Rotamer optimization for protein design through MAP estimation and problem‐size reduction

The search for the global minimum energy conformation (GMEC) of protein side chains is an important computational challenge in protein structure prediction and design. Using rotamer models, the problem is formulated as a NP‐hard optimization problem. Dead‐end elimination (DEE) methods combined with systematic A* search (DEE/A*) has proven useful, but may not be strong enough as we attempt to solve protein design problems where a large number of similar rotamers is eligible and the network of interactions between residues is dense. In this work, we present an exact solution method, named BroMAP (branch‐and‐bound rotamer optimization using MAP estimation), for such protein design problems. The design goal of BroMAP is to be able to expand smaller search trees than conventional branch‐and‐bound methods while performing only a moderate amount of computation in each node, thereby reducing the total running time. To achieve that, BroMAP attempts reduction of the problem size within each node through DEE and elimination by lower bounds from approximate maximum‐a‐posteriori (MAP) estimation. The lower bounds are also exploited in branching and subproblem selection for fast discovery of strong upper bounds. Our computational results show that BroMAP tends to be faster than DEE/A* for large protein design cases. BroMAP also solved cases that were not solved by DEE/A* within the maximum allowed time, and did not incur significant disadvantage for cases where DEE/A* performed well. Therefore, BroMAP is particularly applicable to large protein design problems where DEE/A* struggles and can also substitute for DEE/A* in general GMEC search. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

随机容错设施布局问题的近似算法

在确定性的容错设施布局问题中, 给定顾客的集合和地址的集合. 在每个地址上可以开设任意数目的不同设施. 每个顾客j有连接需求r_j. 允许将顾客j连到同一地址的不同设施上. 目标是开设一些设施并将每个顾客j连到r_j个不同的设施上, 使得总开设费用和连接费用最小. 研究两阶段随机容错设施布局问题(SFTFP), 顾客的集合事先不知道, 但是具有有限多个场景并知道其概率分布. 每个场景指定需要服务的顾客的子集. 并且每个设施有两种类型的开设费用. 在第一阶段根据顾客的随机信息确定性地开设一些设施, 在第二阶段根据顾客的真实信息再增加开设一些设施．给出随机容错布局问题的线性整数规划和基于线性规划舍入的5-近似算法.     

城市水供需系统投资的鲁棒控制

针对城市水需求具有增长性和周期性的情形,建立城市水供需系统投资的离散时间控制模型.由于城市水管理系统参数估计值可能具有不确定性和时变性,为使此情形下仍能有效满足城市水需求,利用内模原理设计了系统补偿器,并证明了其可行性,然后利用补偿器对系统实施鲁棒控制.在预测城市水需求的基础上,通过合理控制城市水供给的投资,使城市的剩余供水能力逐渐准确逼近给定目标值,且系统具有鲁棒性.     

Combining variable neighborhood search and estimation of distribution algorithms in the protein side chain placement problem

The aim of this work is to introduce several proposals for combining two metaheuristics: variable neighborhood search (VNS) and estimation of distribution algorithms (EDAs). Although each of these metaheuristics has been previously hybridized in several ways, this paper constitutes the first attempt to combine both optimization methods. The different ways of combining VNS and EDAs will be classified into three groups. In the first group, we will consider combinations where the philosophy underlying VNS is embedded in EDAs. Considering different neighborhood spaces (points, populations or probability distributions), we will obtain instantiations for the approaches in this group. The second group of algorithms is obtained when probabilistic models (or any other machine learning paradigm) are used in order to exploit the good and bad shakes of the randomly generated solutions in a reduced variable neighborhood search. The last group of algorithms contains the results of alternating VNS and EDAs. An application of the first approach is presented in the protein side chain placement problem. The results obtained show the superiority of the hybrid algorithm in comparison with EDAs and VNS.     

