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February 2012

Volume 6, Issue 2

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Combined depletion and electrostatic forces in polymer-induced membrane adhesion: A theoretical model

Antonio Raudino, Martina Pannuzzo, and Mikko Karttunen

J. Chem. Phys. 136, 055101 (2012); http://dx.doi.org/10.1063/1.3678836 (16 pages)

Online Publication Date: 1 February 2012

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We develop a semi-quantitative analytical theory to describe adhesion between two identical planar charged surfaces embedded in a polymer-containing electrolyte solution. Polymer chains are uncharged and differ from the solvent by their lower dielectric permittivity. The solution mimics physiological fluids: It contains 0.1 M of monovalent ions and a small number of divalent cations that form tight bonds with the headgroups of charged lipids. The components have heterogeneous spatial distributions. The model was derived self-consistently by combining: (a) a Poisson-Boltzmann like equation for the charge densities, (b) a continuum mean-field theory for the polymer profile, (c) a solvation energy forcing the ions toward the polymer-poor regions, and (d) surface interactions of polymers and electrolytes. We validated the theory via extensive coarse-grained Molecular Dynamics (MD) simulations. The results confirm our analytical model and reveal interesting details not detected by the theory. At high surface charges, polymer chains are mainly excluded from the gap region, while the concentration of ions increases. The model shows a strong coupling between osmotic forces, surface potential and salting-out effects of the slightly polar polymer chains. It highlights some of the key differences in the behaviour of monomeric and polymeric mixed solvents and their responses to Coulomb interactions. Our main findings are: (a) the onset of long-ranged ion-induced polymer depletion force that increases with surface charge density and (b) a polymer-modified repulsive Coulomb force that increases with surface charge density. Overall, the system exhibits homeostatic behaviour, resulting in robustness against variations in the amount of charges. Applications and extensions of the model are briefly discussed.
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82.39.Wj Ion exchange, dialysis, osmosis, electro-osmosis, membrane processes
82.45.Mp Thin layers, films, monolayers, membranes
77.22.Ch Permittivity (dielectric function)
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Mg impurity in helium droplets

J. Navarro, D. Mateo, M. Barranco, and A. Sarsa

J. Chem. Phys. 136, 054301 (2012); http://dx.doi.org/10.1063/1.3675919 (9 pages)

Online Publication Date: 1 February 2012

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Within the diffusion Monte Carlo approach, we have determined the structure of isotopically pure and mixed helium droplets doped with one magnesium atom. For pure 4He clusters, our results confirm those of Mella et al. [J. Chem. Phys. 123, 054328 (2005)] that the impurity experiences a transition from a surface to a bulk location as the number of helium atoms in the droplet increases. Contrarily, for pure 3He clusters Mg resides in the bulk of the droplet due to the smaller surface tension of this isotope. Results for mixed droplets are presented. We have also obtained the absorption spectrum of Mg around the 3s3p 1P1 ← 3s2 1S0 transition.
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36.40.Mr Spectroscopy and geometrical structure of clusters

Correlated intermolecular coupling fluctuations in photosynthetic complexes

Sebastiaan M. Vlaming and Robert J. Silbey

J. Chem. Phys. 136, 055102 (2012); http://dx.doi.org/10.1063/1.3682988 (10 pages)

Online Publication Date: 6 February 2012

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The functioning and efficiency of natural photosynthetic complexes is strongly influenced by their embedding in a noisy protein environment, which can even serve to enhance the transport efficiency. Interactions with the environment induce fluctuations of the transition energies and couplings between the chlorophyll molecules, and due to the fact that different fluctuations will partially be caused by the same environmental factors, correlations between the various fluctuations will occur. We argue that fluctuations of the couplings should, in general, not be neglected, as these have a considerable impact on population transfer rates, decoherence rates, and the efficiency of photosynthetic complexes. Furthermore, while correlations between transition energy fluctuations have been studied, we provide the first quantitative study of the effect of correlations between coupling fluctuations and transition energy fluctuations, and of correlations between the various coupling fluctuations. It is shown that these additional correlations typically lead to changes in interchromophore transfer rates and population oscillations and can lead to a limited enhancement of the light harvesting efficiency.
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82.50.-m Photochemistry
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
34.20.Gj Intermolecular and atom-molecule potentials and forces

