A5037695758- Spectroscopy and Quantum Chemical Studies
- Protein Structure and Dynamics
- Advanced Chemical Physics Studies
- Photoreceptor and optogenetics research
- Advanced NMR Techniques and Applications
- Quantum, superfluid, helium dynamics
- Photosynthetic Processes and Mechanisms
- Molecular spectroscopy and chirality
- Computational Drug Discovery Methods
- Linguistics, Language Diversity, and Identity
- Advanced Data Storage Technologies
- DNA and Nucleic Acid Chemistry
- Natural Language Processing Techniques
- Lexicography and Language Studies
- Lattice Boltzmann Simulation Studies
- Scientific Computing and Data Management
- Photochemistry and Electron Transfer Studies
- Bioinformatics and Genomic Networks
- Parallel Computing and Optimization Techniques
- Linguistic research and analysis
- Distributed and Parallel Computing Systems
- Neuroscience and Neuropharmacology Research
- Electrostatics and Colloid Interactions
- Language, Metaphor, and Cognition
- Japanese History and Culture
Bavarian Academy of Sciences and Humanities
2020-2023
Leibniz Supercomputing Centre
2020-2023
Ludwig-Maximilians-Universität München
2004-2016
Ruhr University Bochum
2004-2012
University of Freiburg
2003
Weizmann Institute of Science
2003
University of Hawaii System
1982
Solvation of molecules in water is at the heart a myriad molecular phenomena and crucial importance to understanding such diverse issues as chemical reactivity or biomolecular function. Complementing well-established approaches, it has been shown that laser spectroscopy THz frequency domain offers new insights into hydration from small solutes proteins. Upon introducing spatially-resolved analyses absorption cross section by simulations, sensitivity traced back characteristic...
Due to the progress of density functional theory (DFT) accurate computations vibrational spectra isolated molecules have become a standard task in computational chemistry. This is not yet case for solution spectra. To contribute exploration corresponding procedures, here we suggest more efficient variant so-called instantaneous normal-mode analysis (INMA). applies conventional molecular dynamics (MD) simulations, which are based on nonpolarizable mechanics (MM) force fields, rapid generation...
Networks of internal water molecules are thought to provide proton transfer pathways in many enzymatic and photosynthetic reactions. Extremely broad absorption continua observed recent IR spectroscopic measurements on the photodriven pump bacteriorhodopsin (BR) suggest such networks may also serve as storage release sites for these By combining electronic structure calculations with molecular mechanical force fields, we examine dynamics resulting spectra two protonated networks, H + ·(H 2 O)...
The race to meet the challenges of global pandemic has served as a reminder that existing drug discovery process is expensive, inefficient and slow. There major bottleneck screening vast number potential small molecules shortlist lead compounds for antiviral development. New opportunities accelerate lie at interface between machine learning methods, in this case, developed linear accelerators, physics-based methods. two
We present a combination of the structure adapted multipole method with reaction field (RF) correction for efficient evaluation electrostatic interactions in molecular dynamics simulations under periodic boundary conditions. The algorithm switches from an explicit electrostatics to continuum description at maximal distance that is consistent minimum image convention, and, thus, avoids use potential. A physically motivated switching function enables charge clusters interacting given smoothly...
Introduction: What is language planning?, policy? How Japanese written History of policy in Japan Language formulation today Underlying imperatives Which script? Some perspectives on The major arguments. Historical background to government action National Research Council kana problem A temporary hiatus Interim Council. Kokutai and kotodama Domestic frustrations External policies Taiwan Korea China southeast Asia. Democracy script early reforms: characters kanazukai reorganized Reforms the...
The computation of vibrational spectra via molecular dynamics (MD) simulations has made lively progress in recent years. In particular, infrared are accessible employing ab initio MD, for which only the total dipole moment to be computed "on fly" from electronic structure along trajectory. analysis such terms normal modes intramolecular motion, however, still poses a challenge theory. Here, we present an algorithm extract MD trajectories by combining several ideas available literature....
The computation of vibrational spectra complex molecules from time correlation functions generated by ab initio molecular dynamics simulations has made lively progress in recent years. However, the analysis such spectra, i.e., assignment bands to atomic motions, is no means straightforward. In a article [J. Chem. Theory Comput.2011, 7, 2028–2039], Mathias and Baer presented corresponding method that derives generalized normal coordinates (GNCs) trajectories, which furnish band positions,...
