Author
Pengfei Huo
Other affiliations: Boston University, California Institute of Technology, The Institute of Optics
Bio: Pengfei Huo is an academic researcher from University of Rochester. The author has contributed to research in topics: Quantum dynamics & Adiabatic process. The author has an hindex of 20, co-authored 49 publications receiving 1522 citations. Previous affiliations of Pengfei Huo include Boston University & California Institute of Technology.
Topics: Quantum dynamics, Adiabatic process, Polariton, Diabatic, Quantum
Papers
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TL;DR: Results are presented which indicate that, even though the method is based on a "mean trajectory" like scheme, it can accurately capture electronic population branching through multiple avoided crossing regions and that the approach offers a robust and reliable way to treat quantum dynamical phenomena in a wide range of condensed phase applications.
Abstract: An approach for treating dissipative, non-adiabatic quantum dynamics in general model systems at finite temperature based on linearizing the density matrix evolution in the forward-backward path difference for the environment degrees of freedom is presented. We demonstrate that the approach can capture both short time coherent quantum dynamics and long time thermal equilibration in an application to excitation energy transfer in a model photosynthetic light harvesting complex. Results are also presented for some nonadiabatic scattering models which indicate that, even though the method is based on a "mean trajectory" like scheme, it can accurately capture electronic population branching through multiple avoided crossing regions and that the approach offers a robust and reliable way to treat quantum dynamical phenomena in a wide range of condensed phase applications.
162 citations
TL;DR: This paper extends the recently developed iterative linearized density matrix (ILDM) propagation scheme and demonstrates that it successfully describes the coherent beating of the site populations on different chromophores and gives good agreement with other methods that have been developed recently for going beyond the usual approximations, thus providing a new reliable theoretical tool to study coherent exciton transfer in light harvesting systems.
Abstract: Rather than incoherent hopping between chromophores, experimental evidence suggests that the excitation energy transfer in some biological light harvesting systems initially occurs coherently, and involves coherent superposition states in which excitation spreads over multiple chromophores separated by several nanometers. Treating such delocalized coherent superposition states in the presence of decoherence and dissipation arising from coupling to an environment is a significant challenge for conventional theoretical tools that either use a perturbative approach or make the Markovian approximation. In this paper, we extend the recently developed iterative linearized density matrix (ILDM) propagation scheme [E. R. Dunkel et al., J. Chem. Phys. 129, 114106 (2008)] to study coherent excitation energy transfer in a model of the Fenna–Matthews–Olsen light harvesting complex from green sulfur bacteria. This approach is nonperturbative and uses a discrete path integral description employing a short time approxim...
151 citations
TL;DR: The most recent crystal structure of the Fenna-Matthews-Olson (FMO) protein complex indicates the presence of an additional eighth chromophore, which has been proposed to serve as a link between th...
Abstract: The most recent crystal structure of the Fenna–Matthews–Olson (FMO) protein complex indicates the presence of an additional eighth chromophore, which has been proposed to serve as a link between th...
137 citations
TL;DR: This article reviews recent progress in the theoretical modeling of excitation energy transfer processes in natural light harvesting complexes and concludes that the iterative partial linearized density matrix path-integral propagation approach provides an accurate and efficient way to model the nonadiabatic quantum dynamics at the heart of these EET processes.
Abstract: This article reviews recent progress in the theoretical modeling of excitation energy transfer (EET) processes in natural light harvesting complexes. The iterative partial linearized density matrix path-integral propagation approach, which involves both forward and backward propagation of electronic degrees of freedom together with a linearized, short-time approximation for the nuclear degrees of freedom, provides an accurate and efficient way to model the nonadiabatic quantum dynamics at the heart of these EET processes. Combined with a recently developed chromophore-protein interaction model that incorporates both accurate ab initio descriptions of intracomplex vibrations and chromophore-protein interactions treated with atomistic detail, these simulation tools are beginning to unravel the detailed EET pathways and relaxation dynamics in light harvesting complexes.
130 citations
TL;DR: Results from direct quantum dynamics simulations reveal basic principles of polariton photochemistry as well as promising reactivities that take advantage of intrinsic quantum behaviors of photons.
Abstract: We perform quantum dynamics simulations to investigate new chemical reactivities enabled by cavity quantum electrodynamics. The quantum light–matter interactions between the molecule and the quanti...
116 citations
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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
28 Jul 2005
TL;DR: 曼氏血吸虫感染后，宿主活化CD4^＋Th2细胞Ｌ分泌IL-4、IL-5和 IL-13。
Abstract: 入侵病原体与宿主之间呈动态平衡，以维持病原体成功地寄生在宿主体内而不致宿主死亡，这是许多寄生虫感染的一个重要特征。包括曼氏血吸虫在内的许多蠕虫感染中，持续的炎症反应比病原体本身对宿主的危害更大，降低宿主的免疫反应具有重要意义。曼氏血吸虫感染后，宿主活化CD4^＋Th2细胞，分泌IL-4、IL-5和IL-13。最近研究表明IL-13是肝组织纤维化的重要调节因子。
583 citations
TL;DR: This Perspective examines the most significant theoretical and computational obstacles to achieving nonadiabatic dynamics realism, and suggests some possible strategies that may prove fruitful.
Abstract: Nonadiabatic dynamics—nuclear motion evolving on multiple potential energy surfaces—has captivated the interest of chemists for decades. Exciting advances in experimentation and theory have combined to greatly enhance our understanding of the rates and pathways of nonadiabatic chemical transformations. Nevertheless, there is a growing urgency for further development of theories that are practical and yet capable of reliable predictions, driven by fields such as solar energy, interstellar and atmospheric chemistry, photochemistry, vision, single molecule electronics, radiation damage, and many more. This Perspective examines the most significant theoretical and computational obstacles to achieving this goal, and suggests some possible strategies that may prove fruitful.
524 citations
Princeton University1, University of California, Berkeley2, Northwestern University3, Argonne National Laboratory4, Harvard University5, University of Freiburg6, Boston University7, University of Chicago8, VU University Amsterdam9, National Institutes of Natural Sciences, Japan10, University of Colorado Boulder11, University of Ottawa12, Michigan State University13, University of California, Irvine14, University of Michigan15, University College London16, Temple University17, Lawrence Berkeley National Laboratory18, Columbia University19
TL;DR: The state of recent discoveries is surveyed, viewpoints that suggest that coherence can be used in complex chemical systems are presented, and the role of coherence as a design element in realizing function is discussed.
Abstract: Coherence phenomena arise from interference, or the addition, of wave-like amplitudes with fixed phase differences. Although coherence has been shown to yield transformative ways for improving function, advances have been confined to pristine matter and coherence was considered fragile. However, recent evidence of coherence in chemical and biological systems suggests that the phenomena are robust and can survive in the face of disorder and noise. Here we survey the state of recent discoveries, present viewpoints that suggest that coherence can be used in complex chemical systems, and discuss the role of coherence as a design element in realizing function.
502 citations
TL;DR: The PYXAID program is introduced, developed for non-adiabatic molecular dynamics simulations in condensed matter systems and used to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states.
Abstract: This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The prog...
501 citations