The role of structure in the nonlinear mechanics of cross-linked semiflexible polymer networks

Nicholas Agung Kurniawan, Søren Enemark, and Raj Rajagopalan

J. Chem. Phys. 136, 065101 (2012); http://dx.doi.org/10.1063/1.3682779 (8 pages)

Online Publication Date: 8 February 2012

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The microstructural basis of the characteristic nonlinear mechanics of biopolymer networks remains unclear. We present a 3D network model of realistic, cross-linked semiflexible fibers to study strain-stiffening and the effect of fiber volume-occupancy. We identify two structural parameters, namely, network connectivity and fiber entanglements, that fully govern the nonlinear response from small to large strains. The results also reveal distinct deformation mechanisms at different length scales and, in particular, the contributions of heterogeneity at short length scales.
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61.41.+e Polymers, elastomers, and plastics
81.40.Lm Deformation, plasticity, and creep
62.20.F- Deformation and plasticity

Folding of small origamis

Jean Michel Arbona, Jean-Pierre Aimé, and Juan Elezgaray

J. Chem. Phys. 136, 065102 (2012); http://dx.doi.org/10.1063/1.3682472 (8 pages)

Online Publication Date: 9 February 2012

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A model that preserves the known thermodynamic properties of double stranded DNA is introduced to study the formation of more complex DNA constructions, such as small origamis or Holliday junctions. We show that the thermodynamic behaviour of these complex DNA constructions is not only given by their sequence but also by their topology.
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87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.14.gk DNA
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Kinetic pathways to peptide aggregation on surfaces: The effects of β-sheet propensity and surface attraction

Alex Morriss-Andrews and Joan-Emma Shea

J. Chem. Phys. 136, 065103 (2012); http://dx.doi.org/10.1063/1.3682986 (11 pages)

Online Publication Date: 10 February 2012

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Mechanisms of peptide aggregation on hydrophobic surfaces are explored using molecular dynamics simulations with a coarse-grained peptide representation. Systems of peptides are studied with varying degrees of backbone rigidity (a measure of β-sheet propensity) and degrees of attraction between their hydrophobic residues and the surface. Multiple pathways for aggregation are observed, depending on the surface attraction and peptide β-sheet propensity. For the case of a single-layered β-sheet fibril forming on the surface (a dominant structure seen in all simulations), three mechanisms are observed: (a) a condensation-ordering transition where a bulk-formed amorphous aggregate binds to the surface and subsequently rearranges to form a fibril; (b) the initial formation of a single-layered fibril in the bulk depositing flat on the surface; and (c) peptides binding individually to the surface and nucleating fibril formation by individual peptide deposition. Peptides with a stiffer chiral backbone prefer mechanism (b) over (a), and stronger surface attractions prefer mechanism (c) over (a) and (b). Our model is compared to various similar experimental systems, and an agreement was found in terms of the surface increasing the degree of fibrillar aggregation, with the directions of fibrillar growth matching the crystallographic symmetry of the surface. Our simulations provide details of aggregate growth mechanisms on scales inaccessible to either experiment or atomistic simulations.
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87.15.ap Molecular dynamics simulation
87.15.bk Structure of aggregates
87.15.R- Reactions and kinetics
87.14.ef Peptides

Absorption by DNA single strands of adenine isolated in vacuo: The role of multiple chromophores

Lisbeth Munksgaard Nielsen, Sara Øvad Pedersen, Maj-Britt Suhr Kirketerp, and Steen Brøndsted Nielsen

