German Research School for Simulation science

Jülich, Germany

German Research School for Simulation science

Jülich, Germany
Time filter
Source Type

Zhang C.,German Research School for Simulation science | Knyazev D.G.,Johannes Kepler University | Vereshaga Y.A.,German Research School for Simulation science | Ippoliti E.,German Research School for Simulation science | And 4 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2012

Fast lateral proton migration along membranes is of vital importance for cellular energy homeostasis and various proton-coupled transport processes. It can only occur if attractive forces keep the proton at the interface. How to reconcile this high affinity to the membrane surface with high proton mobility is unclear. Here, we tested whether a minimalistic model interface between an apolar hydrophobic phase (n-decane) and an aqueous phase mimics the biological pathway for lateral proton migration. The observed diffusion span, on the order of tens of micrometers, and the high proton mobility were both similar to the values previously reported for lipid bilayers. Extensive ab initio simulations on the same water?n-decane interface reproduced the experimentally derived free energy barrier for the excess proton. The free energy profile G H+ adopts the shape of a well at the interface, having a width of two water molecules and a depth of 6 ± 2RT. The hydroniums in direct contact with n-decane have a reduced mobility. However, the hydroniums in the second layer of water molecules are mobile. Their in silico diffusion coefficient matches that derived from our in vitro experiments, (5.7 ± 0.7) × 10 -5 cm 2 s -1. Conceivably, these are the protons that allow for fast diffusion along biological membranes.

Ramasamy K.,University of Alabama | Ramasamy K.,Los Alamos National Laboratory | Sims H.,University of Alabama | Sims H.,German Research School for Simulation Science | And 2 more authors.
Chemistry of Materials | Year: 2014

A wide variety of copper-based semiconducting chalcogenides have been investigated in recent years to address the need for sustainable solar cell materials. An attractive class of materials consisting of nontoxic and earth abundant elements is the copper-antimony-sulfides. The copper-antimony-sulfide system consists of four major phases, namely, CuSbS2 (Chalcostibite), Cu12Sb4S13 (Tetrahedrite), Cu 3SbS3 (Skinnerite), and Cu3SbS4 (Fematinite). All four phases are p-type semiconductors having energy band gaps between 0.5 and 2 eV, with reported large absorption coefficient values over 105 cm-1. We have for the first time developed facile colloidal hot-injection methods for the phase-pure synthesis of nanocrystals of all four phases. Cu12Sb4S13 and Cu 3SbS3 are found to have direct band gaps (1.6 and 1.4 eV, respectively), while the other two phases display indirect band gaps (1.1 and 1.2 eV for CuSbS2 and Cu3SbS4, respectively). The synthesis methods yield nanocrystals with distinct morphology for the different phases. CuSbS2 is synthesized as nanoplates, and Cu 12Sb4S13 is isolated as hollow structures, while uniform spherical Cu3SbS3 and oblate spheroid nanocrystals of Cu3SbS4 are obtained. In order to understand the optical and electrical properties, we have calculated the electronic structures of all four phases using the hybrid functional method (HSE 06) and PBE generalized gradient approximation to density functional theory. Consistent with experimental results, the calculations indicate that CuSbS 2 and Cu3SbS4 are indirect band gap materials but with somewhat higher band gap values of 1.6 and 2.5 eV, respectively. Similarly, Cu3SbS3 is determined to be a direct band gap material with a gap of 1.5 eV. Interestingly, both PBE and HSE06 methods predict metallic behavior in fully stoichiometric Cu12Sb4S 13 phase, with opening up of bands leading to semiconducting or insulating behavior for off-stoichiometric compositions with a varying number of valence electrons. The absorption coefficient values at visible wavelengths for all the phases are estimated to range between 104 and 105 cm-1, confirming their potential for solar energy conversion applications. © 2014 American Chemical Society.

Ramasamy K.,University of Alabama | Sims H.,University of Alabama | Sims H.,German Research School for Simulation Science | Butler W.H.,University of Alabama | Gupta A.,University of Alabama
Journal of the American Chemical Society | Year: 2014

