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Todd J. Martínez

Bio: Todd J. Martínez is an academic researcher from Stanford University. The author has contributed to research in topics: Excited state & Ab initio multiple spawning. The author has an hindex of 85, co-authored 370 publications receiving 23083 citations. Previous affiliations of Todd J. Martínez include Nanyang Technological University & Arizona State University.


Papers
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Journal ArticleDOI
07 May 2009-Nature
TL;DR: It is found that pronounced changes in colour and fluorescence emerge with the accumulation of plastic deformation, indicating that in these polymeric materials the transduction of mechanical force into the ring-opening reaction is an activated process.
Abstract: Biology is replete with materials systems that actively and functionally respond to mechanical stimuli and thereby enable physiological processes such as the sense of touch, hearing or the growth of tissue and bone. In contrast, exposing polymers to large stresses tends to result in covalent bond rupture and hence damage or failure. Davis et al. now demonstrate that synthetic materials can be rationally designed to ensure that mechanical stress alters their properties in a useful manner. This is realized by incorporating a chemical group that responds to mechanical stress by changing its colour to red as it undergoes a ring-opening reaction, enabling the team to directly monitor the accumulation of plastic deformation. The principles underpinning this work should enable the development of other force-responsive chemical groups that could impart synthetic materials with desirable functionalities ranging from damage sensing to fully regenerative self-healing. Exposing synthetic materials to large stresses tends to result in simple failure, unlike many biological systems, which respond by enabling physiological processes such as hearing and balance. But by incorporating a chemical group that responds to mechanical stress by changing its colour, it is possible to monitor the accumulation of plastic deformation directly in a synthetic polymer. This principle could be used to design synthetic materials with desirable functionalities ranging from damage sensing to fully regenerative self-healing. Mechanochemical transduction enables an extraordinary range of physiological processes such as the sense of touch, hearing, balance, muscle contraction, and the growth and remodelling of tissue and bone1,2,3,4,5,6. Although biology is replete with materials systems that actively and functionally respond to mechanical stimuli, the default mechanochemical reaction of bulk polymers to large external stress is the unselective scission of covalent bonds, resulting in damage or failure7. An alternative to this degradation process is the rational molecular design of synthetic materials such that mechanical stress favourably alters material properties. A few mechanosensitive polymers with this property have been developed8,9,10,11,12,13,14; but their active response is mediated through non-covalent processes, which may limit the extent to which properties can be modified and the long-term stability in structural materials. Previously, we have shown with dissolved polymer strands incorporating mechanically sensitive chemical groups—so-called mechanophores—that the directional nature of mechanical forces can selectively break and re-form covalent bonds15,16. We now demonstrate that such force-induced covalent-bond activation can also be realized with mechanophore-linked elastomeric and glassy polymers, by using a mechanophore that changes colour as it undergoes a reversible electrocyclic ring-opening reaction under tensile stress and thus allows us to directly and locally visualize the mechanochemical reaction. We find that pronounced changes in colour and fluorescence emerge with the accumulation of plastic deformation, indicating that in these polymeric materials the transduction of mechanical force into the ring-opening reaction is an activated process. We anticipate that force activation of covalent bonds can serve as a general strategy for the development of new mechanophore building blocks that impart polymeric materials with desirable functionalities ranging from damage sensing to fully regenerative self-healing.

1,367 citations

Journal ArticleDOI
TL;DR: The role of conical intersections and charge transfer in the photoisomerization mechanism is emphasized and the standard model for photoinduced cis-trans isomerization about carbon double bonds is framed in terms of two electronic states and a one-dimensional reaction coordinate.
Abstract: The standard model for photoinduced cis-trans isomerization about carbon double bonds is framed in terms of two electronic states and a one-dimensional reaction coordinate. We review recent work that suggests that a minimal picture of the reaction mechanism requires the consideration of at least two molecular coordinates and three electronic states. In this chapter, we emphasize the role of conical intersections and charge transfer in the photoisomerization mechanism.