J. Chem. Phys. 136, 064302 (2012); http://dx.doi.org/10.1063/1.3679444 (5 pages)

Online Publication Date: 10 February 2012

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The degree of electronic coupling between DNA bases is a topic being up for much debate. Here we report on the intrinsic electronic properties of isolated DNA strands in vacuo free of solvent, which is a good starting point for high-level excited states calculations. Action spectra of DNA single strands of adenine reveal sign of exciton coupling between stacked bases from blueshifted absorption bands (∼3 nm) relative to that of the dAMP mononucleotide (one adenine base). The bands are blueshifted by about 10 nm compared to those of solvated strands, which is a shift similar to that for the adenine molecule and the dAMP mononucleotide. Desolvation has little effect on the bandwidth, which implies that inhomogenous broadening of the absorption bands in aqueous solution is of minor importance compared to, e.g., conformational disorder. Finally, at high photon energies, internal conversion competes with electron detachment since dissociation of the bare photoexcited ions on the microsecond time scale is measured.
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87.15.Pc Electronic and electrical properties
36.20.Kd Electronic structure and spectra
87.14.gk DNA
87.15.M- Spectra of biomolecules

Spontaneous tunneling and near-infrared-induced interconversion between the amino-hydroxy conformers of cytosine

Igor Reva, Maciej J. Nowak, Leszek Lapinski, and Rui Fausto

J. Chem. Phys. 136, 064511 (2012); http://dx.doi.org/10.1063/1.3683217 (8 pages)

Online Publication Date: 13 February 2012

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Spontaneous and near-infrared∕infrared (NIR∕IR)-induced interconversions between two amino-hydroxy conformers of monomeric cytosine have been investigated for the compound isolated in a low-temperature argon matrix. Combined use of a laser source (which provides narrowband NIR radiation) and a broadband NIR/IR source of excitation light allowed a detailed investigation of mutual conversions of the two conformers in question. The experiments carried out within the current work demonstrated that upon broadband NIR∕IR irradiation (with the IR source of FTIR spectrometer) the population ratio of the two amino-hydroxy conformers changes towards a ratio corresponding to a photostationary state. Evolution of the conformer population ratio towards the photostationary ratio occurred independent of the initial ratio of conformers, which could be prepared by a population shift (in favor of one of the forms) induced by narrowband NIR excitation. Moreover, spontaneous tunneling conversion of the higher-energy conformer into a lower-energy form was observed for cytosine isolated in a low-temperature argon matrix kept in the dark. This process is slow and occurs on a time scale of days. The tunneling process, studied for matrix-isolated cytosine, clearly follows a dispersive type of kinetics rather than the classical monoexponential kinetics.
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87.15.hp Conformational changes
82.30.Qt Isomerization and rearrangement
82.50.Bc Processes caused by infrared radiation
87.15.R- Reactions and kinetics
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)

Non-Hermitian exciton dynamics in a photosynthetic unit system

A. Thilagam

J. Chem. Phys. 136, 065104 (2012); http://dx.doi.org/10.1063/1.3684654 (9 pages)

Online Publication Date: 13 February 2012

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The non-Hermitian quantum dynamics of excitonic energy transfer in photosynthetic systems is investigated using a dissipative two-level dimer model. The approach is based on Green's function formalism which permits consideration of decoherence and intersite transfer processes on comparable terms. The results indicate a combination of coherent and incoherent behavior at higher temperatures with the possibility of exceptional points occurring at the coherent-incoherent crossover regime at critical temperatures. When each dimer site is coupled equally to the environmental sources of dissipation, the excitonic wavepacket evolves with time with a coherent component, which can be attributed to the indistinguishability of the sources of dissipation. The time evolution characteristics of the B850 Bchls dimer system is analysed using typical parameter estimates in photosynthetic systems, and the quantum brachistochrone passage times are obtained for a range of parameters.
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71.35.-y Excitons and related phenomena
03.67.Mn Entanglement measures, witnesses, and other characterizations
03.65.Ud Entanglement and quantum nonlocality (e.g. EPR paradox, Bell's inequalities, GHZ states, etc.)
02.30.-f Function theory, analysis
05.30.-d Quantum statistical mechanics
03.65.Yz Decoherence; open systems; quantum statistical methods

