The effective geometry Monte Carlo algorithm: Applications to molecular communication

In this work, we address the systematic biases and random errors stemming from finite step sizes encountered in diffusion simulations. We introduce the Effective Geometry Monte Carlo (EG-MC) simulation algorithm which modifies the geometry of the receiver. We motivate our approach in a 1D toy model and then apply our findings to a spherical absorbing receiver in a 3D unbounded environment. We show that with minimal computational cost the impulse response of this receiver can be precisely simulated using EG-MC. Afterwards, we demonstrate the accuracy of our simulations and give tight constraints on the single free parameter in EG-MC. Finally, we comment on the range of applicability of our results. While we present the EG-MC algorithm for the specific case of molecular diffusion, we believe that analogous methods with effective geometry manipulations can be utilized to approach a variety of problems in other branches of physics such as condensed matter physics and cosmological large scale structure simulations.     

Homogenization of Periodically Heterogeneous Thin Beams

Consider an elastic thin three-dimensional body made of a periodic distribution of elastic inclusions. When both the thickness of the beam and the size of the heterogeneities tend simultaneously to zero the authors obtain three different one-dimensional models of beam depending upon the limit of the ratio of these two small parameters.     

Order-Stability in Complex Biological,Social, and AI-Systems from Quantum Information Theory

This paper is our attempt, on the basis of physical theory, to bring more clarification on the question “What is life?” formulated in the well-known book of Schrödinger in 1944. According to Schrödinger, the main distinguishing feature of a biosystem’s functioning is the ability to preserve its order structure or, in mathematical terms, to prevent increasing of entropy. However, Schrödinger’s analysis shows that the classical theory is not able to adequately describe the order-stability in a biosystem. Schrödinger also appealed to the ambiguous notion of negative entropy. We apply quantum theory. As is well-known, behaviour of the quantum von Neumann entropy crucially differs from behaviour of classical entropy. We consider a complex biosystem S composed of many subsystems, say proteins, cells, or neural networks in the brain, that is, S=(Si). We study the following problem: whether the compound system S can maintain “global order” in the situation of an increase of local disorder and if S can preserve the low entropy while other Si increase their entropies (may be essentially). We show that the entropy of a system as a whole can be constant, while the entropies of its parts rising. For classical systems, this is impossible, because the entropy of S cannot be less than the entropy of its subsystem Si. And if a subsystems’s entropy increases, then a system’s entropy should also increase, by at least the same amount. However, within the quantum information theory, the answer is positive. The significant role is played by the entanglement of a subsystems’ states. In the absence of entanglement, the increasing of local disorder implies an increasing disorder in the compound system S (as in the classical regime). In this note, we proceed within a quantum-like approach to mathematical modeling of information processing by biosystems—respecting the quantum laws need not be based on genuine quantum physical processes in biosystems. Recently, such modeling found numerous applications in molecular biology, genetics, evolution theory, cognition, psychology and decision making. The quantum-like model of order stability can be applied not only in biology, but also in social science and artificial intelligence.     

The self-assemblies of a newly designed star-shaped molecule end-capped with bromine atoms studied by scanning tunneling microscopy

A new star-shaped molecule StOF-Br_3 containing oligofluorenes and halogen atoms(Bromine) has been synthesized and studied by Scanning Tunneling Microscopy(STM) at the highly oriented pyrolytic graphite(HOPG) surface.We have obtained the high-resolution self-assembled STM images,from which the highly ordered and closely packed non-porous arrangements of the StOF-Br_3 molecular selfassemblies at the heptanoic acid/HOPG surface could be observed.The molecular models and selfassembled StOF-Br_3 architectures have been given in the following text.Besides,we have also figured out the surface free energy by the density functional theory(DFT) calculation,which proved that the halogen...halogen interaction was strong enough to stabilize the ordered molecular self-assemblies.This work verifies the existence of bromine...bromine interactions,and meanwhile provides a kind of effective approach for quickly building ordered molecular nanoarchitectures with large areas and different geometries.     

Interactions of human islet amyloid polypeptide with lipid structure of different curvatures

Curvature is one of the most important features of lipid membranes in living cells, which significantly influences the structure of lipid membranes and their interaction with proteins. Taken the human islet amyloid polypeptide (hIAPP), an important protein related to the pathogenesis of type II diabetes, as an example, we performed molecular dynamics (MD) simulations to study the interaction between the protein and the lipid structures with varied curvatures. We found that the lipids in the high curvature membrane pack loosely with high mobility. The hIAPP initially forms H-bonds with the membrane surface that anchored the protein, and then inserts into the membrane through the hydrophobic interactions between the residues and the hydrophobic tails of the lipids. hIAPP can insert into the membrane more deeply with a larger curvature and with a stronger binding strength. Our result provided important insights into the mechanism of the membrane curvature-dependent property of proteins with molecular details.     

