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May 2012

Volume 6, Issue 5

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Communication: Spectroscopic measurement of the binding energy of a carboxylic acid-water dimer

Quanli Gu and J. L. Knee

J. Chem. Phys. 136, 171101 (2012); http://dx.doi.org/10.1063/1.4711862 (4 pages)

Online Publication Date: 2 May 2012

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Infrared-ultraviolet two color pump-probe spectroscopy is used to measure the binding energy, D0, of a carboxylic acid-water dimer where the acid is 9-hydroxy-9-fluorenecarboxylic acid. The acid-water configuration presents a standard structure for the general acid-water interaction where the water bonds to the carboxylic acid group through two intermolecular hydrogen bonds. Photodissociation studies with product vibrational state resolution have enabled an accurate determination of the binding energy for this acid-water system to be D0 = 2975 ± 30 cm−1. Quantum chemical calculations are performed to compare with the experimental observations and a recent measurement on the water dimer (D0 = 1105 ± 10 cm−1).
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33.20.Ea Infrared spectra
33.20.Tp Vibrational analysis
33.80.Gj Diffuse spectra; predissociation, photodissociation
33.15.Fm Bond strengths, dissociation energies
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.20.Lg Ultraviolet spectra
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Mimicking trimeric interactions in the aromatic side chains of the proteins: A gas phase study of indole…(pyrrole)2 heterotrimer

Sumit Kumar and Aloke Das

J. Chem. Phys. 136, 174302 (2012); http://dx.doi.org/10.1063/1.4706517 (9 pages)

Online Publication Date: 1 May 2012

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Aromatic trimeric interactions are extremely significant in the stabilization of the specific structures of the proteins as well as protein-protein, and protein-ligand interactions. Here we have reported a direct evidence of the observation of a cyclic asymmetric structure of indole…(pyrrole)2 trimer bound by three N–H…π hydrogen bonding interactions in a supersonic jet. The experiment has been performed by using resonant two-photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques. Density functional theory (DFT) calculations nicely corroborate the experimental results showing one weakly allowed IR-active band due to symmetric stretch of the N–H bonds and two strongly allowed IR-active bands due to two types of asymmetric stretches of the N–H bonds in the trimer. The present spectroscopic investigation demonstrates that the strength of the three N–H…π bound intermolecular interactions in the cyclic asymmetric trimer is quite different unlike the corresponding interactions of similar strength in a cyclic symmetric trimer.
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87.14.E- Proteins
87.15.km Protein-protein interactions
87.15.kp Protein-ligand interactions
87.15.mn Photoionization

How does water-nanotube interaction influence water flow through the nanochannel?

Xiaoyi Li, Yanchao Shi, Yuling Yang, Huailiang Du, Ruhong Zhou, and Yuliang Zhao

J. Chem. Phys. 136, 175101 (2012); http://dx.doi.org/10.1063/1.4707346 (6 pages)

Online Publication Date: 1 May 2012

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Water permeation across various nitrogen-doped double-walled carbon nanotubes (N-DWCNT) has been studied with molecular dynamics simulations to better understand the influence of water-nanopore interaction on the water permeation rate. There exists a threshold interaction energy at around –34.1 kJ∕mol. Over the threshold energy, the water flow through N-DWCNT decreases monotonically with the strengthening of the water-nanotube interaction. The effect on the water flow across the channel is found to be negligible when the interaction energy is weaker than the threshold. The water-nanotube interaction energy can be controlled by doping nitrogen atoms into the nanotube walls. Although the van der Waals interaction energy is much stronger than the electrostatic interaction energy, it is less sensitive to the proportion of doped nitrogen atoms. On the other hand, the electrostatic interaction energy weakens after the initial strengthening when the percentage of doped nitrogen atoms increases to ∼25%. The doped nitrogen atoms make less influence on the overall electrostatic interaction energy when the proportion is over 25%, due to the repulsions among themselves. Thus, the monotonous strengthening of the van der Waals interaction energy seems to dominate the overall trend of the total interaction energy, whereas the change of the long-range electrostatic interaction energy characterizes the shape of the correlation curve, as the percentage of doped nitrogen atoms increases.
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61.25.Em Molecular liquids
61.20.Ja Computer simulation of liquid structure
47.61.-k Micro- and nano- scale flow phenomena
47.60.Dx Flows in ducts and channels
34.20.Gj Intermolecular and atom-molecule potentials and forces

