedral restrictions [M. Dolgushev and A. Blumen, J. Chem. Phys. 138, 204902 (2013)], are treated under exact closure constraints. This allows us to obtain semianalytic results for their dynamics, based on sets of Langevin equations. The dihedral restrictions clearly manifest themselves in the behavior of the mean-square monomer displacement. The determination of the equilibrium ring conformations shows that the dihedral constraints influence the ring curvature, leading to compact folded structures. The method for imposing such constraints in Gaussian systems is very general and it allows to account for heterogeneous (site-dependent) restrictions. We show it by considering rings in which one site differs from the others.

NMR relaxation of the orientation of single segments in semiflexible dendrimers.

We study the orientational properties of labeled segments in semiflexible dendrimers making use of the viscoelastic approach of Dolgushev and Blumen [J. Chem. Phys. 131, 044905 (2009)]. We focus on the segmental orientational autocorrelation functions (ACFs), which are fundamental for the frequency-dependent spin-lattice relaxation times T1(ω). We show that semiflexibility leads to an increase of the contribution of large-scale motions to the ACF. This fact influences the position of the maxima of the [1/T1]-functions. Thus, going from outer to inner segments, the maxima shift to lower frequencies. Remarkably, this feature is not obtained in the classical bead-spring model of flexible dendrimers, although many experiments on dendrimers manifest such a behavior.

Dynamics of discrete semiflexible chains under dihedral constraints: analytic results.

Here we consider the dynamics of semiflexible polymers subject both to angular and to dihedral constraints. We succeed in obtaining analytically the dynamical matrix of such systems by extending the formalism developed by Dolgushev and Blumen [J. Chem. Phys. 131, 044905 (2009)]. This leads to a set of Langevin equations whose eigenvalues determine many dynamical properties. Exemplarily, we display the mechanical relaxation loss moduli [G"(ω)] as a function of several, distinct sets of microscopic stiffness parameters; it turns out that such differences lead to macroscopically distinct patterns.

Dynamics of semiflexible regular hyperbranched polymers.

We study the dynamics of semiflexible Vicsek fractals (SVF) following the framework established by Dolgushev and Blumen [J. Chem. Phys. 131, 044905 (2009)], a scheme which allows to model semiflexible treelike polymers of arbitrary architecture. We show, extending the methods used in the treatment of semiflexible dendrimers by Fürstenberg et al. [J. Chem. Phys. 136, 154904 (2012)], that in this way the Langevin-dynamics of SVF can be treated to a large part analytically. For this we show for arbitrary Vicsek fractals (VF) how to construct complete sets of eigenvectors; these reduce considerably the diagonalization problem of the corresponding equations of motion. In fact, such eigenvector sets arise naturally from a hierarchical procedure which follows the iterative construction of the VF. We use the obtained eigenvalues to calculate the loss moduli G(")(ω) of SVF for different degrees of stiffness of the junctions. Finally, we compare the results for SVF to those found for semiflexible dendrimers.

Geometrical aspects of quantum walks on random two-dimensional structures.

We study the transport properties of continuous-time quantum walks (CTQWs) over finite two-dimensional structures with a given number of randomly placed bonds and with different aspect ratios (ARs). Here, we focus on the transport from, say, the left side to the right side of the structure where absorbing sites are placed. We do so by analyzing the long-time average of the survival probability of CTQWs. We compare the results to the classical continuous-time random walk case (CTRW). For small ARs (landscape configurations) we observe only small differences between the quantum and the classical transport properties, i.e., roughly the same number of bonds is needed to facilitate the transport. However, with increasing ARs (portrait configurations) a much larger number of bonds is needed in the CTQW case than in the CTRW case. While for CTRWs the number of bonds needed decreases when going from small ARs to large ARs, for CTQWs this number is large for small ARs, has a minimum for the square configuration, and increases again for increasing ARs. We explain our findings by analyzing the average eigenstates of the corresponding structures: The participation ratios allow us to distinguish between localized and nonlocalized (average) eigenstates. In particular, for large ARs we find for CTQWs that the eigenstates are localized for bond numbers exceeding the bond numbers needed to facilitate transport in the CTRW case. Thus, a rather large number of bonds is needed in order for quantum transport to be efficient for large ARs.