761 citations

Journal ArticleDOI
TL;DR: The ab initio multiple spawning (AIMS) method is a time-dependent formulation of quantum chemistry, whereby the nuclear dynamics and electronic structure problems are solved simultaneously as mentioned in this paper. But it does not consider the nonadiabatic effects which are crucial in modeling dynamics on multiple electronic states.
Abstract: The ab initio multiple spawning (AIMS) method is a time-dependent formulation of quantum chemistry, whereby the nuclear dynamics and electronic structure problems are solved simultaneously. Quantum mechanical effects in the nuclear dynamics are included, especially the nonadiabatic effects which are crucial in modeling dynamics on multiple electronic states. The AIMS method makes it possible to describe photochemistry from first principles molecular dynamics, with no empirical parameters. We describe the method and present the application to two molecules of interest in organic photochemistryethylene and cyclobutene. We show that the photodynamics of ethylene involves both covalent and ionic electronic excited states and the return to the ground state proceeds through a pyramidalized geometry. For the photoinduced ring opening of cyclobutene, we show that the disrotatory motion predicted by the Woodward−Hoffmann rules is established within the first 50 fs after optical excitation.

724 citations

Journal ArticleDOI
TL;DR: It is demonstrated that a video gaming machine containing two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree-Fock energy + gradient calculations.
Abstract: We demonstrate that a video gaming machine containing two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree−Fock energy + gradient calculations. Such performance makes it possible to run large scale Hartree−Fock and Density Functional Theory calculations, which typically require hundreds of traditional processor cores, on a single workstation. Benchmark Born−Oppenheimer molecular dynamics simulations are performed on two molecular systems using the 3-21G basis set - a hydronium ion solvated by 30 waters (94 atoms, 405 basis functions) and an aspartic acid molecule solvated by 147 waters (457 atoms, 2014 basis functions). Our GPU implementation can perform 27 ps/day and 0.7 ps/day of ab initio molecular dynamics simulation on a single desktop computer for these systems.

719 citations

Journal ArticleDOI
TL;DR: In this paper, a new method for minimal energy conical intersection (MECI) searches was proposed, which does not require knowledge of the non-adiabatic coupling vector.
Abstract: There is a clear need for computationally inexpensive electronic structure theory methods which can model excited state potential energy surfaces. Time-dependent density functional theory (TDDFT) has emerged as one of the most promising contenders in this context. Many previous tests have concentrated on vertical excitation energies, which can be compared to experimental absorption maxima. Here, we focus attention on more global aspects of the resulting potential energy surfaces, especially conical intersections which play a key role in photochemical mechanisms. We introduce a new method for minimal energy conical intersection (MECI) searches which does not require knowledge of the non-adiabatic coupling vector. Using this new method, we compute MECI geometries with multi-state complete active space perturbation theory (MS-CASPT2) and TDDFT. We show that TDDFT in the linear response and adiabatic approximations can predict MECI geometries and energetics quite accurately, but that there are a number of qualitative deficiencies which need to be addressed before TDDFT can be used routinely in photochemical problems.

562 citations


Cited by
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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: The all-atom additive CHARMM36 protein force field is refinement is presented, with improved accuracy in generating polypeptide backbone conformational ensembles for intrinsically disordered peptides and proteins.
Abstract: An all-atom protein force field, CHARMM36m, offers improved accuracy for simulating intrinsically disordered peptides and proteins. The all-atom additive CHARMM36 protein force field is widely used in molecular modeling and simulations. We present its refinement, CHARMM36m ( http://mackerell.umaryland.edu/charmm_ff.shtml ), with improved accuracy in generating polypeptide backbone conformational ensembles for intrinsically disordered peptides and proteins.

3,299 citations

01 Jan 2016
TL;DR: The principles of fluorescence spectroscopy is universally compatible with any devices to read and is available in the digital library an online access to it is set as public so you can download it instantly.
Abstract: Thank you very much for downloading principles of fluorescence spectroscopy. As you may know, people have look hundreds times for their favorite novels like this principles of fluorescence spectroscopy, but end up in malicious downloads. Rather than reading a good book with a cup of tea in the afternoon, instead they cope with some harmful bugs inside their desktop computer. principles of fluorescence spectroscopy is available in our digital library an online access to it is set as public so you can download it instantly. Our digital library spans in multiple locations, allowing you to get the most less latency time to download any of our books like this one. Kindly say, the principles of fluorescence spectroscopy is universally compatible with any devices to read.

2,960 citations