On using compressibility to detect when slime mould completed computation

Slime mould Physarum polycephalum is a single cell visible by an unaided eye. The slime mould optimizes its network of protoplasmic tubes in gradients of attractants and repellents. This behavior is interpreted as computation. Several prototypes of the slime mould computers were designed to solve problems of computation geometry, graphs, transport networks, and to implement universal computing circuits. Being a living substrate, the slime mould does not halt its behavior when a task is solved but often continues foraging the space thus masking the solution found. We propose to use temporal changes in compressibility of the slime mould patterns as indicators of the halting of the computation. Compressibility of a pattern characterizes the pattern's morphological diversity, that is, a number of different local configurations. At the beginning of computation the slime explores the space, thus generating less compressible patterns. After gradients of attractants and repellents are detected the slime spans data sites with its protoplasmic network and retracts scouting branches, thus generating more compressible patterns. We analyze the feasibility of the approach on results of laboratory experiments and computer modelling. © 2015 Wiley Periodicals, Inc. Complexity 21: 162–175, 2016     

Colourings of cubic graphs inducing isomorphic monochromatic subgraphs

A -bisection of a bridgeless cubic graph is a -colouring of its vertex set such that the colour classes have the same cardinality and all connected components in the two subgraphs induced by the colour classes ( monochromatic components in what follows) have order at most . Ban and Linial Conjectured that every bridgeless cubic graph admits a -bisection except for the Petersen graph. A similar problem for the edge set of cubic graphs has been studied: Wormald conjectured that every cubic graph with has a -edge colouring such that the two monochromatic subgraphs are isomorphic linear forests (ie, a forest whose components are paths). Finally, Ando conjectured that every cubic graph admits a bisection such that the two induced monochromatic subgraphs are isomorphic. In this paper, we provide evidence of a strong relation of the conjectures of Ban-Linial and Wormald with Ando's Conjecture. Furthermore, we also give computational and theoretical evidence in their support. As a result, we pose some open problems stronger than the above-mentioned conjectures. Moreover, we prove Ban-Linial's Conjecture for cubic-cycle permutation graphs. As a by-product of studying -edge colourings of cubic graphs having linear forests as monochromatic components, we also give a negative answer to a problem posed by Jackson and Wormald about certain decompositions of cubic graphs into linear forests.     

峨山褐煤的分子结构和分子模拟

作为重要的化石能源，褐煤资源潜力巨大、分布广泛但综合利用率低。研究褐煤的分子结构模型，有助于预测褐煤在热解、液化和气化过程中的化学反应机理及反应路径，进而提高褐煤的综合应用水平。以云南峨山褐煤为研究对象，利用傅里叶变换红外光谱、13C核磁共振波谱及X射线光电子能谱等分析测试方法，获取了峨山褐煤的含碳、含氧及含氮结构参数。在此基础上，借助Gaussian 09计算平台，采用量子化学建模的方法构建并优化了峨山褐煤的分子结构模型。研究结果表明：峨山褐煤的芳碳率为39.20%，芳香碳结构主要为苯和萘，且芳香桥头碳与周边碳的比值χ_b为0.07；脂碳率为49.51%，脂肪碳结构主要为亚甲基，季碳和氧接脂碳；氧原子主要存在于羟基、醚氧、羰基和羧基结构中；含氮结构则以吡啶为主。基于元素分析、13C 核磁共振波谱分析，又经过热重实验消除褐煤中残余水分的影响后，计算出峨山褐煤的分子式为C₁₅₃H₁₃₇O₃₅N₂。依据分子式及分析结果计算出峨山褐煤的结构单元含量并构建出其初始结构模型，采用半经验法PM 3基组及密度泛函理论M06-2X/3-21G基组对初始分子构型进行优化。优化后的分子模型具有明显的三维立体特征，芳香环之间较为分散且在空间中排列不规则，芳香簇主要通过亚甲基、醚氧基、羰基、酯基和脂肪环连接，含氧官能团主要分布在分子边缘，脂肪族侧链较多。对优化后的分子模型进行振动频率计算进而获得了分子模型的模拟红外光谱，其与实验红外谱图吻合度良好，证明了峨山褐煤分子结构模型的准确性、合理性。分子结构模型的构建有利于直观地了解峨山褐煤的分子结构特征，从而有助于从微观分子角度研究峨山褐煤的宏观性质。同时，峨山褐煤分子结构模型可为其在热解、液化和气化等领域研究中提供理论指导。     

含分布时滞的时滞微分系统多步龙格-库塔方法的时滞相关稳定性

本文研究了一类含分布时滞的时滞微分系统的多步龙格-库塔方法的稳定性.基于辐角原理，本文给出了多步龙格-库塔方法弱时滞相关稳定性的充分条件，并通过数值算例验证了理论结果的有效性.     

Overwriting information: Correlations,physical costs,and environment models

In this sequel to our previous study of the entropic and energetic costs of information erasure [N.G. Anderson, Phys. Lett. A 372 (2008) 5552], we consider direct overwriting of classical information encoded in a quantum-mechanical memory system interacting with a heat bath. Lower bounds on physical costs of overwriting – in both “single-shot” and “sequential” overwriting scenarios – are obtained from globally unitary quantum dynamics and entropic inequalities alone, all within a referential approach that grounds information content in correlations between physical system states. A heterogeneous environment model, required for consistent treatment of sequential overwriting, is introduced and used to establish and relate bounds for various cases.     

A fast parallel clustering algorithm for molecular simulation trajectories

We implemented a GPU‐powered parallel k‐centers algorithm to perform clustering on the conformations of molecular dynamics (MD) simulations. The algorithm is up to two orders of magnitude faster than the CPU implementation. We tested our algorithm on four protein MD simulation datasets ranging from the small Alanine Dipeptide to a 370‐residue Maltose Binding Protein (MBP). It is capable of grouping 250,000 conformations of the MBP into 4000 clusters within 40 seconds. To achieve this, we effectively parallelized the code on the GPU and utilize the triangle inequality of metric spaces. Furthermore, the algorithm's running time is linear with respect to the number of cluster centers. In addition, we found the triangle inequality to be less effective in higher dimensions and provide a mathematical rationale. Finally, using Alanine Dipeptide as an example, we show a strong correlation between cluster populations resulting from the k‐centers algorithm and the underlying density. © 2012 Wiley Periodicals, Inc.     

Construction of conformal mappings by generalized polarization tensors

We present a new systematic method to compute the Riemann mapping from the outside of the unit disc to the outside of a simply connected domain. We derive explicit relations between the coefficients of the Riemann mapping and the generalized polarization tensors associated with the domain. Because the generalized polarization tensors can be computed numerically, we are able to compute the coefficients of the Riemann mapping using these relations. Effectiveness of the method is validated by numerical examples. Copyright © 2014 John Wiley & Sons, Ltd.     

Fast enclosure for the minimum norm least squares solution of the matrix equation AXB = C

Fast algorithms for enclosing the minimum norm least squares solution of the matrix equation AXB = C are proposed. To develop these algorithms, theories for obtaining error bounds of numerical solutions are established. The error bounds obtained by these algorithms are verified in the sense that all the possible rounding errors have been taken into account. Techniques for accelerating the enclosure and obtaining smaller error bounds are introduced. Numerical results show the properties of the proposed algorithms. Copyright © 2015 John Wiley & Sons, Ltd.