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

‡We describe the use of singular value decomposition in transforming genome-wide expression data from genes 3 arrays space to reduced diagonalized ‘‘eigengenes’’ 3 ‘‘eigenarrays’’ space, where the eigengenes (or eigenarrays) are unique orthonormal superpositions of the genes (or arrays). Normalizing the data by filtering out the eigengenes (and eigenarrays) that are inferred to represent noise or experimental artifacts enables meaningful comparison of the expression of different genes across different arrays in different experiments. Sorting the data according to the eigengenes and eigenarrays gives a global picture of the dynamics of gene expression, in which individual genes and arrays appear to be classified into groups of similar regulation and function, or similar cellular state and biological phenotype, respectively. After normalization and sorting, the significant eigengenes and eigenarrays can be associated with observed genome-wide effects of regulators, or with measured samples, in which these regulators are overactive or underactive, respectively.

Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling

Preface 1.General Considerations 2.Basic Processes in Atomization 3.Drop Size Distributions of Sprays 4.Atomizers 5.Flow in Atomizers 6.Atomizer Performance 7.External Spray Charcteristics 8.Drop Evaporation 9.Drop Sizing Methods Index

Atomization and Sprays

To improve the performance of particle image velocimetry in measuring instantaneous velocity fields, direct cross-correlation of image fields can be used in place of auto-correlation methods of interrogation of double- or multiple-exposure recordings. With improved speed of photographic recording and increased resolution of video array detectors, cross-correlation methods of interrogation of successive single-exposure frames can be used to measure the separation of pairs of particle images between successive frames. By knowing the extent of image shifting used in a multiple-exposure and by a priori knowledge of the mean flow-field, the cross-correlation of different sized interrogation spots with known separation can be optimized in terms of spatial resolution, detection rate, accuracy and reliability.

Theory of cross-correlation analysis of PIV images : Image analysis as measuring technique in flows

流体力学杂志“Journal of Fluid Mechanics”由剑桥大学教授George Batchelor在1956年5月创办，在国际流体力学界享有很高的学术声望，被公认为是流体力学最著名的学术刊物之一，2005年的影响因子为2．061，雄居同类期刊之首．在它创刊50周年之际，2006年5月JFM出版了第554卷的纪念特刊，其中刊登了现任主编（美国西北大学S．H．Davis教授和英国剑桥大学T．J．Pedley教授）合写的述评：“Editorial：JFM at50”，以JFM为背景，从独特的视角对近50年来流体力学的发展进行了简明的回顾和展望，并归纳了一系列非常有启发性的有趣统计数字．2006年7月21日在剑桥大学应用数学和理论物理研究所（DAMTP）举行了创刊50周年的庆祝会．下午2点，JFM的新老编辑和来宾会聚一堂，Pedley教授致开幕词，其后是5个精彩的报告：The mysterious rattleback and its fluid counterpart（Keith Moffatt），Developments in shear instabilities（Patrick Huerre），Falling clouds（Elisabeth Guazzelli），Ecotectural fluid mechanics（Paul Linden），The success of JFM（Herbert Huppert），最后由Davis教授致闭幕词．

Journal of Fluid Mechanics创刊50周年

https://apm.iitm.ac.in/fmlab/mvp/files/Fuel_mahesh.pdf

Spatial droplet velocity and size profiles in effervescent atomizer-produced sprays

The utility of the Cassie-Baxter formula to predict the apparent contact angle of a drop on rough hydrophobic surfaces has been questioned recently. To resolve this issue, experimental and numerical data for advancing and receding contact angles are reported. In all cases considered it is seen that contact angles follow the overall trend of the Cassie-Baxter formula, except for the advancing front on pillar type roughness. It is shown that deviations from the Cassie-Baxter angle have a one-to-one correlation with microscopic distortions of the contact line with respect to its configuration in the Cassie-Baxter state.

Is the Cassie-Baxter formula relevant?

We introduce a phase field model of wetting of surfaces by sessile drops. The theory uses a two-dimensional non-conserved phase field variable to parametrize the Gibbs free energy of the three-dimensional system. Contact line tension and contact angle hysteresis arise from the gradient term in the free energy and the kinetic coefficient respectively. A significant advantage of this approach is in the constitutive specification of hysteresis. The advancing and receding angles of a surface, the liquid–vapor interfacial energy and three-phase line tension are the only required constitutive inputs to the model. We first simulate hysteresis on a smooth chemically homogeneous surface using this theory. Next we show that it is possible to study heterogeneous surfaces whose component surfaces are themselves hysteretic. We use this theory to examine the wetting of a surface containing a circular heterogeneous island. The contact angle for this case is found to be determined solely by the material properties at the contact line in accord with recent experimental data.

/pdf/constitutive-modeling-of-contact-angle-hysteresis-k1z2z16e3v.pdf

Constitutive modeling of contact angle hysteresis.

We report a simple evaporation process using liquid marbles as precursors to produce high sphericity, precisely diameter controlled polyelectrolyte microspheres. We use poly(diallyldimethylammonium chloride) (PDDA) as the test polyelectrolyte for this experimental study. We present measurements of the rate of mass loss during evaporation to demonstrate evidence of two limiting physical processes. At short times, the rate of mass loss is well described by the "D(2) law" regime, which is vapor diffusion limited. At long times, the rate of water diffusion inside the nearly solid polyelectrolyte microsphere becomes the rate-limiting step. The transition between these two limiting processes is accompanied by changes in the physical morphology inside the microsphere. We compare the estimated values of the water diffusion coefficients with the values reported in the literature to demonstrate good agreement.

On synthesizing solid polyelectrolyte microspheres from evaporating liquid marbles.

We propose a novel approach to describe wetting of plane solid surfaces by liquid drops. A two-dimensional nonconserved phase field variable is employed to distinguish between wetted and nonwetted regions on the surface. The imbalance in the Young's force provides for the exchange of relative stability of the two phases. The three-phase contact line tension arises from the gradient energy and contact angle hysteresis from the kinetic coefficient. Using this theory, we discuss contact angle hysteresis on chemically heterogeneous surfaces. We show significant departure from the classical Cassie theory, which is attributed to defect pinning of the continuous triple line.

/pdf/phase-field-modeling-of-hysteresis-in-sessile-drops-45i7htyvwf.pdf

Mahesh V. Panchagnula

Papers

Spatial droplet velocity and size profiles in effervescent atomizer-produced sprays

Is the Cassie-Baxter formula relevant?

Constitutive modeling of contact angle hysteresis.

On synthesizing solid polyelectrolyte microspheres from evaporating liquid marbles.

Phase field modeling of hysteresis in sessile drops.