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

Introduction Statistical mechanics Molecular dynamics Monte Carlo methods Some tricks of the trade How to analyse the results Advanced simulation techniques Non-equilibrium molecular dynamics Brownian dynamics Quantum simulations Some applications Appendix A: Computers and computer simulation Appendix B: Reduced units Appendix C: Calculation of forces and torques Appendix D: Fourier transforms Appendix E: The gear predictor - corrector Appendix F: Programs on microfiche Appendix G: Random numbers References Index.

Computer Simulation of Liquids

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

Although gold is the subject of one of the most ancient themes of investigation in science, its renaissance now leads to an exponentially increasing number of publications, especially in the context of emerging nanoscience and nanotechnology with nanoparticles and self-assembled monolayers (SAMs). We will limit the present review to gold nanoparticles (AuNPs), also called gold colloids. AuNPs are the most stable metal nanoparticles, and they present fascinating aspects such as their assembly of multiple types involving materials science, the behavior of the individual particles, size-related electronic, magnetic and optical properties (quantum size effect), and their applications to catalysis and biology. Their promises are in these fields as well as in the bottom-up approach of nanotechnology, and they will be key materials and building block in the 21st century. Whereas the extraction of gold started in the 5th millennium B.C. near Varna (Bulgaria) and reached 10 tons per year in Egypt around 1200-1300 B.C. when the marvelous statue of Touthankamon was constructed, it is probable that “soluble” gold appeared around the 5th or 4th century B.C. in Egypt and China. In antiquity, materials were used in an ecological sense for both aesthetic and curative purposes. Colloidal gold was used to make ruby glass 293 Chem. Rev. 2004, 104, 293−346

Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology.

Intermolecular And Surface Forces

Thermal gradients impart a force on colloidal particles pushing the colloids towards cold or hot regions, a phenomenon called thermophoresis. Existing theories describe thermophoresis by considering the local perturbation of the thermal field around the colloid. While these approaches incorporate interfacial surface free energies, they have consistently ignored the impact of the Kapitza resistance associated with the colloid-solvent interface. We propose a theoretical approach to include interfacial Kapitza resistance effects, and we test the new equations using non-equilibrium molecular dynamics simulations. We demonstrate that the Kapitza resistance influences the local thermal field around a colloid, modifying the Soret coefficient. We conclude that interfacial thermal conductance effects must be included to describe thermophoresis.

The impact of the interfacial Kapitza resistance on colloidal thermophoresis

Using non-equilibrium molecular dynamics simulations and a coarse grained model of ionic liquids, we have investigated the impact that the shape and the intramolecular charge distribution of the ions have on the electrotuneable friction with ionic-liquid nanoscale films. We show that the electric-field induces significant structural changes in the film, leading to dramatic modifications of the friction force. Comparison of the present work with previous studies using different models of ionic liquids indicate that the phenomenology presented here applies to a wide range of ionic liquids. In particular, the electric-field-induced shift of the slippage plane from the solid-liquid interface to the interior of the film and the non-monotonic variation of the friction force are common features of ionic lubricants under strong confinement. We also demonstrate that the molecular structure of the ions plays an important role in determining the electrostriction and electroswelling of the confined film, hence showing the importance of ion-specific effects in electrotuneable friction.

Electrotunable friction with ionic liquid lubricants: how important is the molecular structure of the ions?

Ellipsoidal Particles at Liquid-Liquid Interfaces Gary B. Davies, a) Timm Kruger, 1, b) Peter V. Coveney, c) Jens Harting, 4, d) and Fernando Bresme 6, e) Centre for Computational Science, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom. Institute for Materials and Processes, Department of Engineering, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JL, Scotland, United Kingdom. Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands. Faculty of Science and Technology, Mesa+ Institute, University of Twente, 7500 AE Enschede, The Netherlands. Department of Chemistry, Imperial College London, London, SW7 2AZ, United Kingdom. Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway.

of Interface Deformation on the Orientation Transition of Ellipsoidal Particles at Liquid-Liquid Interfaces

Neutron News 6 Meeting Report Current Challenges in Materials for Thermal Energy Storage In June 2022, over 40 scientists from 13 countries across four continents came together in stunning Caesar Augusta (Zaragoza, Spain) to participate in a 3-day CECAM Flagship Workshop entitled “Current Challenges in Materials for Thermal Energy Storage.” Originally planned for 2021, the intensity of the COVID pandemic at the time could not guarantee a face-to-face meeting. With the benefit of hindsight, its postponement to 2022 was a gratifying turn of fate, as only a handful of registered participants had to join us online for the event (see Figure 1). The record-high temperatures we all experienced in Zaragoza during the meeting were certainly a vivid reminder of the primary driver behind the workshop, as well as of the challenges associated with securing a sustainable future for all: human activities continue to produce and require vast amounts of energy, and its efficient storage and subsequent use has far-reaching economic and societal impacts. This latter objective drives current efforts in the search for improved Thermal Energy-Storage Materials (TESMs), to store and release energy via sensible heat, adsorption-desorption phenomena or well-defined phase transitions either in the bulk or under confinement. In all cases, the search for improved TESMs has relied primarily on empirical knowledge focused on a handful of observables like the heat capacity, melting/desorption enthalpy & temperature or the thermal conductivity, albeit with quite limited physical insight and success. Motivated by the above, this workshop brought together computational and experimental efforts for their coordinated deployment in order to move beyond the stateof-the-art in the rational design of TESMs. These included ongoing developments of versatile and accurate computer-simulation tools in tandem with increasingly elaborate experimental campaigns, with an emphasis on the exploitation of last-generation radiation-scattering techniques (neutrons and X-rays) and the use of robust methodologies to gain access to much-needed thermophysical data in and out-of equilibrium. During the event, we enjoyed over twenty presentations from leading practitioners across a plethora

/pdf/current-challenges-in-materials-for-thermal-energy-storage-13d1xubc.pdf

Current Challenges in Materials for Thermal Energy Storage

Pseudopeptides based on poly(l-lysine isophthalamide) backbone have emerged as promising drug delivery candidates due to their pH-activated membrane disruption ability. To gain molecular understanding on these novel polymeric species, we have constructed force-field parameters and simulated the behaviors of polymers with and without phenylalanine grafted as side chains under conditions compatible with different pHs. The free energy changes upon polymer permeation through membrane were calculated using the umbrella sampling technique. We show that both polymers with and without grafts interact better with the membrane under conditions compatible with lower pH. The conformational states of the polymers were investigated in water and at a water–membrane interface. On the basis of Markov state modeling results, we propose a possible advantage of the grafted polymer over the ungrafted polymer for membrane rupture because of its quicker conformational rearrangement kinetics.

Simulation Studies on the Lipid Interaction and Conformation of Novel Drug-Delivery Pseudopeptidic Polymers

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