Long range excitonic transport in a biomimetic system inspired by the bacterial light-harvesting apparatus

Elad Harel

J. Chem. Phys. 136, 174104 (2012); http://dx.doi.org/10.1063/1.4704656 (10 pages)

Online Publication Date: 1 May 2012

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Photosynthesis, the process by which energy from sunlight drives cellular metabolism, relies on a unique organization of light-harvesting and reaction center complexes. Recently, the organization of light-harvesting LH2 complexes and dimeric reaction center-light-harvesting I-PufX core complexes in membranes of purple non-sulfur bacteria was revealed by atomic force microscopy [S. Bahatyrova et al., Nature (London) 430, 1058 (2004)]. Here, we discuss optimal exciton transfer in a biomimetic system closely modeled on the structure of LH2 and its organization within the membrane using a Markovian quantum model with dissipation and trapping added phenomenologically. In a deliberate manner, we neglect the high level detail of the bacterial light-harvesting complex and its interaction with the phonon bath in order to elucidate a set of design principles that may be incorporated in artificial pigment-scaffold constructs in a supramolecular assembly. We show that our scheme reproduces many of the most salient features found in their natural counterpart and may be largely explained by simple electrostatic considerations. Most importantly, we show that quantum effects act primarily to enforce robustness with respect to spatial and spectral disorder between and within complexes. The implications of such an arrangement are discussed in the context of biomimetic photosynthetic analogs capable of transferring energy efficiently across tens to hundreds of nanometers.
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87.16.-b Subcellular structure and processes
87.15.M- Spectra of biomolecules
82.50.-m Photochemistry

Osmotic virial coefficients for model protein and colloidal solutions: Importance of ensemble constraints in the analysis of light scattering data

Daniel W. Siderius, William P. Krekelberg, Christopher J. Roberts, and Vincent K. Shen

J. Chem. Phys. 136, 175102 (2012); http://dx.doi.org/10.1063/1.4709613 (9 pages)

Online Publication Date: 3 May 2012

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Protein-protein interactions in solution may be quantified by the osmotic second virial coefficient (OSVC), which can be measured by various experimental techniques including light scattering. Analysis of Rayleigh light scattering measurements from such experiments requires identification of a scattering volume and the thermodynamic constraints imposed on that volume, i.e., the statistical mechanical ensemble in which light scattering occurs. Depending on the set of constraints imposed on the scattering volume, one can obtain either an apparent OSVC, A2,app, or the true thermodynamic OSVC, B22osm, that is rigorously defined in solution theory [M. A. Blanco, E. Sahin, Y. Li, and C. J. Roberts, J. Chem. Phys. 134, 225103 (2011)]. However, it is unclear to what extent A2,app and B22osm differ, which may have implications on the physical interpretation of OSVC measurements from light scattering experiments. In this paper, we use the multicomponent hard-sphere model and a well-known equation of state to directly compare A2,app and B22osm. Our results from the hard-sphere equation of state indicate that A2,app underestimates B22osm, but in a systematic manner that may be explained using fundamental thermodynamic expressions for the two OSVCs. The difference between A2,app and B22osm may be quantitatively significant, but may also be obscured in experimental application by statistical uncertainty or non-steric interactions. Consequently, the two OSVCs that arise in the analysis of light scattering measurements do formally differ, but in a manner that may not be detectable in actual application.
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82.70.Dd Colloids
64.75.Ef Mixing
78.35.+c Brillouin and Rayleigh scattering; other light scattering
82.39.Wj Ion exchange, dialysis, osmosis, electro-osmosis, membrane processes
82.60.Lf Thermodynamics of solutions

