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

The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

A smooth particle mesh Ewald method

The authors present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.

Canonical sampling through velocity rescaling

Co-Planar Stereotaxic Atlas of the Human Brain—3-Dimensional Proportional System: An Approach to Cerebral Imaging, J. Talairach, P. Tournoux. Georg Thieme Verlag, New York (1988), 122 pp., 130 figs. DM 268

The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such clusters, or communities, can be considered as fairly independent compartments of a graph, playing a similar role like, e. g., the tissues or the organs in the human body. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. This problem is very hard and not yet satisfactorily solved, despite the huge effort of a large interdisciplinary community of scientists working on it over the past few years. We will attempt a thorough exposition of the topic, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists, from the discussion of crucial issues like the significance of clustering and how methods should be tested and compared against each other, to the description of applications to real networks.

/pdf/community-detection-in-graphs-34rogm3r6p.pdf

Community detection in graphs

We review the history of the parallel tempering simulation method. From its origins in data analysis, the parallel tempering method has become a standard workhorse of physicochemical simulations. We discuss the theory behind the method and its various generalizations. We mention a selected set of the many applications that have become possible with the introduction of parallel tempering, and we suggest several promising avenues for future research.

/pdf/parallel-tempering-theory-applications-and-new-perspectives-58zv195vra.pdf

Parallel tempering: Theory, applications, and new perspectives

A general recursion algorithm is described for calculating kinematical diffraction intensities from crystals containing coherent planar faults. The method exploits the self-similar stacking sequences that occur when layers stack non-deterministically. Recursion gives a set of simple relations between average interference terms from a statistical crystal, which can be solved as a set of simultaneous equations. The diffracted intensity for a polycrystalline sample is given by the incoherent sum of scattered intensities over an ensemble of crystallites. The relations between this and previous approaches, namely the Hendricks-Teller matrix formulation, the difference equation method, the summed series formula of Cowley, and Michalski’s recurrence relations between average phase factors, are discussed. Although formally identical to these previous methods, the present recursive description has an intuitive appeal and proves easier to apply to complex crystal structure types. The method is valid for all types of planar faults, can accommodate long-range stacking correlations, and is applicable to crystals that contain only a finite number of layers. A FORTRAN program DIFFaX , based on this recursion algorithm, has been written and used to simulate powder X-ray (and neutron) diffraction patterns and single crystal electron (kinematical) diffraction patterns. Calculations for diamond-lonsdaleite and for several synthetic zeolite systems that contain high densities of stacking faults are presented as examples.

A general recursion method for calculating diffracted intensities from crystals containing planar faults

One of the main bottlenecks to deploying large-scale carbon dioxide capture and storage (CCS) in power plants is the energy required to separate the CO(2) from flue gas. For example, near-term CCS technology applied to coal-fired power plants is projected to reduce the net output of the plant by some 30% and to increase the cost of electricity by 60-80%. Developing capture materials and processes that reduce the parasitic energy imposed by CCS is therefore an important area of research. We have developed a computational approach to rank adsorbents for their performance in CCS. Using this analysis, we have screened hundreds of thousands of zeolite and zeolitic imidazolate framework structures and identified many different structures that have the potential to reduce the parasitic energy of CCS by 30-40% compared with near-term technologies.

/pdf/in-silico-screening-of-carbon-capture-materials-3rusdx9cl5.pdf

In silico screening of carbon-capture materials

A description of Monte Carlo methods for simulation of proteins is given. Advantages and disadvantages of the Monte Carlo approach are presented. The theoretical basis for calculating equilibrium properties of biological molecules by the Monte Carlo method is presented. Some of the standard and some of the more recent ways of performing Monte Carlo on proteins are presented. A discussion of the estimation of errors in properties calculated by Monte Carlo is given.

Monte Carlo simulations.

This invention provides methods by which biologically derived DNA sequences in a mixed sample or in an arrayed single sequence clone can be determined and classified without sequencing. The methods make use of information on the presence of carefully chosen target subsequences, typically of length from 4 to 8 base pairs, and preferably the length between target subsequences in a sample DNA sequence together with DNA sequence databases containing lists of sequences likely to be present in the sample to determine a sample sequence. The preferred method uses restriction endonucleases to recognize target subsequences and cut the sample sequence. Then carefully chosen recognition moieties are ligated to the cut fragments, the fragments amplified, and the experimental observation made. Polymerase chain reaction (PCR) is the preferred method of amplification. Another embodiment of the invention uses information on the presence or absence of carefully chosen target subsequences in a single sequence clone together with DNA sequence databases to determine the clone sequence. Computer implemented methods are provided to analyze the experimental results and to determine the sample sequences in question and to carefully choose target subsequences in order that experiments yield a maximum amount of information.

Michael W. Deem

Papers

Parallel tempering: Theory, applications, and new perspectives

A general recursion method for calculating diffracted intensities from crystals containing planar faults

In silico screening of carbon-capture materials

Monte Carlo simulations.

Method and apparatus for identifying classifying or quantifying DNA sequences in a sample without sequencing