Dominik Marx

Bio: Dominik Marx is an academic researcher from Ruhr University Bochum. The author has contributed to research in topics: Solvation & Ab initio. The author has an hindex of 54, co-authored 257 publications receiving 11488 citations.

Proton transfer 200 years after von Grotthuss: insights from ab initio simulations.

Abstract: In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.

Density-functional study of the structure and stability of ZnO surfaces

Abstract: An extensive theoretical investigation of the nonpolar $(101\ifmmode\bar\else\textasciimacron\fi{}0)$ and $(112\ifmmode\bar\else\textasciimacron\fi{}0)$ surfaces as well as the polar zinc-terminated (0001)-Zn and oxygen-terminated $(0001\ifmmode\bar\else\textasciimacron\fi{})$-O surfaces of ZnO is presented. Particular attention is given to the convergence properties of various parameters such as basis set, k-point mesh, slab thickness, or relaxation constraints within local-density and generalized-gradient approximation pseudopotential calculations using both plane-wave and mixed-basis sets. The pros and cons of different approaches to deal with the stability problem of the polar surfaces are discussed. Reliable results for the structural relaxations and the energetics of these surfaces are presented and compared to previous theoretical and experimental data, which are also concisely reviewed and commented.

Aqueous Basic Solutions: Hydroxide Solvation, Structural Diffusion, and Comparison to the Hydrated Proton

Abstract: Many hydrogen-bonded liquids, molecular solids, and lowdimensional systems support anomalous diffusion mechanisms of topological charge defects created by the addition or removal of protons. The most familiar examples are the “classic” cases of aqueous acidic and basic solutions,1 where the defects appear in the form of hydrated hydronium (H3O) and hydroxide (OH-) ions, denoted as H+(aq) and OH-(aq), respectively.2 While anomalous charge migration has important consequences in chemical,1,3,4 biological,5-8 and technological9,10 applications, Vide infra, providing a molecular-level, mechanistic understanding of the fascinating physical principles underlying the charge transport process is a challenging, yet fundamental, problem in physical chemistry.11

Dissecting the THz spectrum of liquid water from first principles via correlations in time and space.

Abstract: Solvation of molecules in water is at the heart of a myriad of molecular phenomena and of crucial importance to understanding such diverse issues as chemical reactivity or biomolecular function. Complementing well-established approaches, it has been shown that laser spectroscopy in the THz frequency domain offers new insights into hydration from small solutes to proteins. Upon introducing spatially-resolved analyses of the absorption cross section by simulations, the sensitivity of THz spectroscopy is traced back to characteristic distance-dependent modulations of absorption intensities for bulk water. The prominent peak at ≈200 cm-1 is dominated by first-shell dynamics, whereas a concerted motion involving the second solvation shell contributes most significantly to the absorption at about 80 cm-1 ≈2.4 THz. The latter can be understood in terms of an umbrella-like motion of two hydrogen-bonded tetrahedra along the connecting hydrogen bond axis. Thus, a modification of the hydrogen bond network, e.g., due to the presence of a solute, is expected to affect vibrational motion and THz absorption intensity at least on a length scale that corresponds to two layers of solvating water molecules. This result provides a molecular mechanism explaining the experimentally determined sensitivity of absorption changes in the THz domain in terms of distinct, solute-induced dynamical properties in solvation shells of (bio)molecules—even in the absence of well-defined resonances.

Efficient and general algorithms for path integral Car–Parrinello molecular dynamics

Abstract: In path integral molecular dynamics, efficient sampling of the phase space is not guaranteed due to the stiff harmonic part of the action arising from the quantum kinetic energy. This problem has been eliminated by incorporating a sufficient number of thermostats into the dynamical scheme and by introducing a transformation of the path ‘‘bead’’ variables. In this paper, an efficient Car–Parrinello path integral molecular dynamics algorithm, sufficiently general to include the use of ultrasoft pseudopotentials is introduced. Difficulties encountered when combining thermostats and transformations of the Cartesian ‘‘bead’’ coordinates with the generalized orthonormality condition are circumvented by employing a constrained nonorthogonal orbital method.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Multiwfn: a multifunctional wavefunction analyzer.

Abstract: Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, in a line, in a plane or in a spatial scope. (2) Population analysis. (3) Bond order analysis. (4) Orbital composition analysis. (5) Plot density-of-states and spectrum. (6) Topology analysis for electron density. Some other useful utilities involved in quantum chemistry studies are also provided. The built-in graph module enables the results of wavefunction analysis to be plotted directly or exported to high-quality graphic file. The program interface is very user-friendly and suitable for both research and teaching purpose. The code of Multiwfn is substantially optimized and parallelized. Its efficiency is demonstrated to be significantly higher than related programs with the same functions. Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn. The program is free of charge and open-source. Its precompiled file and source codes are available from http://multiwfn.codeplex.com.

Understanding TiO2 photocatalysis: mechanisms and materials.

Abstract: Jenny Schneider,*,† Masaya Matsuoka,‡ Masato Takeuchi,‡ Jinlong Zhang, Yu Horiuchi,‡ Masakazu Anpo,‡ and Detlef W. Bahnemann*,† †Institut fur Technische Chemie, Leibniz Universitaẗ Hannover, Callinstrasse 3, D-30167 Hannover, Germany ‡Faculty of Engineering, Osaka Prefecture University, 1 Gakuen-cho, Sakai Osaka 599-8531, Japan Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237, China