Polymer translocation in solid-state nanopores: Dependence of scaling behavior on pore dimensions and applied voltage

Christopher M. Edmonds, Yeny C. Hudiono, Amir G. Ahmadi, Peter J. Hesketh, and Sankar Nair

J. Chem. Phys. 136, 065105 (2012); http://dx.doi.org/10.1063/1.3682777 (10 pages)

Online Publication Date: 14 February 2012

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We investigate unforced and forced translocation of a Rouse polymer (in the absence of hydrodynamic interactions) through a silicon nitride nanopore by three-dimensional Langevin dynamics simulations, as a function of pore dimensions and applied voltage. Our nanopore model consists of an atomistically detailed nanopore constructed using the crystal structure of β-Si3N4. We also use realistic parameters in our simulation models rather than traditional dimensionless quantities. When the polymer length is much larger than the pore length, we find the translocation time versus chain length scales as τ ∼ N2+ν for the unforced case and as τ ∼ N(1+2ν)∕(1+ν) for the forced case. Our results agree with theoretical predictions which indicate that memory effects and tension on the polymer chain play an important role during the translocation process. We also find that the scaling exponents are highly dependent on the applied voltage (force). When the length of the polymer is on the order of the length of the pore, we do not find a continuous scaling law, but rather scaling exponents that increase as the length of the polymer increases. Finally, we investigate the scaling behavior of translocation time versus applied voltage for different polymer and pore lengths. For long pores, we obtain the theoretical scaling law of τ ∼ 1∕Vα, where α ≅ 1 for all voltages and polymer lengths. For short pores, we find that α decreases for very large voltages and∕or small polymer lengths, indicating that the value of α = 1 is not universal. The results of our simulations are discussed in the context of experimental measurements made under different conditions and with differing pore geometries.
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61.46.-w Structure of nanoscale materials
61.41.+e Polymers, elastomers, and plastics
61.43.Gt Powders, porous materials

Unzipping and binding of small interfering RNA with single walled carbon nanotube: A platform for small interfering RNA delivery

Mogurampelly Santosh, Swati Panigrahi, Dhananjay Bhattacharyya, A. K. Sood, and Prabal K. Maiti

J. Chem. Phys. 136, 065106 (2012); http://dx.doi.org/10.1063/1.3682780 (10 pages)

Online Publication Date: 14 February 2012

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In an effort to design efficient platform for siRNA delivery, we combine all atom classical and quantum simulations to study the binding of small interfering RNA (siRNA) by pristine single wall carbon nanotube (SWCNT). Our results show that siRNA strongly binds to SWCNT surface via unzipping its base-pairs and the propensity of unzipping increases with the increase in the diameter of the SWCNTs. The unzipping and subsequent wrapping events are initiated and driven by van der Waals interactions between the aromatic rings of siRNA nucleobases and the SWCNT surface. However, molecular dynamics (MD) simulations of double strand DNA (dsDNA) of the same sequence show that the dsDNA undergoes much less unzipping and wrapping on the SWCNT in the simulation time scale of 70 ns. This interesting difference is due to smaller interaction energy of thymidine of dsDNA with the SWCNT compared to that of uridine of siRNA, as calculated by dispersion corrected density functional theory (DFT) methods. After the optimal binding of siRNA to SWCNT, the complex is very stable which serves as one of the major mechanisms of siRNA delivery for biomedical applications. Since siRNA has to undergo unwinding process with the effect of RNA-induced silencing complex, our proposed delivery mechanism by SWCNT possesses potential advantages in achieving RNA interference.
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87.15.K- Molecular interactions; membrane-protein interactions
87.14.gk DNA
87.14.gn RNA
87.15.ap Molecular dynamics simulation
87.15.B- Structure of biomolecules
87.15.hg Dynamics of intermolecular interactions

