Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 9 de 9
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
Sci Rep ; 9(1): 12424, 2019 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-31455833

RESUMO

Recent progress in the improvement of organic solar cells lead to a power conversion efficiency to over 16%. One of the key factors for this improvement is a more favorable energy level alignment between donor and acceptor materials, which demonstrates that the properties of interfaces between donor and acceptor regions are of paramount importance. Recent investigations showed a significant dependence of the energy levels of organic semiconductors upon admixture of different materials, but its origin is presently not well understood. Here, we use multiscale simulation protocols to investigate the molecular origin of the mixing induced energy level shifts and show that electrostatic properties, in particular higher-order multipole moments and polarizability determine the strength of the effect. The findings of this study may guide future material-design efforts in order to improve device performance by systematic modification of molecular properties.

2.
J Phys Condens Matter ; 27(13): 134202, 2015 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-25767089

RESUMO

A recently developed methodology to simulate photoinduced electron transfer processes at dye-semiconductor interfaces is outlined. The methodology employs a first-principles-based model Hamiltonian and accurate quantum dynamics simulations using the multilayer multiconfiguration time-dependent Hartree approach. This method is applied to study electron injection in the dye-semiconductor system coumarin 343-TiO2. Specifically, the influence of electronic-vibrational coupling is analyzed. Extending previous work, we consider the influence of Dushinsky rotation of the normal modes as well as anharmonicities of the potential energy surfaces on the electron transfer dynamics.

3.
BMC Bioinformatics ; 15: 292, 2014 Aug 29.
Artigo em Inglês | MEDLINE | ID: mdl-25176255

RESUMO

BACKGROUND: Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face several challenges: the fastest atomic movements require time steps of a few femtoseconds which are small compared to biomolecular relevant timescales of milliseconds or even seconds for large conformational motions. At the same time, scalability to a large number of cores is limited mostly due to long-range interactions. An appealing alternative to atomic-level simulations is coarse-graining the resolution of the system or reducing the complexity of the Hamiltonian to improve sampling while decreasing computational costs. Native structure-based models, also called Go-type models, are based on energy landscape theory and the principle of minimal frustration. They have been tremendously successful in explaining fundamental questions of, e.g., protein folding, RNA folding or protein function. At the same time, they are computationally sufficiently inexpensive to run complex simulations on smaller computing systems or even commodity hardware. Still, their setup and evaluation is quite complex even though sophisticated software packages support their realization. RESULTS: Here, we establish an efficient infrastructure for native structure-based models to support the community and enable high-throughput simulations on remote computing resources via GridBeans and UNICORE middleware. This infrastructure organizes the setup of such simulations resulting in increased comparability of simulation results. At the same time, complete workflows for advanced simulation protocols can be established and managed on remote resources by a graphical interface which increases reusability of protocols and additionally lowers the entry barrier into such simulations for, e.g., experimental scientists who want to compare their results against simulations. We demonstrate the power of this approach by illustrating it for protein folding simulations for a range of proteins. CONCLUSIONS: We present software enhancing the entire workflow for native structure-based simulations including exception-handling and evaluations. Extending the capability and improving the accessibility of existing simulation packages the software goes beyond the state of the art in the domain of biomolecular simulations. Thus we expect that it will stimulate more individuals from the community to employ more confidently modeling in their research.


Assuntos
Simulação de Dinâmica Molecular , Proteínas/química , Software , Gráficos por Computador , Dobramento de Proteína , Interface Usuário-Computador
4.
Stud Health Technol Inform ; 175: 162-72, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22942007

RESUMO

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cß chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.


Assuntos
Disciplinas das Ciências Biológicas , Armazenamento e Recuperação da Informação/métodos , Internet , Modelos Químicos , Modelos Moleculares , Software , Interface Usuário-Computador , Simulação por Computador , Pesquisa sobre Serviços de Saúde/métodos , Disseminação de Informação/métodos , Fluxo de Trabalho
5.
Comput Biol Chem ; 35(4): 230-9, 2011 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-21864792

RESUMO

The presence of disulfide bonds in proteins has very important implications on the three-dimensional structure and folding of proteins. An adequate treatment of disulfide bonds in de-novo protein simulations is therefore very important. Here we present a computational study of a set of small disulfide-bridged proteins using an all-atom stochastic search approach and including various constraining potentials to describe the disulfide bonds. The proposed potentials can easily be implemented in any code based on all-atom force fields and employed in simulations to achieve an improved prediction of protein structure. Exploring different potential parameters and comparing the structures to those from unconstrained simulations and to experimental structures by means of a scoring function we demonstrate that the inclusion of constraining potentials improves the quality of final structures significantly. For some proteins (1KVG and 1PG1) the native conformation is visited only in simulations in presence of constraints. Overall, we found that the Morse potential has optimal performance, in particular for the ß-sheet proteins.


