Finding pathways between distant local minima

We report a new algorithm for constructing pathways between local minima that involve a large number of intervening transition states on the potential energy surface. A significant improvement in efficiency has been achieved by changing the strategy for choosing successive pairs of local minima that serve as endpoints for the next search. We employ Dijkstra's algorithm [E. W. Dijkstra, Numer. Math. 1, 269 (1959)] to identify the "shortest" path corresponding to missing connections within an evolving database of local minima and the transition states that connect them. The metric employed to determine the shortest missing connection is a function of the minimized Euclidean distance. We present applications to the formation of buckminsterfullerene and to the folding of various biomolecules: the B1 domain of protein G, tryptophan zippers, and the villin headpiece subdomain. The corresponding pathways contain up to 163 transition states and will be used in future discrete path sampling calculations.     

A doubly nudged elastic band method for finding transition states

A modification of the nudged elastic band (NEB) method is presented that enables stable optimizations to be run using both the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) quasi-Newton and slow-response quenched velocity Verlet minimizers. The performance of this new "doubly nudged" DNEB method is analyzed in conjunction with both minimizers and compared with previous NEB formulations. We find that the fastest DNEB approach (DNEB/L-BFGS) can be quicker by up to 2 orders of magnitude. Applications to permutational rearrangements of the seven-atom Lennard-Jones cluster (LJ7) and highly cooperative rearrangements of LJ38 and LJ75 are presented. We also outline an updated algorithm for constructing complicated multi-step pathways using successive DNEB runs.     

Nonuniform stability properties and perturbing lyapunov functions

In this paper, without assuming the conditions everywhere, we study nonuniform stability properties of differential systems by employing the method of perturbing Lyapunov functions and splitting the given system suitably     

Unusual contributions of molecular architecture to rheology and flow birefringence in hyperbranched polystyrene melts

With the increase in sophisticated synthesis methods, it appears that polymer architecture may be a tunable property. Therefore, the role of architecture in rheological and processing properties has received renewed attention, mainly because of dendrimer synthesis and metallocene‐catalyst technology. Linear polymers and hyperbranched polymers represent two ends of branching complexity. Some previous studies have suggested that hyperbranched polymers may behave like unentangled polymers, whereas others have proposed that they exhibit the properties of soft colloids. In an effort to compare the responses of linear and hyperbranched polymers, we synthesized starlike hyperbranched polystyrenes (HBPSs) of various branch lengths and numbers of branches. The HBPSs used in this study were unentangled or weakly entangled, allowing us to study the effect of branch density more readily. Two linear polystyrene (L‐PS) melts and two HBPSs were studied. Using a custom‐built rheooptical apparatus, we characterized the rheology and flow birefringence of these materials. To our knowledge, these are the first flow birefringence measurements on highly branched polymer melts. Our results suggest that the flow behavior of HBPS is significantly different from that of L‐PS: (1) HBPS shows nonterminal behavior in the low‐frequency rheological response; (2) when the stress‐optical rule (SOR) holds, the stress‐optical coefficient of HBPS is much lower than those of analogous linear polymers; and (3) when the branch density is high and the branch length is sufficiently low, the SOR fails for these homopolymer melts. A significant increase in the birefringence for a given amount of stress in the low‐frequency region suggests that there may be a soft core in these materials due to the strong preferential radial orientation of chain segments near the center of a molecule versus those near the periphery. The predominantly elastic response of the soft structures may be responsible for the enhanced form birefringence. Our preliminary results indicate that these materials may exhibit both polymeric and soft‐colloid natures. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 2562–2571, 2001     

Acyl pyruvates as synthons in the Biginelli reaction

Chlorotrimethylsilane-promoted Biginelli-type reaction of ethyl 2,4-dioxo-4-phenylbutanoate, benzaldehyde, and various (thio)ureas is explored. The outcome of the reaction depends on the structure of the (thio)urea used and is strongly affected by the acceptor electronic properties of the COOEt substituent in the molecule of the starting β-dicarbonyl compound. The di- and tetrahydropyrimidine derivatives obtained possess two functional groups with orthogonal reactivity, and thus represent promising building blocks for drug discovery.     

Commutativity of first‐order discrete‐time linear time‐varying systems

After introducing the concept of commutativity for continuous‐time linear time‐varying systems, the related literature and the results obtained so far are presented. For a simple introduction of the commutativity of discrete‐time linear time‐varying systems, the problem is formulated for first‐order systems. Finally, explicit necessary and sufficient conditions for the commutativity of first‐order discrete‐time linear time‐varying systems are derived, and their advantageous use in digital system design is illustrated, which are the main objectives of the paper. The results are verified by examples which include an application in amplitude modulation for digital telecommunication.     

Modeling of Thermal Conductivity of Concrete with Vermiculite by Using Artificial Neural Networks Approaches

In this article, the thermal conductivity of concrete with vermiculite is determined and also predicted by using artificial neural networks approaches, namely the radial basis neural network and multi-layer perceptron. In these models, 20 datasets were used. For the training set, 12 datasets (60%) were randomly selected, and the residual datasets (8 datasets, 40%) were selected as the test set. The root mean square error, the mean absolute error, and determination coefficient statistics are used as evaluation criteria of the models, and the experimental results are compared with these models. It is found that the radial basis neural network model is superior to the other models.     

Comment on “Role of the velocity frame of reference in thermodiffusion in liquid mixtures” by M. Eslamian,C.G. Jiang and M.Z. Saghir

We analyze the material transport equations (MTE) derived by Eslamian and co-authors and address the criticism expressed regarding the approach formulated in our previous work. In doing so, we show that the MTE formulated by Eslamian and co-authors are valid only in closed stationary non-isothermal systems in combination with the restrictions on the Onsager coefficients formulated in our work which is criticized, and that for non-stationary systems the approach we took can be used.