Layered materials with controlled thickness down to monolayer are being intensively investigated for unraveling and harnessing their dimension-dependent properties. Copper antimony sulfide (CuSbS2) is a ternary layered semiconductor material that has been considered as an absorber material in thin film solar cells due to its optimal band gap (∼1.5 eV) with high absorption coefficient of over >104 cm-1. We have for the first time developed solution-based approaches for the synthesis of mono-, few-, and multiple layers of CuSbS2. These include a colloidal bottom-up approach for the synthesis of CuSbS2 nanoplates with thicknesses from six layers to several layers, and a hybrid bottom-up-top-down approach for the formation of CuSbS2 mesobelts. The latter can be exfoliated by Li-ion intercalation and sonication to obtain layers down to monolayer thickness. Time-dependent TEM studies provide important insights into the growth mechanism of mesobelts. At the initial stage the nanoplates grow laterally to form nanosheets as the primary structure, followed by their folding and attachment through homoepitaxy to form prolate-like secondary structures. Eventually, these prolate-like structures form mesocrystals by oriented attachment crystal growth. The changes in optical properties with layer thickness down to monolayers have been studied. In order to understand the thickness-dependent optical and electrical properties, we have calculated the electronic structures of mono- and multiple layers (bulk) of CuSbS2 using the hybrid functional method (HSE 06). We find that the monolayers exhibit noticeably different properties from the multilayered or the bulk system, with a markedly increased band gap that is, however, compromised by the presence of localized surface states. These localized states are predominantly composed of energetically favorable Sb pz states, which break off from the rest of the Sb p states that would otherwise be at the top of the gap. The developed solution-based synthesis approaches are versatile and can likely be extended to other complex layered sulfides. © 2014 American Chemical Society.

Finnerty J.J.,German Research School for Simulation science | Eisenberg R.,Rush University | Carloni P.,German Research School for Simulation science | Carloni P.,Jülich Research Center
Journal of Chemical Theory and Computation | Year: 2013

The simplified coarse grained models of selectivity of Nonner and co-workers predict ion selectivity for a variety of different ion channels. The model includes the charged atoms of the channel's charged residues and permeant ions. However its MC implementation does not take advantage of the increasingly large body of structural information available. Here, we introduce the location of the channel's charged residues into the model's Hamiltonian. In the DEKA Na+ channel, this allows us to correlate the lysine's topological location directly with the predicted selectivity. In the NanC channel, from Escherichia coli, the dramatic variation in the resulting ion population predicts novel selectivity regions and binding sites that can be directly correlated with structural information. These results have well-defined thermodynamic properties that are significantly modified by structural detail allowing new insights with molecular detail. © 2012 American Chemical Society.

Do T.N.,International School for Advanced Studies | Carloni P.,German Research School for Simulation science | Carloni P.,Jülich Research Center | Varani G.,University of Washington | Bussi G.,International School for Advanced Studies
Journal of Chemical Theory and Computation | Year: 2013

RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking methods are insufficient. We here present a computational method which allows studying the binding of RNA molecules and charged peptides with atomistic, explicit-solvent molecular dynamics. In our method, a suitable estimate of the electrostatic interaction is used as an order parameter (collective variable) which is then accelerated using bidirectional pulling simulations. Since the electrostatic interaction is only used to enhance the sampling, the approximations used to compute it do not affect the final accuracy. The method is employed to characterize the binding of TAR RNA from HIV-1 and a small cyclic peptide. Our simulation protocol allows blindly predicting the binding pocket and pose as well as the binding affinity. The method is general and could be applied to study other electrostatics-driven binding events. © 2013 American Chemical Society.

Zhang W.,RWTH Aachen | Thiess A.,Jülich Research Center | Thiess A.,German Research School for Simulation science | Zalden P.,RWTH Aachen | And 7 more authors.
Nature Materials | Year: 2012

The study of metal-insulator transitions (MITs) in crystalline solids is a subject of paramount importance, both from the fundamental point of view and for its relevance to the transport properties of materials. Recently, a MIT governed by disorder was observed in crystalline phase-change materials. Here we report on calculations employing density functional theory, which identify the microscopic mechanism that localizes the wavefunctions and is driving this transition. We show that, in the insulating phase, the electronic states responsible for charge transport are localized inside regions having large vacancy concentrations. The transition to the metallic state is driven by the dissolution of these vacancy clusters and the formation of ordered vacancy layers. These results provide important insights on controlling the wavefunction localization, which should help to develop conceptually new devices based on multiple resistance states. © 2012 Macmillan Publishers Limited. All rights reserved.

Karakatsanis L.P.,Democritus University of Thrace | Pavlos G.P.,Democritus University of Thrace | Xenakis M.N.,German Research School for Simulation science
Physica A: Statistical Mechanics and its Applications | Year: 2013

