Introduction

Research of atomic and molecular physics under extreme conditions is an important direction of physics study in 21st century,which are of great scientific significance but also  can push forward the national strategic high technology and the related interdisciplinary research. Our group focus on the research of cold atomic physics, ultraclold neutral plasma  and the interaction of matter with a strong laser field. Such investigation are not only a fundamental problem of atomic and molecular physics, plasma physics and  condensed matter physics and quantum information sciences,  , but also have comprehensive applications in inertial-confinement fusion ,and  new energy weapon physics, etc.

Introduction

Founded in 2003, the Laboratory for Biomechanics of Animal Locomotion (BALL) addresses itself to the research on biomechanics and bionics of the flying and swimming animals, such as insects, bats, fish and dolphins. The interaction between the animal’s flexible physical bodies and the surrounding fluid (air or water) can generate the forces which are needed in its locomotion. The high performance of animal locomotion is magic and interesting, with that more and more researchers and students fall in study. The subjects involve not only the fluid dynamics, but also the motor nerve, muscle mechanics, structure dynamics, mechanical constitutive relations of biomaterials et al.

The research on fish swimming in this lab can be traced back to the 1980s. The group, led by Professor TONG Bing-Gang, developed the three-dimensional waving plate theory to investigate the swimming performance of fish undulatory motion. The three-dimensional effects, considered firstly following Lighthill’s classical elongated body theory and T.Y. Wu’s 2D waving plate, can be reduced by the undulatory motion. This work was cited around the world, and it has been reviewed in Triantafyllou’s paper (Annual Review of Fluid Mechanics, 2000).

By the turn of the century, Professor TONG organized an effective research team in the biomechanics, including his group and the big mechanical engineering group in the University of Science and Technology of China (USTC). In this team, the materials and methods, including in vivo visualization of experiments, model experiments, numerical simulation and theoretical modeling, has been developed systematicly. The interactional exchange is frequent day by day.

In 2003, the Laboratory for Biomechanics of Animal Locomotion was founded in the Graduate School of Chinese Academy of Sciences. In the same year, the team prepared and organized the 214th XiangShan-Science Conference – “Biomechanics and Bionics of flying and swimming animals”. Prof. TONG’s principal speech, as one of the two keynote speeches, and the other 5 special reports from this team were the part of total 19 reports in this conference. The team has been supported by 2 and 2 long-term funded projects from the National Science Funding of China (NSFC) and Chinese Academy of Sciences (CAS) respectively.

In the recent paper(Ann. Rev. Fluid Mech., 2011), T.Y. Wu’s reviewed the 7 papers, published by Prof. TONG and his PH.D students. in which the paper on theoretical modeling has been regarded as one of four representative articles for insect flapping flight under large angles of attack. He also has mentioned their in-house numerical platform two times, which coupled the deformable body dynamics and the fluid dynamics and successfully used in the study of free fish swimming.

The laboratory now is equipped with a set of high performance parallel computing cluster (160 CPU) and a circulating water channel, which can help the lab members to work on theoretical modeling, numerical studies and small experiments.

Welcome to the laboratory for biomechanics of animal locomotion.

Introduction
Theoretical and computational biophysics is a fast-evolving research field of biophysics, building theoretical models and using multiscale computer simulations to study the physical properties (structures, kinetics and thermodynamics) and biological functions of biomolecules and their complexes. Recently, we are particularly interested in macromolecules DNA and proteins.
 