Assuntos
Dissulfetos/química , Proteínas/química , Animais , Simulação por Computador , Modelos Moleculares , Estrutura Secundária de Proteína , Termodinâmica
6.
Biochemistry ; 48(34): 8195-205, 2009 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-19610617

RESUMO

The presence of disulfide bonds leads to an interesting interplay between noncovalent intramolecular interactions and disulfide bond formation even in small proteins. Here we have investigated the folding mechanism of the 23-residue potassium channel blocker 1WQE and the 18-residue antimicrobial peptide protegrin-1 1PG1 , as two proteins containing disulfide bridges, in all-atom basin hopping simulations starting from completely extended conformations. The minimal-energy conformations deviate by only 2.1 and 1.2 A for 1WQE and 1PG1 , respectively, from their structurally conserved experimental conformations. A detailed analysis of their free energy surfaces demonstrates that the folding mechanism of disulfide-bridged proteins can vary dramatically from Levinthal's single-path scenario to a cooperative process consistent with the funnel paradigm of protein folding.


Assuntos
Peptídeos Catiônicos Antimicrobianos/química , Dissulfetos , Modelos Moleculares , Bloqueadores dos Canais de Potássio/química , Dobramento de Proteína , Sequência de Aminoácidos , Peptídeos Catiônicos Antimicrobianos/metabolismo , Dados de Sequência Molecular , Oxirredução , Bloqueadores dos Canais de Potássio/metabolismo , Probabilidade , Estrutura Secundária de Proteína , Termodinâmica , Fatores de Tempo
7.
J Phys Chem A ; 112(24): 5467-77, 2008 Jun 19.
Artigo em Inglês | MEDLINE | ID: mdl-18491878

RESUMO

A computational study of the ground- and excited-state properties of the mixed-valence complex [(NH 3) 5Ru (III)NCRu (II)(CN) 5] (-) is presented. Employing DFT and TDDFT calculations for the complex in the gas phase and in aqueous solution, we investigate the vibrational and electronic structure of the complex in the electronic ground state as well as the character of the electronically excited states. The relevance of the various excited states for the intervalence metal-metal charge-transfer process in the complex is analyzed based on the change of charge density, spin density, and dipole moment upon photoexcitation as well as by a Mulliken-Hush analysis. Furthermore, those intramolecular modes, which are important for the charge-transfer process, are identified and characterized.

8.
J Phys Chem A ; 110(4): 1364-74, 2006 Feb 02.
Artigo em Inglês | MEDLINE | ID: mdl-16435796

RESUMO

A theoretical study of photoinduced heterogeneous electron transfer in the dye-semiconductor system coumarin 343-TiO(2) is presented. The study is based on a generic model for heterogeneous electron transfer reactions, which takes into account the coupling of the electronic states to the nuclear degrees of freedom of coumarin 343 as well as to the surrounding solvent. The quantum dynamics of the electron injection process is simulated employing the recently proposed multilayer formulation of the multiconfiguration time-dependent Hartree method. The results reveal an ultrafast injection dynamics of the electron from the photoexcited donor state into the conduction band of the semiconductor. Furthermore, the mutual influence of electronic injection dynamics and nuclear motion is analyzed in some detail. The analysis shows that--depending on the time scale of nuclear motion--electronic vibrational coupling can result in electron transfer driven by coherent vibrational motion or vibrational motion induced by ultrafast electron transfer.

9.
Phys Rev E Stat Nonlin Soft Matter Phys ; 66(3 Pt 2B): 037701, 2002 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-12366307

RESUMO

A method for stochastic unraveling of general time-local quantum master equations (QME) which involve the reduced density operator at time t only is proposed. The present kind of jump algorithm enables a numerically efficient treatment of QMEs that are not of Lindblad form. So it opens large fields of application for stochastic methods. The unraveling can be achieved by allowing for trajectories with negative weight. We present results for the quantum Brownian motion and the Redfield QMEs as test examples. The algorithm can also unravel non-Markovian QMEs when they are in a time-local form like in the time-convolutionless formalism.

SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA