There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

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

Physical Review B

Yield stress materials flow if a sufficiently large shear stress is applied. Although such materials are ubiquitous and relevant for industry, there is no accepted microscopic description of how they yield, even in the simplest situations in which temperature is negligible and in which flow inhomogeneities such as shear bands or fractures are absent. Here we propose a scaling description of the yielding transition in amorphous solids made of soft particles at zero temperature. Our description makes a connection between the Herschel-Bulkley exponent characterizing the singularity of the flow curve near the yield stress Σc, the extension and duration of the avalanches of plasticity observed at threshold, and the density P(x) of soft spots, or shear transformation zones, as a function of the stress increment x beyond which they yield. We argue that the critical exponents of the yielding transition may be expressed in terms of three independent exponents, θ, df, and z, characterizing, respectively, the density of soft spots, the fractal dimension of the avalanches, and their duration. Our description shares some similarity with the depinning transition that occurs when an elastic manifold is driven through a random potential, but also presents some striking differences. We test our arguments in an elasto-plastic model, an automaton model similar to those used in depinning, but with a different interaction kernel, and find satisfying agreement with our predictions in both two and three dimensions.

/pdf/scaling-description-of-the-yielding-transition-in-soft-2dtgcfyrkz.pdf

Scaling description of the yielding transition in soft amorphous solids at zero temperature

Non-reciprocal transmission of motion is potentially highly beneficial to a wide range of applications, ranging from wave guiding to shock and vibration damping and energy harvesting. To date, large levels of non-reciprocity have been realized using broken spatial or temporal symmetries, yet mostly in the vicinity of resonances, bandgaps or using nonlinearities, thereby non-reciprocal transmission remains limited to narrow ranges of frequencies or input magnitudes and sensitive to attenuation. Here, we create a robotic mechanical metamaterials wherein we use local control loops to break reciprocity at the level of the interactions between the unit cells. We show theoretically and experimentally that first-of-their-kind spatially asymmetric standing waves at all frequencies and unidirectionally amplified propagating waves emerge. These findings realize the mechanical analogue of the non-Hermitian skin effect. They significantly advance the field of active metamaterials for non hermitian physics and open avenues to channel mechanical energy in unprecedented ways.

/pdf/non-reciprocal-robotic-metamaterials-4x8xgpjyhf.pdf

Non-reciprocal robotic metamaterials

Low-frequency vibrational modes play a central role in determining various basic properties of glasses, yet their statistical and mechanical properties are not fully understood. Using extensive numerical simulations of several model glasses in three dimensions, we show that in systems of linear size L sufficiently smaller than a crossover size L_{D}, the low-frequency tail of the density of states follows D(ω)∼ω^{4} up to the vicinity of the lowest Goldstone mode frequency. We find that the sample-to-sample statistics of the minimal vibrational frequency in systems of size L<L_{D} is Weibullian, with scaling exponents in excellent agreement with the ω^{4} law. We further show that the lowest-frequency modes are spatially quasilocalized and that their localization and associated quartic anharmonicity are largely frequency independent. The effect of preparation protocols on the low-frequency modes is elucidated, and a number of glassy length scales are briefly discussed.

/pdf/statistics-and-properties-of-low-frequency-vibrational-modes-37p4nrro5s.pdf

Statistics and Properties of Low-Frequency Vibrational Modes in Structural Glasses.

While the rheology of non-Brownian suspensions in the dilute regime is well understood, their behavior in the dense limit remains mystifying. As the packing fraction of particles increases, particle motion becomes more collective, leading to a growing length scale and scaling properties in the rheology as the material approaches the jamming transition. There is no accepted microscopic description of this phenomenon. However, in recent years it has been understood that the elasticity of simple amorphous solids is governed by a critical point, the unjamming transition where the pressure vanishes, and where elastic properties display scaling and a diverging length scale. The correspondence between these two transitions is at present unclear. Here we show that for a simple model of dense flow, which we argue captures the essential physics near the jamming threshold, a formal analogy can be made between the rheology of the flow and the elasticity of simple networks. This analogy leads to a new conceptual framework to relate microscopic structure to rheology. It enables us to define and compute numerically normal modes and a density of states. We find striking similarities between the density of states in flow, and that of amorphous solids near unjamming: both display a plateau above some frequency scale ω∗ ∼ |zc - z|, where z is the coordination of the network of particle in contact, zc = 2D where D is the spatial dimension. However, a spectacular difference appears: the density of states in flow displays a single mode at another frequency scale ωmin ≪ ω∗ governing the divergence of the viscosity.

https://www.pnas.org/content/pnas/109/13/4798.full.pdf

A unified framework for non-Brownian suspension flows and soft amorphous solids

Non-reciprocal transmission of motion is potentially highly beneficial to a wide range of applications, ranging from wave guiding, to shock and vibration damping and energy harvesting. To date, large levels of non-reciprocity have been realized using broken spatial or temporal symmetries, yet only in the vicinity of resonances or using nonlinearities, thereby nonreciprocal transmission remains limited to narrow ranges of frequencies or input magnitudes and sensitive to attenuation. Here, we devise a novel type of robotic mechanical metamaterials wherein we use local control loops to break reciprocity at the level of the interactions between the unit cells. We show theoretically that first-of-their-kind asymmetric standing waves at all frequencies and unidirectionally amplified propagating waves emerge. We demonstrate experimentally and numerically that this property leads to tunable, giant, broadband and attenuation-free non-reciprocal performances, namely a level of 50dB non-reciprocal isolation over 3.5 decades in frequency, as well as one-way amplification of pulses.

/pdf/non-reciprocal-robotic-metamaterials-31m4wmx0cn.pdf

Edan Lerner

Papers

Scaling description of the yielding transition in soft amorphous solids at zero temperature

Non-reciprocal robotic metamaterials

Statistics and Properties of Low-Frequency Vibrational Modes in Structural Glasses.

A unified framework for non-Brownian suspension flows and soft amorphous solids

Non-reciprocal robotic metamaterials.