Representative works
 
Stress-induced sequence-specific transition of DNA
dsDNA in vivo is topologically constrained. In mesophilic organisms dsDNA is usually negatively supercoiled (to the extent of 5-8% of supercoil density), which imposes significant twisting force on dsDNA and hence destabilizes the paring and stacking between bases. This inevitably induces structural transitions on dsDNA. Note that DNA is a heterogeneous macromolecule (DNA sequence is composed of 4 letters, A, G, T, C) , the transitions are always sequence-specific. Among the various transitions, local melting of the two strands of DNA ( i.e., bubble formation) is the most common case and has an impact on the functioning of DNA, for instance, to facilitating DNA duplication and gene transcription. Based on a well-known model (Benham model) to describe the bubble formation, we developed a novel and fast algorithm to calculate the melting profile of any DNA sequence, and observed an ubiquitous phenomenon in stress-induced melting, the inhibitory competition among distinct melted local regions, which is referred as Long-Range Allosteric Transition (LRAT) of DNA. After a detailed analysis of some eukaryotic DNA sequences, we found that LRAT may play a very important role in gene transcriptional regulation.
Related publications:
[1] Ming Li* and Zhong-can Ou-Yang, Predicting the function of eukaryotic scaffold/matrix attachment regions via DNA mechanics, J. Phys.: Condens. Matter, 2005,17:S2853-S2860
[2] Ming Li* and Zhong-can Ou-Yang, An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model, Thin Solid Film, 2006, 499:207-212
[3] Ming Li*, Zhong-Can Ou-Yang,DNA as active polymer: long-range allosteric effect and chromatin loop structure,Computer Physics Communications,2007,177:176–179
Walking mechanism of the motor protein kinesin-1
Conventional kinesin 1, the world’s tiniest biped porter, is one of the most intriguing and the best studied biomolecular machines. It is a protein homodimer, and each monomer consists of an N-terminal globular head domain, a stalk region responsible for dimerization, a neck linker that connects the head and stalk, and a C-terminal fan-shaped tail domain which can be linked to external loads. The N-terminal head domain contains a microtubule binding site, and a nucleotide binding site which can also catalyze ATP hydrolysis. Powered by the chemical energy of ATP hydrolysis, kinesin can perform a unidirectional and hand-over-hand walk along the microtubule for a long distance. How the chemical reaction couples to the walking and how the structure determines the walking behavior (e.g., direction, velocity, processivity ) are the central issues in the study of kinesin-1. The neck linker is believed to be one of the most important elements to shape the walking behavior. We have carried out several theoretical studies is that aspect. In particular, we studied how the neck linker length can significantly affect the stepping velocity of the motor, by using a highly simplified chemically powered ratchet model. We found that the length of the wild-type neck linker (_15 a.a.) might be optimally designed for kinesin-1 to approach the largest stepping velocity.
Related publications:
[1] Y.Shu, X. Zhang, Z.C. Ou-yang, and M. Li*, The neck linker of kinesin 1 seems optimally designed to approach the largest stepping velocity: a simulation study of an ideal model, J. Phys.: Condens. Matter 24 (2012) 035105
[2] Ming Li, Yaogen Shu, Zhong-can Ou-Yang,Mechanochemical coupling of kinesin studied with a neck-linker swing model, Communications in Theoretical Physics 51:1143-1148 (2009)
[3] Yaogen Shu, Ming Li*, Substeps of kinesin studied with a neck linker swing model, Modern Physics letters.B. 24(6) : 539–548 (2010)
Multiscale modeling and simulations
The understanding of complex life phenomena bases on the widely knowledge of individual behaviors of biopolymers and their interplays in cell, which have been very actively studied in experiments. Computer simulations of these macromolecules are expected to largely improve our knowledge in explanation of experiments and formation of theories. Due to very slow dynamics and the complexity of biologic macromolecules, the simulating researches are very initial even in single molecule or dilute solution of polymers. The most interesting properties of biological macromolecules are dependent on their local chemical details (such as, changes of key bases in DNA or RNA molecules strongly vary their global conformations and function). However, usual simulations with complete chemical details can not catch the long-time dynamics. For example, the present most simulations of protein folding are based on simple models without chemical details or only arrive at very short time. The situation is being improved by developing and applying multiscale modeling and simulating techniques in some particular systems. General multiscale methodology is also attempting. We focus on the development and applications of multiscale simulations to stude slow dynamics of DNA and proteins, including coarse-graining, enhanced sampling, accelerating molecular simulation, metastable state analyzing, sampling technique in path space etc.
Related publications:
[1] Shun Xu, Xin Zhou*, and Zhong-can Ou-Yang, Parallel Tempering Simulation on Generalized Canonical Ensemble,Parallel Tempering Simulation on Generalized Canonical Ensemble,Comm. in Comput. Phys. (in press),2012. 
[2] Linchen Gong, Xin Zhou*, Kinetic Transition Network based on Trajectory Mapping,Kinetic Transition Network based on Trajectory Mapping,J. Phys. Chem. B114, 10266,2010.
[3] Linchen Gong, Xin Zhou*, Structuring and Sampling in Complex Conformational Space: Weighted Ensemble Dynamics,Structuring and Sampling in Complex Conformational Space: Weighted Ensemble Dynamics,Phys. Rev. E80, 026707,2009.
[4] Xin Zhou*, Yi Jiang, Steen Rasmussen, and Hans Ziock, Bridging coarse-grained models by jump-in-sample simulations,Bridging coarse-grained models by jump-in-sample simulations,J. Chem. Phys. 128, 174017,2008
[5] Xin Zhou*, Yi Jiang, Kurt Kremer, Hans Ziock, and Steen Rasmussen, Hyperdynamics for entropic systems: Time-space compression and pair correlation function approximation, Phys. Rev. E Rapid Comm. 74, 035701, 2006.
[6] Xin Zhou, Denis Andrienko, Luigi Delle Site, and Kurt Kremer, Flow boundary conditions for chain-end adsorbing polymer blends, J Chem. Phys. 123, (2005) 104904-1 - 104904-6.
[7] Xin Zhou, Denis Andrienko, Luigi Delle Site, and Kurt Kremer,Dynamic surface decoupling in a sheared polymer melt polycarbonate melt sheared over a nickel surface, Europhys. Lett. 70, (2004) 264 - 270.