云计算中面向能耗降低的虚拟机多资源放置算法

为降低云计算系统产生的能耗,实现系统多类型资源的合理利用,提出虚拟机多资源能耗优化放置模型,并给出虚拟机多目标资源随机多组优化算法(RMRO)。RMRO算法随机生成多组虚拟机放置序列,并对每组序列进行优化,从中选出最优的序列作为最终的虚拟机序列。基于RMRO,进一步提出了3种虚拟机放置序列的再优化策略,通过实验对比,选择MMBA策略作为最佳策略。仿真结果表明,RMRO相比传统的MBFD和MBFH算法,能明显降低数据中心的能耗,同时使系统多种资源利用更合理。     

Effect of Four-Wave Mixing on Optimal Placement of Optical Amplifier in WDM Star Networks

In this article, the effect of four-wave mixing (FWM) and amplified spontaneous emission (ASE) noise on WDM optical star networks has been investigated. Analysis for the evaluation of probability of error has been carried out (a) when only FWM is present and (b) when both FWM and ASE noise are present. Numerical results are presented in the graphical and tabular forms for the practical values of parameters. Finally, optimal location of the amplifier in the network has been identified as being before the star coupler preceding the receiver.     

Robust prediction of complex spatiotemporal states through machine learning with sparse sensing

Complex spatiotemporal states arise frequently in material as well as biological systems consisting of multiple interacting units. A specific, but rather ubiquitous and interesting example is that of “chimeras”, existing in the edge between order and chaos. We use Machine Learning methods involving “observers” to predict the evolution of a system of coupled lasers, comprising turbulent chimera states and of a less chaotic biological one, of modular neuronal networks containing states that are synchronized across the networks. We demonstrated the necessity of using “observers” to improve the performance of Feed-Forward Networks in such complex systems. The robustness of the forecasting capabilities of the “Observer Feed-Forward Networks” versus the distribution of the observers, including equidistant and random, and the motion of them, including stationary and moving was also investigated. We conclude that the method has broader applicability in dynamical system context when partial dynamical information about the system is available.     

云环境下面向复杂资源需求的虚拟机能效部署研究

针对云环境下在线虚拟机部署这一矢量装箱问题进行了研究,提出了多维空间划分模型和在线虚拟机能效部署算法OEEVMP。多维空间划分模型可以引导虚拟机部署,避免多维资源的不均衡利用;基于此模型,提出的OEEVMP算法在物理机运行数量局部最优和全局最优之间取得均衡,从而提高虚拟机部署能效。通过仿真实验,将OEEVMP算法与MFFD算法进行了对比,实验结果验证了所提算法的可行性和有效性。最后,对控制模型的两个参数进行了分析,给出了最佳的参数组合。     

带惩罚的容错设施布局问题的近似算法

在带惩罚的容错设施布局问题中, 给定顾客集合、地址集合、以及每个顾客和各个地址之间的连接费用, 这里假设连接费用是可度量的. 每位顾客有各自的服务需求, 每个地址可以开设任意多个设施, 顾客可以被安排连接到某些地址的一些开设的设施上以满足其需求, 也可以被拒绝, 但这时要支付拒绝该顾客所带来的惩罚费用. 目标是确定哪些顾客的服务需求被拒绝并开设一些设施, 将未被拒绝的顾客连接到不同的开设设施上, 使得开设费用、连接费用和惩罚费用总和最小. 给出了带惩罚的容错设施布局问题的线性整数规划及其对偶规划, 进一步, 给出了基于其线性规划和对偶规划舍入的4-近似算法.     

Concentrated Loads on Light Gauge Steel Diaphragms

ABSTRACT

When a point load is applied within the length of a side of a diaphragm, significant local forces may arise. A theory is developed whereby both the forces induced in the edge fasteners and the bending moments induced in the edge members may be evaluated from simple explicit expressions. This theory is verified by comparison with finite element investigations.

The behavior of sheeting in compression surrounding edge fasteners is investigated experimentally and a simple approach to the resulting buckling failure is derived. Finally, some tests on complete diaphragm assemblies subject to compressive concentrated loads are described and the results compared with the theory.