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

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

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

/pdf/charmm-the-biomolecular-simulation-program-4kexem0xkx.pdf

CHARMM: the biomolecular simulation program.

Some of the richest dynamical phenomena occur in both space and time. In view of the substantial developments that have taken place in the understanding of the onset of chaos in spatially homogeneous systems, which are described by systems of ordinary differential equations, there is some hope that parallel developments may take place in the study of spatially distributed systems that are usually described by partial differential equations. It is safe to say that this goal has not yet been achieved. The problem is twofold: not only are the phenomena diverse so that a set of organizing features like the major routes to chaos in spatially homogeneous systems has yet to be discovered, but some of the most useful nonlinear dynamics techniques, like surface of section plots, fractal dimensions and Lyapunov numbers, lose some of their utility for these high-dimensional systems. While all of the above tools can and have been brought to bear on the problem of spatio-temporal structure there is no one definitive diagnostic method.

Phase Dynamics, Phase Resetting, Correlation Functions and Coupled Map Lattices

Nonadiabatic molecular dynamics methods for diffusion

Dynamical correlations in rough sphere fluids

The dynamic structure factor of a dilute solution of flexible polymer molecules in a binary mixture near the critical point is studied using mode coupling techniques. The strong concentration fluctuations of the solvent near the criticcal point lead to modifications of the hydrodynamic interactions between the monomer units in a chain. A set of equations is derived which describes the decay of the coupled solvent and polymer modes. The critical fluctuations of the solvent lead to a change in the wave vector dependence of the dynamic structure factor and a change in the center of mass diffusion coefficient of the polymer.

Polymer dynamics in a binary critical mixture

The general formalism for periodic dichotomous noise on nonpotential flows is considered. This uncorrelated noise process switches suddenly at integer values of period $\ensuremath{\tau}$. The effect of additive noise of this kind on the planar FitzHugh-Nagumo ordinary differential equations [R. FitzHugh, Biophys. J. 1, 445 (1961); J. Nagumo, S. Arimoto, and Y. Yoshikawa, Proc. IRE 50, 2061 (1962)] is examined. For large $\ensuremath{\tau}$, quasifractal attractors are observed, whereas for the white-noise limit, where $\ensuremath{\tau}$ is small, a Fokker-Planck equation describes the evolution. The magnitude of $\ensuremath{\tau}$ determines the smoothness of the transient evolution and equilibrium density of the system. Typically the stochastic equations give rise to two regions of high density near the stable fixed points of the underlying autonomous system. The stiffness parameter $\ensuremath{\varepsilon}$ in the differential equations determines the fast variable, its associated nullcline, and the resulting flow structure. For small $\ensuremath{\varepsilon}$ the cubic nullcline controls the motion and transitions between the high-density peaks occur along segments of a noisy limit cycle. For large $\ensuremath{\varepsilon}$ the linear nullcline governs the transitions and the peaks are joined by a single band. The statistical behavior of the oscillatory and direct transitions is examined.

Dichotomously switched phase flows

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