First passage times for a tracer particle in single file diffusion and fractional Brownian motion

Lloyd P. Sanders and Tobias Ambjörnsson

J. Chem. Phys. 136, 175103 (2012); http://dx.doi.org/10.1063/1.4707349 (12 pages)

Online Publication Date: 4 May 2012

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We investigate the full functional form of the first passage time density (FPTD) of a tracer particle in a single-file diffusion (SFD) system whose population is: (i) homogeneous, i.e., all particles having the same diffusion constant and (ii) heterogeneous, with diffusion constants drawn from a heavy-tailed power-law distribution. In parallel, the full FPTD for fractional Brownian motion [fBm—defined by the Hurst parameter, H ∊ (0, 1)] is studied, of interest here as fBm and SFD systems belong to the same universality class. Extensive stochastic (non-Markovian) SFD and fBm simulations are performed and compared to two analytical Markovian techniques: the method of images approximation (MIA) and the Willemski-Fixman approximation (WFA). We find that the MIA cannot approximate well any temporal scale of the SFD FPTD. Our exact inversion of the Willemski-Fixman integral equation captures the long-time power-law exponent, when H ⩾ 1∕3, as predicted by Molchan [Commun. Math. Phys. 205, 97 (1999)] for fBm. When H < 1∕3, which includes homogeneous SFD (H = 1∕4), and heterogeneous SFD (H < 1∕4), the WFA fails to agree with any temporal scale of the simulations and Molchan's long-time result. SFD systems are compared to their fBm counter parts; and in the homogeneous system both scaled FPTDs agree on all temporal scales including also, the result by Molchan, thus affirming that SFD and fBm dynamics belong to the same universality class. In the heterogeneous case SFD and fBm results for heterogeneity-averaged FPTDs agree in the asymptotic time limit. The non-averaged heterogeneous SFD systems display a lack of self-averaging. An exponential with a power-law argument, multiplied by a power-law pre-factor is shown to describe well the FPTD for all times for homogeneous SFD and sub-diffusive fBm systems.
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05.60.-k Transport processes
02.60.Gf Algorithms for functional approximation
02.30.Rz Integral equations
02.50.Ga Markov processes
05.40.Jc Brownian motion

Multipartite entanglement in the Fenna-Matthews-Olson (FMO) pigment-protein complex

A. Thilagam

J. Chem. Phys. 136, 175104 (2012); http://dx.doi.org/10.1063/1.4705396 (14 pages)

Online Publication Date: 4 May 2012

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We investigate multipartite states in the Fenna-Matthews-Olson (FMO) pigment-protein complex of the green sulfur bacteria using a Lorentzian spectral density of the phonon reservoir fitted with typical parameter estimates of the species, Prosthecochloris aestuarii. The evolution of the entanglement measure of the excitonic W qubit states is evaluated in the picosecond time range, showing increased revivals in the non-Markovian regime. Similar trends are observed in the evolution dynamics of the Meyer-Wallach measure of the N-exciton multipartite state, with results showing that multipartite entanglement can last from 0.5 to 1 ps, between the bacteriochlorophylls of the FMO complex. The teleportation and quantum information splitting fidelities associated with the Greenberger-Horne-Zeilinger and W-like resource states formed by the excitonic qubit channels of the FMO complex show that revivals in fidelities increase with the degree of non-Markovian strength of the decoherent environment. Quantum information processing tasks involving teleportation followed by the decodification process involving W-like states of the FMO complex may play a critical role during coherent oscillations at physiological temperatures.
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03.67.Bg Entanglement production and manipulation
03.67.Lx Quantum computation architectures and implementations
03.67.Mn Entanglement measures, witnesses, and other characterizations
87.14.E- Proteins
87.15.hg Dynamics of intermolecular interactions
87.23.Kg Dynamics of evolution