The accurate description of vibrational spectra isolated dye molecules such as quinones has become a standard task in computational chemistry due to the progress density functional theory. This is by no means case for solution spectra. To contribute this issue, we have carried out QM/MM hybrid molecular dynamics (MD) simulation p-benzoquinone water, so derive its IR We explored two different procedures that allow calculation an spectrum from simulation. One based on Fourier transforms...
We have carried out "first-principles" Born–Oppenheimer molecular dynamics (BOMD) simulations of the phosphate ions H2PO4– and HPO42– in liquid water calculated their IR spectra by Fourier transform techniques from trajectories. bands were assigned a so-called "generalized normal coordinate analysis". The effects including Hartree–Fock (HF) exchange into density functional theory (DFT) computation forces studied comparing results obtained with well-known BP, BLYP, B3LYP functionals. neglect...
The combination of vibrational spectroscopy and molecular dynamics simulations provides a powerful tool to obtain insights into the details water structure in bulk aqueous solutions. Applying newly developed approaches analyze correlations charge currents, dipole fluctuations, motion real k-space, we compare results from nonpolarizable models, widely used biomolecular modeling, ab initio dynamics. For first time, unfold infrared response contributions correlated fluctuations...
The drug discovery process currently employed in the pharmaceutical industry typically requires about 10 years and $2–3 billion to deliver one new drug. This is both too expensive slow, especially emergencies like COVID-19 pandemic. In silico methodologies need be improved select better lead compounds, so as improve efficiency of later stages protocol, identify those compounds more quickly. No known methodological approach can this combination higher quality speed. Here, we describe an...
Water clusters revisited: The vibrational predissociation spectra of microsolvated Zundel cations has been an experimental and theoretical puzzle for more than two decades. Now it can be shown that the influence tagging with H2 understood in terms a superposition tightly bound weakly adduct species, which offers concise interpretation action spectra. Detailed facts importance to specialist readers are published as "Supporting Information". Such documents peer-reviewed, but not copy-edited or...
Nucleoside triphosphate hydrolysis is an essential component of all living systems. Despite extensive research, the exact modus and mechanism this ubiquitous reaction still remain elusive. In work, we examined detailed mechanisms a model nucleoside in acidic neutral solution by means ab initio simulations. The timescale was accessed through use accelerated sampling method, metadynamics. Both hydrolyses were found to proceed via different mechanisms; system reacted concerted general acid...
A class of photoreceptors occurring in various organisms consists domains that are blue light sensing using flavin (BLUF). The vibrational spectra the chromophore spectroscopically well characterized for dark-adapted resting states and light-adapted signaling BLUF solution. Here we present a theoretical analysis such by applying density functional theory (DFT) to embedded molecular mechanics (MM) models its protein solvent environment. By DFT/MM calculate seven different X-ray NMR structures...
Hybrid molecular dynamics (MD) simulations, in which the forces acting on atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and polarizable mechanics (PMM) force field large solvent environment composed of several 103–105 molecules, pose challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions electron at interface between DFT PMM fragments, treat long-range electrostatic interactions within...
Light-induced isomerization of rhodopsin's retinal chromophore to the activating all-trans geometry initializes formation active receptor state, Meta II. In absence peripheral regulatory proteins, activity II is switched off spontaneously by two independent pathways: either hydrolysis Schiff base and dissociation light into apoprotein opsin plus free or III, an inactive species with intact protonated absorbing at 470 nm. By FTIR spectroscopy on rhodopsin reconstituted isotopically labeled...
The structures of the ubiquinones QA and QB in bacterial photosynthetic reaction center Rhodobacter sphaeroides are calculated by a quantum mechanical/molecular mechanics hybrid technique. orientations their methoxy groups found to differ less than 30°. Calculation vibrational spectra reveals that one CO stretching mode is considerably shifted lower frequencies agreement with experimental data. orientational differences at too small as provide an explanation for this shift. Instead, it must...
The functional reactions in blue light photoreceptors generally involve transiently reduced flavins exhibiting characteristic infrared (IR) spectra. To approach a theoretical understanding, here we apply density theory (DFT) to flavin radicals embedded molecular mechanics (MM) model of an aqueous solution. Combining DFT/MM with instantaneous normal-mode analyses (INMA), compute the IR solution spectra anionic and neutral radicals. For set mid-IR marker bands, identify those changes spectral...
We investigate the dipolar correlations in liquid water at angular resolution by molecular-dynamics simulations of a large periodic simulation system containing about 40,000 molecules. Because we are particularly interested long-range ordering, use simple three-point model for these The electrostatics is treated both Ewald summation and minimum image truncation combined with reaction field approach. To gain insight into dependence simulated ordering introduce suitable expansion molecular...