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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

BACKGROUND With a rising global population, increasing energy demands, and impending climate change, major concerns have been raised over the security of our energy future. Developing sustainable, fossil-free pathways to produce fuels and chemicals of global importance could play a major role in reducing carbon dioxide emissions while providing the feedstocks needed to make the products we use on a daily basis. One prospective goal is to develop electrochemical conversion processes that can convert molecules in the atmosphere (e.g., water, carbon dioxide, and nitrogen) into higher-value products (e.g., hydrogen, hydrocarbons, oxygenates, and ammonia) by coupling to renewable energy. Electrocatalysts play a key role in these energy conversion technologies because they increase the rate, efficiency, and selectivity of the chemical transformations involved. Today’s electrocatalysts, however, are inadequate. The grand challenge is to develop advanced electrocatalysts with the enhanced performance needed to enable widespread penetration of clean energy technologies. ADVANCES Over the past decade, substantial progress has been made in understanding several key electrochemical transformations, particularly those that involve water, hydrogen, and oxygen. The combination of theoretical and experimental studies working in concert has proven to be a successful strategy in this respect, yielding a framework to understand catalytic trends that can ultimately provide rational guidance toward the development of improved catalysts. Catalyst design strategies that aim to increase the number of active sites and/or increase the intrinsic activity of each active site have been successfully developed. The field of hydrogen evolution, for example, has seen important breakthroughs over the years in the development of highly active non–precious metal catalysts in acid. Notable advancements have also been made in the design of oxygen reduction and evolution catalysts, although there remains substantial room for improvement. The combination of theory and experiment elucidates the remaining challenges in developing further improved catalysts, often involving scaling relations among reactive intermediates. This understanding serves as an initial platform to design strategies to circumvent technical obstacles, opening up opportunities and approaches to develop higher-performance electrocatalysts for a wide range of reactions. OUTLOOK A systematic framework of combining theory and experiment in electrocatalysis helps to uncover broader governing principles that can be used to understand a wide variety of electrochemical transformations. These principles can be applied to other emerging and promising clean energy reactions, including hydrogen peroxide production, carbon dioxide reduction, and nitrogen reduction, among others. Although current paradigms for catalyst development have been helpful to date, a number of challenges need to be successfully addressed in order to achieve major breakthroughs. One important frontier, for example, is the development of both experimental and computational methods that can rapidly elucidate reaction mechanisms on broad classes of materials and in a wide range of operating conditions (e.g., pH, solvent, electrolyte). Such efforts would build on current frameworks for understanding catalysis to provide the deeper insights needed to fine-tune catalyst properties in an optimal manner. The long-term goal is to continue improving the activity and selectivity of these catalysts in order to realize the prospects of using renewable energy to provide the fuels and chemicals that we need for a sustainable energy future.

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Combining theory and experiment in electrocatalysis: Insights into materials design

Nanocrystals are fundamental to modern science and technology. Mastery over the shape of a nanocrystal enables control of its properties and enhancement of its usefulness for a given application. Our aim is to present a comprehensive review of current research activities that center on the shape-controlled synthesis of metal nanocrystals. We begin with a brief introduction to nucleation and growth within the context of metal nanocrystal synthesis, followed by a discussion of the possible shapes that a metal nanocrystal might take under different conditions. We then focus on a variety of experimental parameters that have been explored to manipulate the nucleation and growth of metal nanocrystals in solution-phase syntheses in an effort to generate specific shapes. We then elaborate on these approaches by selecting examples in which there is already reasonable understanding for the observed shape control or at least the protocols have proven to be reproducible and controllable. Finally, we highlight a number of applications that have been enabled and/or enhanced by the shape-controlled synthesis of metal nanocrystals. We conclude this article with personal perspectives on the directions toward which future research in this field might take.

Shape‐Controlled Synthesis of Metal Nanocrystals: Simple Chemistry Meets Complex Physics?

