Drude polarizable force field for aliphatic ketones and aldehydes,and their associated acyclic carbohydrates

The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (d-allose and d-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars d-allose and d-psicose, thereby extending the available biomolecules in the Drude polarizable FF.     

Behavior of protonated cyclopropyl intermediates during polyalphaolefin synthesis: Mechanism and predicted product distribution

A new mechanism for the origin of multiple skeletal isomers observed in the cationic dimerization of 1‐decene is proposed, and products that should form based on this mechanism are predicted. A protonated cyclopropyl intermediate appeared to form directly from combination of 2‐decyl carbocation with 1‐decene; formation of this intermediate did not appear to occur via ring closure of a branched secondary carbocation. The authors propose that rapid, repeated isomerizations of the protonated cyclopropyl intermediates lead to multiple skeletal isomers in decene dimers. The proposed mechanism can account for structures previously identified in mixtures of decene dimers and butene dimers. Copyright © 2012 John Wiley & Sons, Ltd.     

Complex network from pseudoperiodic time series: topology versus dynamics

We construct complex networks from pseudoperiodic time series, with each cycle represented by a single node in the network. We investigate the statistical properties of these networks for various time series and find that time series with different dynamics exhibit distinct topological structures. Specifically, noisy periodic signals correspond to random networks, and chaotic time series generate networks that exhibit small world and scale free features. We show that this distinction in topological structure results from the hierarchy of unstable periodic orbits embedded in the chaotic attractor. Standard measures of structure in complex networks can therefore be applied to distinguish different dynamic regimes in time series. Application to human electrocardiograms shows that such statistical properties are able to differentiate between the sinus rhythm cardiograms of healthy volunteers and those of coronary care patients.     

REPAIR OF PYRIMIDINE DIMERS IN ULTRAVIOLET-IRRADIATED CHLAM YDOMONAS

Abstract— A UV-specific endonuclease was used to monitor the presence of UV-induced pyrimidine dimers in the DNA of Chlamydomonas reinhardi . All of the dimers induced by 50 J/m² of 254 nm light are removed by a 2 h exposure to photoreactivating light. Nearly all of the dimers are removed by the wild-type strain of Chlamydomonas upon incubation for 24h in the dark. Two UV-sensitive mutants, UVS 1 and UVS 6, are deficient in removal of dimers in the dark. These results are interpreted to mean that Chlamydomonas has an excision-repair pathway for coping with UV-induced damage.     

Adjusting learning motivation to promote cooperation

An evolutionary prisoner’s dilemma game with players adjusting their learning motivation is studied. At each time step, each player can adjust his/her learning motivation according to the difference between the current payoff and payoff aspiration. Greater payoff aspiration means stronger learning motivation, and vice versa. We find that the density of cooperation in a spatial prisoner’s dilemma game is enhanced when the learning motivation mechanism is considered. Meanwhile, we show that proper noise can not only induce the highest cooperation level but also can maintain the cooperation phenomenon even though there is more temptation to defect.     

Node importance for dynamical process on networks: a multiscale characterization

Defining the importance of nodes in a complex network has been a fundamental problem in analyzing the structural organization of a network, as well as the dynamical processes on it. Traditionally, the measures of node importance usually depend either on the local neighborhood or global properties of a network. Many real-world networks, however, demonstrate finely detailed structure at various organization levels, such as hierarchy and modularity. In this paper, we propose a multiscale node-importance measure that can characterize the importance of the nodes at varying topological scale. This is achieved by introducing a kernel function whose bandwidth dictates the ranges of interaction, and meanwhile, by taking into account the interactions from all the paths a node is involved. We demonstrate that the scale here is closely related to the physical parameters of the dynamical processes on networks, and that our node-importance measure can characterize more precisely the node influence under different physical parameters of the dynamical process. We use epidemic spreading on networks as an example to show that our multiscale node-importance measure is more effective than other measures.     

Parameter inference in small world network disease models with approximate Bayesian Computational methods

Small world network models have been effective in capturing the variable behaviour of reported case data of the SARS coronavirus outbreak in Hong Kong during 2003. Simulations of these models have previously been realized using informed “guesses” of the proposed model parameters and tested for consistency with the reported data by surrogate analysis. In this paper we attempt to provide statistically rigorous parameter distributions using Approximate Bayesian Computation sampling methods. We find that such sampling schemes are a useful framework for fitting parameters of stochastic small world network models where simulation of the system is straightforward but expressing a likelihood is cumbersome.     

(N‐Phosphinoamidinate)cobalt‐Catalyzed Hydroboration: Alkene Isomerization Affords Terminal Selectivity

Herein we establish the utility of a three‐coordinate (N‐phosphinoamidinate)cobalt(amido) pre‐catalyst that is capable of effecting challenging alkene isomerization/hydroboration processes at room temperature, leading to the selective terminal addition of the boron group.