There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

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

J. Appl. Cryst.の発刊に際して

https://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/202086/1/j.scriptamat.2015.07.021.pdf

First principles phonon calculations in materials science

Phonon plays essential roles in dynamical behaviors and thermal properties, which are central topics in fundamental issues of materials science. The importance of first principles phonon calculations cannot be overly emphasized. Phonopy is an open source code for such calculations launched by the present authors, which has been world-widely used. Here we demonstrate phonon properties with fundamental equations and show examples how the phonon calculations are applied in materials science.

DL_POLY_3 is a general-purpose massively parallel molecular dynamics simulation package embedding a highly efficient set of methods and algorithms such as: Domain Decomposition (DD), Linked Cells (LC), Daresbury Advanced Fourier Transform (DAFT), Trotter derived Velocity Verlet (VV) integration and RATTLE. Written to support academic research, it has a wide range of applications and can run on a wide range of computers; from single processor workstations to multi-processor computers. The code development has placed particular emphasis on the efficient utilization of multi-processor power by optimised memory workload and distribution, which makes it possible to simulate systems of the order of tens of millions of particles and beyond. In this paper we discuss the new DL_POLY_3 design, and report on the performance, capability and scalability. We also discuss new features implemented to simulate highly non-equilibrium processes of radiation damage and analyse the structural damage during such processes.

/pdf/dl-poly-3-new-dimensions-in-molecular-dynamics-simulations-z4v2wlhc49.pdf

DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism

Foreword Acknowledgements Definitions of symbols used 1. Some fundamentals 2. The harmonic approximation and lattice dynamics of very simple systems 3. Dynamics of diatomic crystals: general principles 4. How far do the atoms move? 5. Lattice dynamics and thermodynamics 6. Formal description 7. Acoustic modes and macroscopic elasticity 8. Anharmonic effects and phase transitions 9. Neutron scattering 10. Infrared and Raman spectroscopy 11. Formal quantum mechanical description of lattice vibrations 12. Molecular dynamics simulations Appendices Problems Bibliography Index.

Introduction to Lattice Dynamics

We show that silver(I) hexacyanocobaltate(III), Ag3[Co(CN)6], exhibits positive and negative thermal expansion an order of magnitude greater than that seen in other crystalline materials. This framework material expands along one set of directions at a rate comparable to the most weakly bound solids known. By flexing like lattice fencing, the framework couples this to a contraction along a perpendicular direction. This gives negative thermal expansion that is 14 times larger than in ZrW2O8. Density functional theory calculations quantify both the low energy associated with this flexibility and the role of argentophilic (Ag+...Ag+) interactions. This study illustrates how the mechanical properties of a van der Waals solid might be engineered into a rigid, useable framework.

https://science.sciencemag.org/content/sci/319/5864/794.full.pdf

Colossal Positive and Negative Thermal Expansion in the Framework Material Ag3[Co(CN)6]

A new approach to the reverse Monte Carlo analysis of total scattering data from polycrystalline materials is presented. The essential new feature is the incorporation of an explicit analysis of the Bragg peaks using a profile refinement, taking account of the instrument resolution function. Other new features including fitting data from magnetic materials, modelling lattice site disorder and new restraint and constraint options. The new method is demonstrated by a brief review of studies carried out during its development. The new program RMCProfile represents a significant advance in the analysis of polycrystalline total scattering data, especially where the local structure is to be explored within the true constraints of the long-range average structure.

https://iopscience.iop.org/article/10.1088/0953-8984/19/33/335218/pdf

Martin T. Dove

Papers

DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism

Introduction to Lattice Dynamics

Colossal Positive and Negative Thermal Expansion in the Framework Material Ag3[Co(CN)6]

Introduction to Lattice Dynamics

RMCProfile: reverse Monte Carlo for polycrystalline materials.