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.

Fast parallel algorithms for short-range molecular dynamics

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。

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

2.2. Fenton’s Chemistry 6575 2.2.1. Origins 6575 2.2.2. Fenton Process 6575 2.3. Photo-Fenton Process 6577 3. H2O2 Electrogeneration for Water Treatment 6577 3.1. Fundamentals 6578 3.2. Cathode Materials 6579 3.3. Divided Cells 6580 3.4. Undivided Cells 6583 4. Electro-Fenton (EF) Process 6585 4.1. Origins 6585 4.2. Fundamentals of EF for Water Remediation 6586 4.2.1. Cell Configuration 6586 4.2.2. Cathodic Fe2+ Regeneration 6586 4.2.3. Anodic Generation of Heterogeneous Hydroxyl Radical 6587

Electro-Fenton process and related electrochemical technologies based on Fenton's reaction chemistry

We present a method for determining the free-energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the physically relevant regions of the order parameter space. The algorithm is tested on the reconstruction of an alanine dipeptide free-energy landscape.

Well-tempered metadynamics: a smoothly converging and tunable free-energy method.

Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.

QM/MM Methods for Biomolecular Systems

The metadynamics or hills method is a relatively new molecular dynamics technique aimed to enhance the sampling of separated regions in phase space and map out the underlying free energy landscape as a function of a small number of order parameters or collective variables. The high efficiency allows for the application of metadynamics in combination with first principles dynamics methods, in particular with Car−Parrinello molecular dynamics, to study processes in which changes in the electronic structure play a dominant role, such as chemical reactions. The option to choose several independent collective variables is important to tackle complex and concerted transformations that lack an obvious a priori choice for a single reaction coordinate. In this Account, we discuss the role of metadynamics in the search of transition states, local minima, reaction paths, free energy profiles, and reaction coordinates among a growing list of alternative methods.

Metadynamics as a tool for exploring free energy landscapes of chemical reactions.

The recently introduced hills method (Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562) is a powerful tool to compute the multidimensional free energy surface of intrinsically concerted reactions. We have extended this method by focusing our attention on localizing the lowest free energy path that connects the stable reactant and product states. This path represents the most probable reaction mechanism, similar to the zero temperature intrinsic reaction coordinate, but also includes finite temperature effects. The transformation of the multidimensional problem to a one-dimensional reaction coordinate allows for accurate convergence of the free energy profile along the lowest free energy path using standard free energy methods. Here we apply the hills method, our lowest free energy path search algorithm, and umbrella sampling to the prototype S(N)2 reaction. The hills method replaces the in many cases difficult problem of finding a good reaction coordinate with choosing relatively simple collective variables, such as the bond lengths of the broken and formed chemical bonds. The second part of the paper presents a guide to using the hills method, in which we test and fine-tune the method for optimal accuracy and efficiency using the umbrella sampling results as a reference.

A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions.

The formation of active intermediates from the Fenton-like reagent (a mixture of iron(III) ions and hydrogen peroxide) in aqueous solution has been investigated using static DFT calculations and Car−Parrinello molecular dynamics simulations. We show the spontaneous formation of the iron(III) hydroperoxo intermediate in a first step. The Fenton-like reaction thus proceeds very differently compared to Fenton's reagent (i.e., the FeII/H2O2 mixture), for which we have recently shown that the first step is the spontaneous O−O lysis of hydrogen peroxide when coordinated to iron(II) in water. For the second step in the reaction mechanism of the Fenton-like reagent, we compare the possibilities of homolysis and heterolysis of the O−O bond and the Fe−O bond of the produced [(H2O)5FeIIIOOH]2+ intermediate. We find that concomitant hydrolysis of the reacting species plays a crucial role and, taking this into account, that O−O homolysis ([(H2O)4(OH)FeIIIOOH]+ → [(H2O)4(OH)FeIVO]+ + OH•) in vacuo is a likely second st...

Fenton-like Chemistry in Water: Oxidation Catalysis by Fe(III) and H2O2

Multiscale computer simulation algorithms are required to describe complex molecular systems with events occurring over a range of time and length scales. True multiscale simulations must solve the interface, or hand-shaking, problem of coupling together different levels of description in different spatial regions of the system. If the spatial regions of different resolution move over time, or if material is allowed to flow over the inter-region boundaries, a mechanism must be introduced into the multiscale algorithm to allow material to dynamically change its representation. While such a mechanism is highly desirable in many instances, it is fraught with technical difficulties. Here, we present a molecular dynamics simulation algorithm which is multiscale in both time and space. We supplement the potential and kinetic energy expressions with auxiliary terms in order to recover the total energy as a conserved quantity, even when the total number of degrees of freedom changes during the simulation. This is crucial for a proper assessment of the quality of adaptive hybrid algorithms, and in particular, it allows us to tune the hierarchy of RESPA levels to optimize the integration scheme.

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Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics

Kohn−Sham solutions are constructed from ab initio densities obtained with multireference configuration interaction (MRCI) calculations for the transition state (TS) and for the intermediate comple...

Bernd Ensing

Papers

Metadynamics as a tool for exploring free energy landscapes of chemical reactions.

A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions.

Fenton-like Chemistry in Water: Oxidation Catalysis by Fe(III) and H2O2

Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics

Comparison of the accurate Kohn-Sham solution with the generalized gradient approximations