A benchmark of optimally folded protein structures using integer programming and the 3D-HP-SC model

The Protein Structure Prediction (PSP) problem comprises, among other issues, forecasting the three-dimensional native structure of proteins using only their primary structure information. Most computational studies in this area use synthetic data instead of real biological data. However, the closer to the real-world, the more the impact of results and their applicability. This work presents 17 real protein sequences extracted from the Protein Data Bank for a benchmark to the PSP problem using the tri-dimensional Hydrophobic-Polar with Side-Chains model (3D-HP-SC). The native structure of these proteins was found by maximizing the number of hydrophobic contacts between the side-chains of amino acids. The problem was treated as an optimization problem and solved by means of an Integer Programming approach. Although the method optimally solves the problem, the processing time has an exponential trend. Therefore, due to computational limitations, the method is a proof-of-concept and it is not applicable to large sequences. For unknown sequences, an upper bound of the number of hydrophobic contacts (using this model) can be found, due to a linear relationship with the number of hydrophobic residues. The comparison between the predicted and the biological structures showed that the highest similarity between them was found with distance thresholds around 5.2–8.2 Å. Both the dataset and the programs developed will be freely available to foster further research in the area.     

Meshless acoustic analysis using a weakly singular Burton-Miller boundary integral formulation

The Burton-Miller boundary integral formulation is solved by a complex variable boundary element-free method (CVBEFM) for the boundary-only meshless analysis of acoustic problems with arbitrary wavenumbers. To regularize both strongly singular and hypersingular integrals and to avoid the computation of the solid angle and its normal derivative, a weakly singular Burton-Miller formulation is derived by considering the normal derivative of the solid angle and adopting the singularity subtraction procedures. To facilitate the implementation of the CVBEFM and the approximation of gradients of the boundary variables, a stabilized complex variable moving least-square approximation is selected in the meshless discretization procedure. The results show the accuracy and efficiency of the present CVBEFM and reveal that the method can produce satisfactory results for all wavenumbers, even for extremely large wavenumbers such as k = 10 000.     

A periodic isoperimetric problem related to the unique games conjecture

We prove the endpoint case of a conjecture of Khot and Moshkovitz related to the unique games conjecture, less a small error. Let n ≥ 2. Suppose a subset Ω of n‐dimensional Euclidean space satisfies ?Ω = Ω^c and Ω + v = Ω^c (up to measure zero sets) for every standard basis vector . For any and for any q ≥ 1, let and let . For any x ∈ ?Ω, let N(x) denote the exterior normal vector at x such that ‖N(x)‖₂ = 1. Let . Our main result shows that B has the smallest Gaussian surface area among all such subsets Ω, less a small error: In particular, Standard arguments extend these results to a corresponding weak inequality for noise stability. Removing the factor 6 × 10^?9 would prove the endpoint case of the Khot‐Moshkovitz conjecture. Lastly, we prove a Euclidean analogue of the Khot and Moshkovitz conjecture. The full conjecture of Khot and Moshkovitz provides strong evidence for the truth of the unique games conjecture, a central conjecture in theoretical computer science that is closely related to the P versus NP problem. So, our results also provide evidence for the truth of the unique games conjecture. Nevertheless, this paper does not prove any case of the unique games conjecture.     

Information percolation and cutoff for the random‐cluster model

We consider the random‐cluster model (RCM) on with parameters p∈(0,1) and q ≥ 1. This is a generalization of the standard bond percolation (with edges open independently with probability p) which is biased by a factor q raised to the number of connected components. We study the well‐known Fortuin‐Kasteleyn (FK)‐dynamics on this model where the update at an edge depends on the global geometry of the system unlike the Glauber heat‐bath dynamics for spin systems, and prove that for all small enough p (depending on the dimension) and any q>1, the FK‐dynamics exhibits the cutoff phenomenon at with a window size , where λ_∞ is the large n limit of the spectral gap of the process. Our proof extends the information percolation framework of Lubetzky and Sly to the RCM and also relies on the arguments of Blanca and Sinclair who proved a sharp mixing time bound for the planar version. A key aspect of our proof is the analysis of the effect of a sequence of dependent (across time) Bernoulli percolations extracted from the graphical construction of the dynamics, on how information propagates.     

From Quantum Probabilities to Quantum Amplitudes

The task of reconstructing the system’s state from the measurements results, known as the Pauli problem, usually requires repetition of two successive steps. Preparation in an initial state to be determined is followed by an accurate measurement of one of the several chosen operators in order to provide the necessary “Pauli data”. We consider a similar yet more general problem of recovering Feynman’s transition (path) amplitudes from the results of at least three consecutive measurements. The three-step histories of a pre- and post-selected quantum system are subjected to a type of interference not available to their two-step counterparts. We show that this interference can be exploited, and if the intermediate measurement is “fuzzy”, the path amplitudes can be successfully recovered. The simplest case of a two-level system is analysed in detail. The “weak measurement” limit and the usefulness of the path amplitudes are also discussed.     

一带一路背景下企业地域影响力发展的规划研究

面对一个分布在新地理区域的新市场,合理规划区域服务影响力的发展战略对企业至关重要。本文假设企业的服务影响力在地理区域上的发展可以用其地理上分布的立足点来表示。单个立足点覆盖有限范围内的地理区域,并且在一个特定时刻用所有立足点所覆盖地理区域的总和来表示企业该时刻的发展状态。由于资源限制,企业对经济发展迅速的区域的覆盖必须在一定时间内逐步完成。因此,在发展时期内如何确定立足点的位置并使其位于知名城市中,是企业管理者亟待解决的问题。针对这个问题,本文首先基于时间序列预测方法建立了区域经济指标评估模型;然后使用集合覆盖理论提出了以成本和满意度为目标的选址优化模型并使用分支定界算法求解该模型;最后,使用从“一带一路”地区收集的数据对模型进行了检验。结果表明,该方法对有相关问题的企业具有较大的参考价值。