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Author

Davide Donadio

Other affiliations: ETH Zurich, Max Planck Society, University of California  ...read more
Bio: Davide Donadio is an academic researcher from University of California, Davis. The author has contributed to research in topics: Thermal conductivity & Phonon. The author has an hindex of 46, co-authored 171 publications receiving 17239 citations. Previous affiliations of Davide Donadio include ETH Zurich & Max Planck Society.


Papers
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Journal ArticleDOI
TL;DR: In this paper, the authors present a new molecular dynamics algorithm for sampling the canonical distribution, where the velocities of all the particles are rescaled by a properly chosen random factor.
Abstract: The authors present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.

11,327 citations

Journal Article
TL;DR: The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution and can be used to measure the accuracy of the sampling.
Abstract: The authors present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.

2,402 citations

Journal ArticleDOI
TL;DR: In this paper, a new molecular dynamics algorithm for sampling the canonical distribution is presented, in which the velocities of all the particles are rescaled by a properly chosen random factor.
Abstract: We present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. We illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent on the thermostat parameter also with regard to the dynamic properties.

2,073 citations

Journal ArticleDOI
TL;DR: A series of routines that can be interfaced with the most popular classical molecular dynamics codes through a simple patching procedure, which leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available.

1,423 citations

Journal ArticleDOI
TL;DR: Interestingly and in contrast to bulk materials, at 300 K, thermal conductivity keeps increasing and remains logarithmically divergent with sample length even for sample lengths much larger than the average phonon mean free path, which provides fundamental understanding of thermal transport in two-dimensional materials.
Abstract: Graphene exhibits extraordinary electronic and mechanical properties, and extremely high thermal conductivity. Being a very stable atomically thick membrane that can be suspended between two leads, graphene provides a perfect test platform for studying thermal conductivity in two-dimensional systems, which is of primary importance for phonon transport in low-dimensional materials. Here we report experimental measurements and nonequilibrium molecular dynamics simulations of thermal conduction in suspended single-layer graphene as a function of both temperature and sample length. Interestingly and in contrast to bulk materials, at 300 K, thermal conductivity keeps increasing and remains logarithmically divergent with sample length even for sample lengths much larger than the average phonon mean free path. This result is a consequence of the two-dimensional nature of phonons in graphene, and provides fundamental understanding of thermal transport in two-dimensional materials.

791 citations


Cited by
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[...]

08 Dec 2001-BMJ
TL;DR: There is, I think, something ethereal about i —the square root of minus one, which seems an odd beast at that time—an intruder hovering on the edge of reality.
Abstract: 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 …

33,785 citations

01 May 1993
TL;DR: 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.
Abstract: 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.

29,323 citations

28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组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�ly.
Abstract: 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。

18,940 citations

Journal ArticleDOI
TL;DR: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules, and provides a rich set of calculation types.

12,985 citations