Two-point approximation to the Kramers problem with coloured noise

Daniel Campos and Vicenç Méndez

J. Chem. Phys. 136, 074506 (2012); http://dx.doi.org/10.1063/1.3685418 (8 pages)

Online Publication Date: 15 February 2012

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We present a method, founded on previous renewal approaches as the classical Wilemski-Fixman approximation, to describe the escape dynamics from a potential well of a particle subject to non-Markovian fluctuations. In particular, we show how to provide an approximated expression for the distribution of escape times if the system is governed by a generalized Langevin equation (GLE). While we show that the method could apply to any friction kernel in the GLE, we focus here on the case of power-law kernels, for which extensive literature has appeared in the last years. The method presented (termed as two-point approximation) is able to fit the distribution of escape times adequately for low potential barriers, even if conditions are far from Markovian. In addition, it confirms that non-exponential decays arise when a power-law friction kernel is considered (in agreement with related works published recently), which questions the existence of a characteristic reaction rate in such situations.
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31.50.Bc Potential energy surfaces for ground electronic states
31.15.bt Statistical model calculations (including Thomas-Fermi and Thomas-Fermi-Dirac models)
05.40.Ca Noise

Electron stimulated desorption of anions from native and brominated single stranded oligonucleotide trimers

Katarzyna Polska, Janusz Rak, Andrew D. Bass, Pierre Cloutier, and Léon Sanche

J. Chem. Phys. 136, 075101 (2012); http://dx.doi.org/10.1063/1.3685587 (8 pages)

Online Publication Date: 21 February 2012

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We measured the low energy electron stimulated desorption (ESD) of anions from thin films of native (TXT) and bromine monosubstituted (TBrXT) oligonucleotide trimers deposited on a gold surface (T = thymidine, X = T, deoxycytidine (C), deoxyadenosine (A) or deoxyguanosine (G), Br = bromine). The desorption of H−, CH3−∕NH−, O−∕NH2−, OH−, CN−, and Br− was induced by 0 to 20 eV electrons. Dissociative electron attachment, below 12 eV, and dipolar dissociation, above 12 eV, are responsible for the formation of these anions. The comparison of the results obtained for the native and brominated trimers suggests that the main pathways of TBrXT degradation correspond to the release of the hydride and bromide anions. Significantly, the presence of bromine in oligonucleotide trimers blocks the electron-induced degradation of nuclobases as evidenced by a dramatic decrease in CN− desorption. An increase in the yields of OH− is also observed. The debromination yield of particular oligonucleotides diminishes in the following order: BrdU > BrdA > BrdG > BrdC. Based on these results, 5-bromo-2′-deoxyuridine appears to be the best radiosensitizer among the studied bromonucleosides.
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87.15.M- Spectra of biomolecules
87.53.-j Effects of ionizing radiation on biological systems
87.14.gk DNA
87.15.rs Dissociation
68.43.Rs Electron stimulated desorption
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)

Far-infrared spectroscopy on free-standing protein films under defined temperature and hydration control

Christian U. Stehle, Wasim Abuillan, Bruno Gompf, and Martin Dressel

J. Chem. Phys. 136, 075102 (2012); http://dx.doi.org/10.1063/1.3686886 (8 pages)

Online Publication Date: 21 February 2012

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The functionality of proteins is governed by their dynamics. We have performed a systematic investigation on four different proteins in the far-infrared spectral region under control of the two external parameters that have the strongest influence on the dynamics, namely temperature and hydration. The absorption measurements covering the frequency range from 40 cm−1 to 690 cm−1 (1–20 THz) close the gap between the well-studied mid-infrared and the recent THz investigations. By preparing the proteins as free-standing films, we achieve unprecedented reproducibility. Besides a featureless slope in the THz range, we can identify absorption peaks characteristic for each protein and others common to several proteins. We fit the spectra to extract the peak positions and suggest assignments for them. The far-infrared absorption spectra of all proteins are basically independent on hydration. By a detailed analysis of the sorption isotherms this can be explained by the low absorption of biological water, which resembles more the behavior of ice than that of liquid water.
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87.14.E- Proteins
87.15.H- Dynamics of biomolecules
87.15.M- Spectra of biomolecules
82.30.-b Specific chemical reactions; reaction mechanisms
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