In this study which is the continuation of the first part (Pavlos et al. 2012) [1], the nonlinear analysis of the solar flares index is embedded in the non-extensive statistical theory of Tsallis (1988) [3]. The q-triplet of Tsallis, as well as the correlation dimension and the Lyapunov exponent spectrum were estimated for the singular value decomposition (SVD) components of the solar flares timeseries. Also the multifractal scaling exponent spectrum f(a), the generalized Renyi dimension spectrum D(q) and the spectrum J(p) of the structure function exponents were estimated experimentally and theoretically by using theq-entropy principle included in Tsallis non-extensive statistical theory, following Arimitsu and Arimitsu (2000) [25]. Our analysis showed clearly the following: (a) a phase transition process in the solar flare dynamics from a high dimensional non-Gaussian self-organized critical (SOC) state to a low dimensional also non-Gaussian chaotic state, (b) strong intermittent solar corona turbulence and an anomalous (multifractal) diffusion solar corona process, which is strengthened as the solar corona dynamics makes a phase transition to low dimensional chaos, (c) faithful agreement of Tsallis non-equilibrium statistical theory with the experimental estimations of the functions: (i) non-Gaussian probability distribution function P(x), (ii) f(a) and D(q), and (iii) J(p) for the solar flares timeseries and its underlying non-equilibrium solar dynamics, and (d) the solar flare dynamical profile is revealed similar to the dynamical profile of the solar corona zone as far as the phase transition process from self-organized criticality (SOC) to chaos state. However the solar low corona (solar flare) dynamical characteristics can be clearly discriminated from the dynamical characteristics of the solar convection zone. © 2013 Elsevier B.V. All rights reserved.

Flesch A.,Jülich Research Center | Zhang G.,Jülich Research Center | Koch E.,German Research School for Simulation science | Pavarini E.,Jülich Research Center
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

We study the mechanism of orbital-order melting observed at temperature T OO in the series of rare-earth manganites. We find that the purely electronic many-body super-exchange mechanism yields a transition temperature T KK that decreases with decreasing rare-earth radius and increases with pressure, opposite to the experimental T OO. We show that the tetragonal crystal-field splitting reduces T KK further increasing the discrepancies with experiments. This proves that super-exchange effects, although very efficient, in the light of experimentally observed trends play a minor role for the melting of orbital ordering in rare-earth manganites. © 2012 American Physical Society.

Zhang G.,Jülich Research Center | Gorelov E.,Jülich Research Center | Koch E.,German Research School for Simulation science | Pavarini E.,Jülich Research Center
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

Spin-state transitions are the hallmark of rare-earth cobaltates. In order to understand them, it is essential to identify all relevant parameters which shift the energy balance between spin states and determine their trends. We find that Δ, the eg-t2g crystal-field splitting, increases by ∼250 meV when increasing pressure to 8 GPa and by about 150 meV when cooling from 1000 K to 5 K. It changes, however, by less than 100 meV when La is substituted with another rare earth. Moreover, the Hund's rule coupling Javg is about the same in systems with very different spin-state transition temperature, like LaCoO3 and EuCoO3. Consequently, in addition to Δ and Javg, the Coulomb-exchange anisotropy δJavg and the superexchange energy gain δESE play a crucial role and are comparable with spin-state-dependent relaxation effects due to covalency. We show that in the LnCoO3 series, with Ln=Y or another rare earth (RE), superexchange progressively stabilizes a low-spin ground state as the Ln3+ ionic radius decreases. We give a simple model to describe spin-state transitions and show that, at low temperature, the formation of isolated high-spin/low-spin pairs is favored, while in the high-temperature phase, the most likely homogeneous state is high spin rather than intermediate spin. An orbital-selective Mott state could be a fingerprint of such a state. © 2012 American Physical Society.

Peyser A.,University of Miami | Peyser A.,German Research School for Simulation science | Nonner W.,University of Miami
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2012

Electrical signaling via voltage-gated ion channels depends upon the function of a voltage sensor (VS), identified with the S1-S4 domain in voltage-gated K + channels. Here we investigate some energetic aspects of the sliding-helix model of the VS using simulations based on VS charges, linear dielectrics, and whole-body motion. Model electrostatics in voltage-clamped boundary conditions are solved using a boundary element method. The statistical mechanical consequences of the electrostatic configurational energy are computed to gain insight into the sliding-helix mechanism and to predict experimentally measured ensemble properties such as gating charge displaced by an applied voltage. Those consequences and ensemble properties are investigated for two alternate S4 configurations, α and 3 10 helical. Both forms of VS are found to have an inherent electrostatic stability. Maximal charge displacement is limited by geometry, specifically the range of movement where S4 charges and countercharges overlap in the region of weak dielectric. Charge displacement responds more steeply to voltage in the α-helical than in the 3 10-helical sensor. This difference is due to differences on the order of 0.1 eV in the landscapes of electrostatic energy. As a step toward integrating these VS models into a full-channel model, we include a hypothetical external load in the Hamiltonian of the system and analyze the energetic input-output relation of the VS. © 2012 American Physical Society.

Loading German Research School for Simulation science collaborators
Loading German Research School for Simulation science collaborators