Chemical reactions are the heart and soul of chemistry. They play an essential role in several fields including materials science, physics, and molecular sciences. A chemical reaction is the process of chemical change, in which one substance is converted into another by the reorganization of atoms (by bond breaking and bond making). The study of the mechanisms, behavior, and rates of chemical reactions is fundamental for understanding nature, life, and designing new or improved chemical processes. In this regard, the book Theories of Molecular Reaction Dynamics: The Microscopic Foundation of Chemical Kinetics provides an excellent discussion of chemical reactions by molecular reaction dynamics. The book Theories of Molecular Reaction Dynamics: The Microscopic Foundation of Chemical Kinetics, by Niels E. Henriksen and Flemming Y. Hansen, with its second edition published in 2019, discusses the foundations of molecular reaction dynamics. Molecular reaction dynamics, as stated by the authors, refer to the microscopic atomic-level description of chemical reactions, which is in contrast to the macroscopic approach known from chemical kinetics [1]. The goal of the book is to provide the readers with a better and deeper understanding of chemical reactions via a microscopic description. It represents a graduate-level introduction to the theme with attention to the basic concepts and a strong emphasis on the clarity of the presentation. It covers basic theories of reaction dynamics in the gas phase and theories of condensed-phase dynamics. The authors of the book, Niels E. Henriksen and Flemming Y. Hansen, are both from the Department of Chemistry at the Technical University of Denmark. Prof. Henriksen’s current interests in research are in the field of femtochemistry, i.e., the detection and control of atomic motion on the femtosecond timescale. To that end, his group studies, in particular, the

Theories of molecular reaction dynamics: the microscopic foundation of chemical kinetics

Tandem reactions consist of a sequence of two or more distinct transformations that can be achieved in a single synthetic step. A new article by Sun and colleagues demonstrates how the catalytic properties of bimetallic nanoparticles can be rationally optimized to enable the one-pot synthesis of polybenzoxazole (PBO).

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Rational Design of Bimetallic Nanocatalysts for Tandem Transformations

We report herein the synthesis of Pd nanostructures ~64–95-nm range in size displaying controlled surface morphologies by a seeded-growth method employing Pd nanoparticles as seeds. Interestingly, we found that the surface texture and thus the surface area of the produced Pd nanomaterials could be tuned by varying the seeded-growth temperature. Pd nanostructures displaying increasingly higher surface textures were obtained as the seeded-growth temperature was decreased from 95 to 30 °C. These results could be explained based on the variations in the relative rates of atom deposition (V
 deposition) and surface diffusion (V
 diffusion) during the Pd growth. The catalytic activities of the Pd nanostructures toward the reduction of 4-nitrophenol augmented with the increase in the surface texture of the produced nanostructures. The results presented herein can have important implications for designing facile approaches to the synthesis of Pd nanostructures with desired features and optimized catalytic performances that can be highly accessible and attractive for large scale production.

Surface diffusion versus atomic addition: using temperature to maneuver the morphology of Pd nanostructures by seeded-growth

The understanding of relaxation dynamics of
metallic nanoshells is important for a range of nanotechnological applications.
In this work, we present a combined experimental-theoretical study of the
relaxation dynamics of AgAu nanoshells. This was investigated using ultrafast
pump-probe experiments resonant with the surface plasmon of the nanoshells, as
well as via atomistic molecular dynamics simulations of relaxation and
temperature-jump (DT-jump) processes. Both
techniques were then discussed and complemented using a non-equilibrium
statistical mechanical model. Data collected at low energies were consistent
with our previously reported work and allowed the characterization of intrinsic
electron-phonon coupling times (EPCT) and of the overall relaxation dynamics in
terms of a two-temperature model. Data at intermediate and higher energies, in
turn, showed a nonlinear dependence of EPCT as a function of the pump power, faster
relaxation being observed at higher pump energies. In the limit of small DT-jumps, relaxation
based on a two-temperature model is recovered, whereas in the limit of large DT-jumps, the
relaxation becomes faster with increasing temperature change. The results
reported here give insight on the ultrafast dynamics of AgAu nanoshells and
might also be applied to other metallic systems, paving the way to the better
understanding of relaxation dynamics of nanoparticles in general.

Stochastic Thermodynamics Analysis of Ultrafast AgAu Nanoshell Dynamics in the Nonlinear Response Regime

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Pedro H. C. Camargo

Papers

Theories of molecular reaction dynamics: the microscopic foundation of chemical kinetics

Rational Design of Bimetallic Nanocatalysts for Tandem Transformations

Surface diffusion versus atomic addition: using temperature to maneuver the morphology of Pd nanostructures by seeded-growth

Stochastic Thermodynamics Analysis of Ultrafast AgAu Nanoshell Dynamics in the Nonlinear Response Regime

Automating 3D Imaging of Inorganic Nanoparticles