Non-stationary forward flux sampling

Nils B. Becker, Rosalind J. Allen, and Pieter Rein ten Wolde

J. Chem. Phys. 136, 174118 (2012); http://dx.doi.org/10.1063/1.4704810 (18 pages)

Online Publication Date: 4 May 2012

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We present a method, Non-Stationary Forward Flux Sampling, that allows efficient simulation of rare events in both stationary and non-stationary stochastic systems. The method uses stochastic branching and pruning to achieve uniform sampling of trajectories in phase space and time, leading to accurate estimates for time-dependent switching propensities and time-dependent phase space probability densities. It is suitable for equilibrium or non-equilibrium systems, in or out of stationary state, including non-Markovian or externally driven systems. We demonstrate the validity of the technique by applying it to a one-dimensional barrier crossing problem that can be solved exactly, and show its usefulness by applying it to the time-dependent switching of a genetic toggle switch.
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05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
02.50.Cw Probability theory
02.50.Ga Markov processes

From A to B: A ride in the free energy surfaces of protein G domains suggests how new folds arise

Ludovico Sutto and Carlo Camilloni

J. Chem. Phys. 136, 185101 (2012); http://dx.doi.org/10.1063/1.4712029 (5 pages)

Online Publication Date: 8 May 2012

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Metamorphic proteins are an extremely intriguing case of protein evolution and a golden opportunity to challenge the current simplified models. In a recent work, we showed that a coarse-grained Gō model can be used to study the thermodynamics of lymphotactin, a naturally occurring metamorphic protein. Here, we extend such model by including the necessary atomic detail to study the effects of the single mutations that artificially bring the GA domain of protein G to fold into the GB domain of the same protein. The results of this all-atom Gō model show how the residual structure of the denatured state is an early indicator of a forthcoming fold and function switch. These findings reconcile the results of previous studies on similar systems highlighting the different role played by secondary and tertiary interactions and suggesting a possible way for new folds to arise.
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87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.15.km Protein-protein interactions
87.14.E- Proteins

Rare switching events in non-stationary systems

Nils B. Becker and Pieter Rein ten Wolde

J. Chem. Phys. 136, 174119 (2012); http://dx.doi.org/10.1063/1.4704812 (15 pages)

Online Publication Date: 4 May 2012

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Physical systems with many degrees of freedom can often be understood in terms of transitions between a small number of metastable states. For time-homogeneous systems with short-term memory these transitions are fully characterized by a set of rate constants. We consider the question how to extend such a coarse-grained description to non-stationary systems and to systems with finite memory. We identify the physical regimes in which time-dependent rates are meaningful, and state microscopic expressions that can be used to measure both externally time-dependent and history-dependent rates in microscopic simulations. Our description can be used to generalize Markov state models to time-dependent Markovian or non-Markovian systems.
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05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
02.50.Ga Markov processes

Polar solvation dynamics of lysozyme from molecular dynamics studies

Sudipta Kumar Sinha and Sanjoy Bandyopadhyay

J. Chem. Phys. 136, 185102 (2012); http://dx.doi.org/10.1063/1.4712036 (6 pages)

Online Publication Date: 9 May 2012

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The solvation dynamics of a protein are believed to be sensitive to its secondary structures. We have explored such sensitivity in this article by performing room temperature molecular dynamics simulation of an aqueous solution of lysozyme. Nonuniform long-time relaxation patterns of the solvation time correlation function for different segments of the protein have been observed. It is found that relatively slower long-time solvation components of the α-helices and β-sheets of the protein are correlated with lower exposure of their polar probe residues to bulk solvent and hence stronger interactions with the dynamically restricted surface water molecules. These findings can be verified by appropriate experimental studies.
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87.15.ap Molecular dynamics simulation
87.14.ej Enzymes
87.15.R- Reactions and kinetics
87.15.H- Dynamics of biomolecules
87.15.K- Molecular interactions; membrane-protein interactions
87.15.bd Secondary structure

