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

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

/pdf/quantum-mechanical-continuum-solvation-models-3edv963g14.pdf

Quantum mechanical continuum solvation models.

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.

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the "multiple segment Viterbi" (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call "sparse rescaling". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.

/pdf/accelerated-profile-hmm-searches-5f0frwnmca.pdf

Accelerated Profile HMM Searches

http://stacks.cdc.gov/view/cdc/37605/cdc_37605_DS1.pdf

Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system.

WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator. A command line interface and the complete, open WebLogo source code are available for local installation and customization.

/pdf/weblogo-a-sequence-logo-generator-n21d3mafc9.pdf

WebLogo: A Sequence Logo Generator

There are only a very few known relations in statistical dynamics that are valid for systems driven arbitrarily far-from-equilibrium. One of these is the fluctuation theorem, which places conditions on the entropy production probability distribution of nonequilibrium systems. Another recently discovered far from equilibrium expression relates nonequilibrium measurements of the work done on a system to equilibrium free energy differences. In this paper, we derive a generalized version of the fluctuation theorem for stochastic, microscopically reversible dynamics. Invoking this generalized theorem provides a succinct proof of the nonequilibrium work relation.

https://arxiv.org/pdf/cond-mat/9901352.pdf

Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences

An equality has recently been shown relating the free energy difference between two equilibrium ensembles of a system and an ensemble average of the work required to switch between these two configurations. In the present paper it is shown that this result can be derived under the assumption that the system's dynamics is Markovian and microscopically reversible.

Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems

The Kawasaki nonlinear response relation, the transient fluctuation theorem, and the Jarzynski nonequilibrium work relation are all expressions that describe the behavior of a system that has been driven from equilibrium by an external perturbation In contrast to linear response theory, these expressions are exact no matter the strength of the perturbation, or how far the system has been driven away from equilibrium In this paper, I show that these three relations (and several other closely related results) can all be considered special cases of a single theorem This expression is explicitly derived for discrete time and space Markovian dynamics, with the additional assumptions that the unperturbed dynamics preserve the appropriate equilibrium ensemble, and that the energy of the system remains finite

http://gold.cchem.berkeley.edu/Pubs/gavin.pdf

Path-ensemble averages in systems driven far from equilibrium

Thermodynamic length is a metric distance between equilibrium thermodynamic states. Among other interesting properties, this metric asymptotically bounds the dissipation induced by a finite time transformation of a thermodynamic system. It is also connected to the Jensen-Shannon divergence, Fisher information, and Rao's entropy differential metric. Therefore, thermodynamic length is of central interest in understanding matter out of equilibrium. In this Letter, we will consider how to define thermodynamic length for a small system described by equilibrium statistical mechanics and how to measure thermodynamic length within a computer simulation. Surprisingly, Bennett's classic acceptance ratio method for measuring free energy differences also measures thermodynamic length.

Gavin E. Crooks

Papers

WebLogo: A Sequence Logo Generator

Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences

Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems

Path-ensemble averages in systems driven far from equilibrium

Measuring Thermodynamic Length