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

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

Understanding the complementary roles of surface energy and roughness on natural nonwetting surfaces has led to the development of a number of biomimetic superhydrophobic surfaces, which exhibit apparent contact angles with water greater than 150 degrees and low contact angle hysteresis. However, superoleophobic surfaces-those that display contact angles greater than 150 degrees with organic liquids having appreciably lower surface tensions than that of water-are extremely rare. Calculations suggest that creating such a surface would require a surface energy lower than that of any known material. We show how a third factor, re-entrant surface curvature, in conjunction with chemical composition and roughened texture, can be used to design surfaces that display extreme resistance to wetting from a number of liquids with low surface tension, including alkanes such as decane and octane.

http://science.sciencemag.org/content/sci/318/5856/1618.full.pdf

Designing Superoleophobic Surfaces

The major strategies for designing surfaces that prevent fouling due to proteins, bacteria, and marine organisms are reviewed. Biofouling is of great concern in numerous applications ranging from biosensors to biomedical implants and devices, and from food packaging to industrial and marine equipment. The two major approaches to combat surface fouling are based on either preventing biofoulants from attaching or degrading them. One of the key strategies for imparting adhesion resistance involves the functionalization of surfaces with poly(ethylene glycol) (PEG) or oligo(ethylene glycol). Several alternatives to PEG-based coatings have also been designed over the past decade. While protein-resistant coatings may also resist bacterial attachment and subsequent biofilm formation, in order to overcome the fouling-mediated risk of bacterial infection it is highly desirable to design coatings that are bactericidal. Traditional techniques involve the design of coatings that release biocidal agents, including antibiotics, quaternary ammonium salts (QAS), and silver, into the surrounding aqueous environment. However, the emergence of antibiotic- and silver-resistant pathogenic strains has necessitated the development of alternative strategies. Therefore, other techniques based on the use of polycations, enzymes, nanomaterials, and photoactive agents are being investigated. With regard to marine antifouling coatings, restrictions on the use of biocide-releasing coatings have made the generation of nontoxic antifouling surfaces more important. While considerable progress has been made in the design of antifouling coatings, ongoing research in this area should result in the development of even better antifouling materials in the future.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/adma.201001215

Antifouling coatings: recent developments in the design of surfaces that prevent fouling by proteins, bacteria, and marine organisms.

We discuss in this review how the roughness of a solid impacts its wettability. We see in particular that both the apparent contact angle and the contact angle hysteresis can be dramatically affected by the presence of roughness. Owing to the development of refined methods for setting very well-controlled micro- or nanotextures on a solid, these effects are being exploited to induce novel wetting properties, such as spontaneous filmification, superhydrophobicity, superoleophobicity, and interfacial slip, that could not be achieved without roughness.

Wetting and Roughness

The apparent contact angle of a drop on a rough surface is often modeled using either Wenzel's or Cassie's formulas. Previous experiments are not conclusive regarding which formula to use and when. This information is critical in designing a superhydrophobic substrate for applications in microscale devices. A drop on a rough substrate can occupy multiple equilibrium states. These equilibrium states denote respective local minima in energy. The particular shape that a drop attains depends on how the drop is formed. We propose a design procedure to develop a rough superhydrophobic substrate that accounts for the multiple equilibrium drop shapes. The theory is expected to work well to maximize the advancing contact angle of a drop. It is noted in the end that appropriate models for the receding contact angles on rough substrate must be investigated further before appropriate design procedures, which will maximize the receding contact angle or minimize hysteresis (i.e., minimize the difference between the adv...

On the Modeling of Hydrophobic Contact Angles on Rough Surfaces

Surface roughness is known to amplify hydrophobicity. The apparent contact angle of a drop on a rough surface is often modeled using either Wenzel's or Cassie's formulas. These formulas, along with an appropriate energy analysis, are critical in designing superhydrophobic substrates for applications in microscale devices. In this paper we propose that double (or multiple) roughness structures or slender pillars are appropriate surface geometries to develop "self-cleaning" surfaces. The key motivation behind the double structured roughness is to mimic the microstructure of superhydrophobic leaves (such as lotus). Theoretical analysis similar to that presented in the paper can be used to obtain optimal geometric parameters for the rough surface. The calculation procedure should result in surface geometries with excellent water repellent properties.

Mimicking the lotus effect: influence of double roughness structures and slender pillars.

Direct numerical simulations of fluid-solid systems using the arbitrary Langrangian-Eulerian technique

Surface roughness is known to amplify hydrophobicity. It is observed that, in general, two drop shapes are possible on a given rough surface. These two cases correspond to the Wenzel (liquid wets the grooves of the rough surface) and Cassie (the drop sits on top of the peaks of the rough surface) formulas. Depending on the geometric parameters of the substrate, one of these two cases has lower energy. It is not guaranteed, though, that a drop will always exist in the lower energy state; rather, the state in which a drop will settle depends typically on how the drop is formed. In this paper, we investigate the transition of a drop from one state to another. In particular, we are interested in the transition of a "Cassie drop" to a "Wenzel drop", since it has implications on the design of superhydrophobic rough surfaces. We propose a methodology, based on energy balance, to determine whether a transition from the Cassie to Wenzel case is possible.

Transition between superhydrophobic states on rough surfaces.

The apparent contact angle on a rough surface is usually modeled by either Cassie's or Wenzel's theory. We show, on the basis of experimental evidence, that there can be two contact angles on the same rough surface, depending on how a drop is formed. A transition can occur between the different states by an external disturbance. This paper compares the theoretical prediction with matching experiments. This leads to the establishment of a design criterion for a robust hydrophobic rough surface on which the apparent contact angle will not change as a result of an external disturbance.

Neelesh A. Patankar

Papers

On the Modeling of Hydrophobic Contact Angles on Rough Surfaces

Mimicking the lotus effect: influence of double roughness structures and slender pillars.

Direct numerical simulations of fluid-solid systems using the arbitrary Langrangian-Eulerian technique

Transition between superhydrophobic states on rough surfaces.

Multiple Equilibrium Droplet Shapes and Design Criterion for Rough Hydrophobic Surfaces