排名聚合算法在少量长列表聚合中的性能比较分析

排名聚合将多个排名列表聚合成一个综合排名列表,可应用于推荐系统、链路预测、元搜索、提案评选等.当前已有工作从不同角度对不同排名聚合算法进行了综述、比较,但存在算法种类较少、数据统计特性不清晰、评价指标不够合理等局限性.不同排名聚合算法在提出时均声称优于已有算法,但是用于比较的方法不同,测试的数据不同,应用的场景不同,因此何种算法最能适应某一任务在很多情况下仍不甚清楚.本文基于Mallows模型,提出一套生成统计特性可控的不同类型的排名列表的算法,使用一个可应用于不同类型排名列表的通用评价指标,介绍9种排名聚合算法以及它们在聚合少量长列表时的表现.结果发现启发式方法虽然简单,但是在排名列表相似度较高、列表相对简单的情况下,能够接近甚至超过一些优化类方法的结果;列表中平局数量的增长会降低聚合排名的一致性并增加波动;列表数量的增加对聚合效果的影响呈现非单调性.整体而言,基于距离优化的分支定界方法 (FAST)优于其他各类算法,在不同类型的排名列表中表现非常稳定,能够很好地完成少量长列表的排名聚合.     

On-chip multiphoton Greenberger–Horne–Zeilinger state based on integrated frequency combs

One of the most important multipartite entangled states, Greenberger–Horne–Zeilinger state (GHZ), serves as a fundamental resource for quantum foundation test, quantum communication and quantum computation. To increase the number of entangled particles, significant experimental efforts should been invested due to the complexity of optical setup and the difficulty in maintaining the coherence condition for high-fidelity GHZ state. Here, we propose an ultra-integrated scalable on-chip GHZ state generation scheme based on frequency combs. By designing several microrings pumped by different lasers, multiple partially overlapped quantum frequency combs are generated to supply as the basis for on-chip polarization-encoded GHZ state with each qubit occupying a certain spectral mode. Both even and odd numbers of GHZ states can be engineered with constant small number of integrated components and easily scaled up on the same chip by only adjusting one of the pump wavelengths. In addition, we give the on-chip design of projection measurement for characterizing GHZ states and show the reconfigurability of the state. Our proposal is rather simple and feasible within the existing fabrication technologies and we believe it will boost the development of multiphoton technologies.     

基于平面度的燃料电池电化学性能模拟

 固体氧化物燃料电池的翘曲会影响电极-盖板界面的接触情况，从而影响电化学性能，对相关制造工艺提出了很大的挑战．为了分析燃料电池平面度对放电过程的影响，揭示其潜在的风险，我们建立了两个基于有限元法的仿真模型，对考虑平面度缺陷的燃料电池封装和放电进行分析．在对固体氧化物燃料电池进行平面度测量的基础上，首先建立了具有真实燃料电池翘曲特性的几何模型，分析封装过程中接触压力的分布情况．然后将接触电阻的仿真结果导入到三维多物理场耦合模型中，模拟具有平面度缺陷的燃料电池电化学性能．计算结果展示了燃料电池两侧封装过程中接触压力的分布情况．通过对比有接触电阻和无接触电阻的燃料电池电流密度，分析了电池与盖板的接触对放电过程的影响．结果表明，燃料电池的凹陷面较难达到满意的接触状态，需要比凸起面更大的封装压力．燃料电池表面接触电阻的变化将引起电流传导路径的变化，产生局部高电流或低电流．这项工作强调了在燃料电池中保持均匀分布的接触电阻的重要性，为今后的优化工作奠定了基础．     

New insights on the role of ROS in the mechanisms of sonoporation-mediated gene delivery

Reactive oxygen species (ROS) are hypothesized to play a role in the sonoporation mechanisms. Nevertheless, the acoustical phenomenon behind the ROS production as well as the exact mechanisms of ROS action involved in the increased cell membrane permeability are still not fully understood. Therefore, we investigated the key processes occurring at the molecular level in and around microbubbles subjected to ultrasound using computational chemistry methods. To confirm the molecular simulation predictions, we measured the ROS production by exposing SonoVue® microbubbles (MBs) to ultrasound using biological assays. To investigate the role of ROS in cell membrane permeabilization, cells were subjected to ultrasound in presence of MBs and plasmid encoding reporter gene, and the transfection level was assessed using flow cytometry. The molecular simulations showed that under sonoporation conditions, ROS can form inside the MBs. These radicals could easily diffuse through the MB shell toward the surrounding aqueous phase and participate in the permeabilization of nearby cell membranes. Experimental data confirmed that MBs favor spontaneous formation of a host of free radicals where HO was the main ROS species after US exposure. The presence of ROS scavengers/inhibitors during the sonoporation process decreased both the production of ROS and the subsequent transfection level without significant loss of cell viability. In conclusion, the exposure of MBs to ultrasound might be the origin of chemical effects, which play a role in the cell membrane permeabilization and in the in vitro gene delivery when generated in its proximity.