 

Introduction
The center has ten faculty members, who can be grouped into four research directions:
  1) Mathematical Physics, string theory, gravity, and Quantum Field Theory: Fu-Zhong Yang and Yu Tian;
2) Particle Physics and Phenomenology: Gang Hao, Cong-Feng Qiao, De-Shan Yang, and Qi-Shu Yan;
3) Nuclear and Many-body physics, Hadronic physics, and Quark and Hadron Matter: Guang-Xiong Peng and Lu Guo;
4) Astrophysics and Cosmology: Yun-Song Piao and Cui-Hua Du
Member
 
Piao, Yunsong: Inflational Cosmology and Theory of dark energy
 

Recently, the field of particle cosmology experienced an extraordinary development. The observations of type Ia supernova, the large-scale structure, and the cosmic microwave background have placed tight constraints on the standard cosmological model. Now it is widely believed that a breakthrough of the relevant theories will come from the intersection between cosmology and particle physics and that it may lead to a revolution in our understanding of fundamental physics. My research aims to understand the inflationary cosmology and the physics of the early universe relevant to inflation, and the theory of dark energy.

Yang, Deshan: Heavy flavor physics, QCD effective field theories, Quarkonium Physics, and origins of fermon masses and their mixings.
 

My research interests involves the following fields:
1. Heavy flavor physics & CP violation: The CP violation of the fundamental interactions is one of the necessary conditions for the existence of our universe. The heavy flavor physics is one of main fields to probe the origin of the CP violation in the Standard Model of particle physics and its possible extensions.

2. QCD factorization and effective field theories: The quantum chromodynamics (QCD) is a well-established theory for the strong interactions. The most important properties of QCD — the asymptotic freedom and color confinement, makes a typical high-energy processes involving strong interactions generally entangled with perturbative and non-perturbative contributions. To disentangle the perturbative contributions from the non-perturbative ones, the QCD factorization must hold. Recently, the effective field theory has been becoming one of the most powerful tools in proving the QCD factorization and perturbative calculations.

3. Quarkonium physics: The study on productions and decays of the quarkonium improves our understanding in the properties of QCD in non-relativistic bound-state system of heavy-quark and anti-heavy quark.

4. Origins of masses and mixings of fermions in the Standard Model and its extensions. In the SM and its various extensions, the origin of masses and mixings of fermions is due to the Yukawa couplings which are not well-constrained. Thus the masses and mixings of fermions become the main sources of the free parameters in the SM and its extensions. The so-called horizontal symmetry and its breaking is one of the most popular way to study the patterns of masses and mixings of fermions observed in reality.

Yan Qishu: Collider Physics, New Physics search at LHC, and Particle Phenomenology
 

The prime goal of LHC and ILC is to discover and to perform a pricision measurement on the TeV structure of the nature, respectively. The running of LHC and its data collection and analysis as well have further prompted the researches on TeV theories and the relevant phenomenological studies. Therefore to study the phenomenologies of various new models of TeV is meansingful, while to study how to test these models at LHC and ILC is practical and useful. I focuses on the study of the electroweak symmetry breaking mechanism and the mass origin at LHC, and plans to study at both LHC and ILC on 1) properties and detection methods of Higgs bosons for varies TeV models,2) the detection of dark matter particles, 3) the detection of other new particles, like new vector bosons, new colored fermion, and so on. I hope that my research can promote and deepen our understanding on the TeV structure of nature.

Peng, Guangxiong:
 

Strangeness physics, color superconductivity, equation of state of nuclear and quark matter, QCD phase transition, chiral condensates and medium effects, astrophysics, gauge theory, string theory, quantum gravity, neutrino physics, hadron physics etc.

Nuclear scince and techmology, analysis of nuclear reactions and applications.

Guo, Lu:
 

My research interests are theoretical nuclear physics and quantum many-body problems. I have been mainly engaged in three research directions, namely, (1) reaction mechanism of exotic nuclei and synthesis mechanism of superheavy elements, (2) theoretical studies of exotic nuclear structure and astrophysical related nuclear structure, (3) many-body theory and relevant numerical simulation.

 

Introduction

 

Theoretical condensed matter physics and computational materials physics [T(CMP)2] laboratory at University of Chinese Academy of Sciences (UCAS) is primarily devoted to studying theoretically the basic issues involved in condensed matter physics and materials science. 

Condensed matter physics is the science that deals with the structures, properties and fundamental laws of condensed matter. It is connecting atomic-scale physics to the properties of macroscopic systems or everyday things. The essence of the subject can be revealed in ten words: "The whole is more than the sum of its parts."The emergent phenomena are its main themes of exploration.

By invoking experimental, theoretical and computational methods, people push forward the advances of condensed matter physics through expected and unexpected discoveries, understanding exotic phenomena as well as properties of new materials, and so forth. Thus, condensed matter physics and materials physics are the twin subjects in physics.

Our research fields involve with quantum magnetism, molecular magnetism, strongly correlated systems, superconductivity, superfluidity, spintronics, computational materials physics and chemistry, mesoscopic physics, statistical physics, nanoscience, clean energy, etc.

The modern analytical and numerical methods in condensed matter physics are applied or proposed in our research, including bosonization, fermionization, conformal field theory, non-equilibrium Green function, various mean-field, quantum Monte Carlo, density-matrix renormalization group and variants, linearized tensor network renormalization group, DFT calculations, etc. The computing facility with PC clusters of 320 nodes is available, and the supercomputing resources in CAS can also be used.

For details, please go to: http://tcmp2.ucas.ac.cn/

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