An adaptive stepsize method for the chemical Langevin equation

Silvana Ilie and Alexandra Teslya

J. Chem. Phys. 136, 184101 (2012); http://dx.doi.org/10.1063/1.4711143 (14 pages)

Online Publication Date: 9 May 2012

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Mathematical and computational modeling are key tools in analyzing important biological processes in cells and living organisms. In particular, stochastic models are essential to accurately describe the cellular dynamics, when the assumption of the thermodynamic limit can no longer be applied. However, stochastic models are computationally much more challenging than the traditional deterministic models. Moreover, many biochemical systems arising in applications have multiple time-scales, which lead to mathematical stiffness. In this paper we investigate the numerical solution of a stochastic continuous model of well-stirred biochemical systems, the chemical Langevin equation. The chemical Langevin equation is a stochastic differential equation with multiplicative, non-commutative noise. We propose an adaptive stepsize algorithm for approximating the solution of models of biochemical systems in the Langevin regime, with small noise, based on estimates of the local error. The underlying numerical method is the Milstein scheme. The proposed adaptive method is tested on several examples arising in applications and it is shown to have improved efficiency and accuracy compared to the existing fixed stepsize schemes.
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87.15.R- Reactions and kinetics
02.50.Ey Stochastic processes
87.10.Mn Stochastic modeling
02.60.-x Numerical approximation and analysis

Dynamics of polymer translocation into a circular nanocontainer through a nanopore

Kehong Zhang and Kaifu Luo

J. Chem. Phys. 136, 185103 (2012); http://dx.doi.org/10.1063/1.4712618 (8 pages)

Online Publication Date: 11 May 2012

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Using Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a circular nanocontainer through a nanopore under a driving force F. We observe that the translocation probability initially increases and then saturates with increasing F, independent of ϕ, which is the average density of the whole chain in the nanocontainer. The translocation time distribution undergoes a transition from a Gaussian distribution to an asymmetric distribution with increasing ϕ. Moreover, we find a nonuniversal scaling exponent of the translocation time as chain length, depending on ϕ and F. These results are interpreted by the conformation of the translocated chain in the nanocontainer and the time of an individual segment passing through the pore during translocation.
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87.15.hj Transport dynamics
87.85.Rs Nanotechnologies-applications
87.15.ap Molecular dynamics simulation
87.15.B- Structure of biomolecules

Distribution of transverse chain fluctuations in harmonically confined semiflexible polymers

Rati Sharma and Binny J. Cherayil

J. Chem. Phys. 136, 184902 (2012); http://dx.doi.org/10.1063/1.4712306 (8 pages)

Online Publication Date: 14 May 2012

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Two different experimental studies of polymer dynamics based on single-molecule fluorescence imaging have recently found evidence of heterogeneities in the widths of the putative tubes that surround filaments of F-actin during their motion in concentrated solution. In one [J. Glaser, D. Chakraborty, K. Kroy, I. Lauter, M. Degawa, N. Kirchesner, B. Hoffmann, R. Merkel, and M. Giesen, Phys. Rev. Lett. 105, 037801 (2010)], the observations were explained in terms of the statistics of a worm-like chain confined to a potential determined self-consistently by a binary collision approximation, and in the other [B. Wang, J. Guan, S. M. Anthony, S. C. Bae, K. S. Schweizer, and S. Granick, Phys. Rev. Lett. 104, 118301 (2010)], they were explained in terms of the scaling properties of a random fluid of thin rods. In this paper, we show, using an exact path integral calculation, that the distribution of the length-averaged transverse fluctuations of a harmonically confined weakly bendable rod (one possible realization of a semiflexible chain in a tube), is in good qualitative agreement with the experimental data, although it is qualitatively different in analytic structure from the earlier theoretical predictions. We also show that similar path integral techniques can be used to obtain an exact expression for the time correlation function of fluctuations in the tube cross section.
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05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
33.50.Dq Fluorescence and phosphorescence spectra
31.15.xr Self-consistent-field methods
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