Analytical model for the dynamics of semiflexible dendritic polymers.

We study the dynamics of semiflexible dendritic polymers following the method of Dolgushev and Blumen [J. Chem. Phys. 131, 044905 (2009)]. The scheme allows to formulate in analytical form the corresponding Langevin equations. We determine the eigenvalues by first block-diagonalizing the problem, which allows to treat even very large dendritic objects. A basic ingredient of the procedure is the observation that a set of eigenmodes in the semiflexible case is similar to that chosen by Cai and Chen [Macromolecules 30, 5104 (1997)] for fully flexible dendritic structures. Varying the flexibility of the macromolecules allows us to better understand their mechanical loss moduli G"(ω) based on their eigenvalue spectra. We present the G"(ω) for a series of stiffness parameters and for different functionalities of the branching points.

Maximum entropy principle applied to semiflexible ring polymers.

Based on the success of the maximum entropy principle (MEP) in the study of semiflexible treelike polymers [M. Dolgushev and A. Blumen, J. Chem. Phys. 131, 044905 (2009)], it is of much interest to establish MEP's potential for general semiflexible polymers which contain loops. Here, we embark on this endeavor by considering discrete semiflexible polymer rings in a Rouse-type scheme. Now, for treelike polymers a beads-and-bonds (i.e., a discrete) picture is essential for an easy inclusion of branching points. Moreover, one may envisage (similar to our former work [M. Dolgushev and A. Blumen, J. Chem. Phys. 131, 044905 (2009)]) to impose for each angle between two bonds a distinct stiffness condition. Working in this way leads already for a polymer ring to a complicated problem. Hence, we follow a reduced variational approach as applied earlier to polymer chains, in which a single Lagrange multiplier is used for each set of identical conditions imposed on topologically equivalent bonds and bonds' orientations. In this way, we obtain for the discrete ring an analytically closed form which involves Chebyshev polynomials. This expression turns out to lead to a series of solutions: Apart from the regular solution, several other solutions appear. One may be tempted to discard the other solutions, since for them the potential energy matrix is not positive definite. A more careful analysis based on topological features suggests, however, that such solutions can be assigned to rings displaying knots. Monte Carlo simulations which take excluded volume interactions into account agree with our interpretation.

Cospectral polymers: Differentiation via semiflexibility.

We consider polymer structures which are known in the mathematical literature as "cospectral." Their graphs have (in spite of the different architectures) exactly the same Laplacian spectra. Now, these spectra determine in Gaussian (Rouse-type) approaches many static as well as dynamical polymer characteristics. Hence, in such approaches for cospectral graphs many mesoscopic quantities are predicted to be indistinguishable. Here we show that the introduction of semiflexibility into the generalized Gaussian structure scheme leads to different spectra and hence to distinct macroscopic patterns. Moreover, particular semiflexible situations allow us to distinguish well between cospectral structures. We confirm our theoretical results through Monte Carlo simulations.

Dissipative dynamics with trapping in dimers.

The trapping of excitations in systems coupled to an environment allows one to study the quantum to classical crossover by different means. We show how to combine the phenomenological description by a non-Hermitian Liouville-von Neumann equation (LvNE) approach with the numerically exact path integral Monte Carlo (PIMC) method, and exemplify our results for a system of two coupled two-level systems. By varying the strength of the coupling to the environment we are able to estimate the parameter range in which the LvNE approach yields satisfactory results. Moreover, by matching the PIMC results with the LvNE calculations, we have a powerful tool to extrapolate the numerically exact PIMC method to long times.

Dynamics of chains and dendrimers with heterogeneous semiflexibility.

Based on our recent model for the dynamics of semiflexlible treelike networks [M. Dolgushev and A. Blumen, J. Chem. Phys. 131, 044905 (2009)], we study the dynamical properties of chain polymers and of dendrimers whose junctions display different stiffness degrees (SD). In these polymers the functionality f of the inner junctions is constant, being f=2 for the linear chains and f=3 for the dendrimers. This allows us to focus on the effects caused by the heterogeneities due to different SD. For this we study alternating, diblock, as well as random arrangements of the SD. Each of these cases shows a particular, macroscopically observable behavior, which allows to distinguish between the different microscopic SD arrangements.

Random walks on Sierpinski gaskets of different dimensions.

We study random walks (RWs) on classical and dual Sierpinski gaskets (SG and DSG), naturally embedded in d-dimensional Euclidian spaces (ESs). For large d the spectral dimension d(s) approaches 2, the marginal RW dimension. In contrast to RW over two-dimensional ES, RWs over SG and DSG show a very rich behavior. First, the time discrete scale invariance leads to logarithmic-periodic (log-periodic) oscillations in the RW properties monitored, which increase in amplitude with d. Second, the asymptotic approach to the theoretically predicted RW power laws is significantly altered depending on d and on the variant of the fractal (SG or DSG) under study. In addition, we discuss the suitability of standard RW properties to determine d(s), a question of great practical relevance.

Dynamics of semiflexible treelike polymeric networks.

We study the dynamics of general treelike networks, which are semiflexible due to restrictions on the orientations of their bonds. For this we extend the generalized Gaussian structure model, in which the dynamics obeys Langevin equations coupled through a dynamical matrix. We succeed in formulating analytically this matrix for arbitrary treelike networks and stiffness coefficients. This allows the straightforward determination of dynamical characteristics relevant to mechanical and dielectric relaxation. We show that our approach also follows from the maximum entropy principle; this principle was previously implemented for linear polymers and we extend it here to arbitrary treelike architectures.

Protein displacements under external forces: An atomistic Langevin dynamics approach.

We present a fully atomistic Langevin dynamics approach as a method to simulate biopolymers under external forces. In the harmonic regime, this approach permits the computation of the long-term dynamics using only the eigenvalues and eigenvectors of the Hessian matrix of second derivatives. We apply this scheme to identify polymorphs of model proteins by their mechanical response fingerprint, and we relate the averaged dynamics of proteins to their biological functionality, with the ion channel gramicidin A, a phosphorylase, and neuropeptide Y as examples. In an environment akin to dilute solutions, even small proteins show relaxation times up to 50 ns. Atomically resolved Langevin dynamics computations have been performed for the stretched gramicidin A ion channel.

Slow excitation trapping in quantum transport with long-range interactions.

Long-range interactions (LRIs) slow down the excitation trapping in quantum transport on a one-dimensional chain with traps at both ends when compared to the case with only nearest-neighbor interactions. This is in contrast to the corresponding classical case, in which LRIs lead to faster excitation trapping. The reason for the slowing down is to be found in subtle changes--due to LRIs--in the spectrum of the Hamiltonian. Pertubation theory allows an analytical analysis of this fact.

Universal behavior of quantum walks with long-range steps.

Continuous-time quantum walks with long-range steps R(-gamma) (R being the distance between sites) on a discrete line behave in similar ways for all gamma > or =2 . This is in contrast to classical random walks, which for gamma>3 belong to a different universality class than for gamma < or =3 . We show that the average probabilities to be at the initial site after time t as well as the mean square displacements are of the same functional form for quantum walks with gamma =2, 4, and with nearest neighbor steps. We interpolate this result to arbitrary gamma > or =2 .

Survival probabilities in coherent exciton transfer with trapping.

In the quest for signatures of coherent transport we consider exciton trapping in the continuous-time quantum walk framework. The survival probability displays different decay domains, related to distinct regions of the spectrum of the Hamiltonian. For linear systems and at intermediate times the decay obeys a power law, in contrast with the corresponding exponential decay found in incoherent continuous-time random walk situations. To differentiate between the coherent and incoherent mechanisms, we present an experimental protocol based on a frozen Rydberg gas structured by optical dipole traps.

Spectra of Husimi cacti: exact results and applications.

Starting from exact relations for finite Husimi cacti we determine their complete spectra to very high accuracy. The Husimi cacti are dual structures to the dendrimers but, distinct from these, contain loops. Our solution makes use of a judicious analysis of the normal modes. Although close to those of dendrimers, the spectra of Husimi cacti differ. From the wealth of applications for measurable quantities which depend only on the spectra, we display for Husimi cacti the behavior of the fluorescence depolarization under quasiresonant Forster energy transfer.