Content of SPECIAL TOPIC—8th IUPAP International Conference on Biological Physics in our journal

Published in last 1 year |  In last 2 years |  In last 3 years |  All Please wait a minute... For selected: Download citations EndNote Ris BibTeX Toggle thumbnails Select The construction of general basis functions in reweighting ensemble dynamics simulations: Reproduce equilibrium distribution in complex systems from multiple short simulation trajectories Zhang Chuan-Biao (张传彪), Li Ming (黎明), Zhou Xin (周昕) Chin. Phys. B, 2015, 24 (12): 120202.   DOI: 10.1088/1674-1056/24/12/120202 Abstract （662）   HTML    PDF （1126KB）（372）       Knowledge map    Ensemble simulations, which use multiple short independent trajectories from dispersive initial conformations, rather than a single long trajectory as used in traditional simulations, are expected to sample complex systems such as biomolecules much more efficiently. The re-weighted ensemble dynamics (RED) is designed to combine these short trajectories to reconstruct the global equilibrium distribution. In the RED, a number of conformational functions, named as basis functions, are applied to relate these trajectories to each other, then a detailed-balance-based linear equation is built, whose solution provides the weights of these trajectories in equilibrium distribution. Thus, the sufficient and efficient selection of basis functions is critical to the practical application of RED. Here, we review and present a few possible ways to generally construct basis functions for applying the RED in complex molecular systems. Especially, for systems with less priori knowledge, we could generally use the root mean squared deviation (RMSD) among conformations to split the whole conformational space into a set of cells, then use the RMSD-based-cell functions as basis functions. We demonstrate the application of the RED in typical systems, including a two-dimensional toy model, the lattice Potts model, and a short peptide system. The results indicate that the RED with the constructions of basis functions not only more efficiently sample the complex systems, but also provide a general way to understand the metastable structure of conformational space. Select Langevin approach with rescaled noise for stochastic channel dynamics in Hodgkin-Huxley neurons Huang Yan-Dong (黄艳东), Li Xiang (李翔), Shuai Jian-Wei (帅建伟) Chin. Phys. B, 2015, 24 (12): 120501.   DOI: 10.1088/1674-1056/24/12/120501 Abstract （590）   HTML    PDF （1088KB）（333）       Knowledge map    The Langevin approach has been applied to model the random open and closing dynamics of ion channels. It has long been known that the gate-based Langevin approach is not sufficiently accurate to reproduce the statistics of stochastic channel dynamics in Hodgkin-Huxley neurons. Here, we introduce a modified gate-based Langevin approach with rescaled noise strength to simulate stochastic channel dynamics. The rescaled independent gate and identical gate Langevin approaches improve the statistical results for the mean membrane voltage, inter-spike interval, and spike amplitude. Select Saturated sodium chloride solution under an external static electric field: A molecular dynamics study Ren Gan (任淦), Wang Yan-Ting (王延颋) Chin. Phys. B, 2015, 24 (12): 126402.   DOI: 10.1088/1674-1056/24/12/126402 Abstract （570）   HTML    PDF （2820KB）（914）       Knowledge map    The behavior of saturated aqueous NaCl solutions under a constant external electric field (E) was studied by molecular dynamics (MD) simulation. Our dynamic MD simulations indicated that the irreversible nucleation process towards crystallization is accelerated by a moderate E but retarded or even prohibited under a stronger E, which can be understood by the competition between self-diffusion and drift motion. The former increases with E, thereby accelerating the nucleation process, whereas the latter pulls oppositely charged ions apart under a stronger E, thereby decelerating nucleation. Additionally, our steady-state MD simulations indicated that a first-order phase transition occurs in saturated solutions at a certain threshold Ec. The magnitude of Ec increases with concentration because larger clusters form more easily when the solution is more concentrated and require a stronger E to dissociate. Select Colloidally deposited nanoparticle wires for biophysical detection Sophie C. Shen, Liu Wen-Tao (刘文韬), Diao Jia-Jie (刁佳杰) Chin. Phys. B, 2015, 24 (12): 127308.   DOI: 10.1088/1674-1056/24/12/127308 Abstract （569）   HTML    PDF （1771KB）（371）       Knowledge map    Among the techniques developed to prepare nanoparticle wires for multiple applications, the colloidal deposition method at interface has been regarded as cost-efficient and eco-friendly, and hence has attracted an increasing amount of research attention. In this report, the recent developments in preparing nanoparticle wires and integrated nanoparticle wire arrays using this technique have been reviewed. Furthermore, we have also discussed the application of these nanoparticle structures in detecting chemical and biological molecules. Select Label-free surface-enhanced infrared spectro-electro-chemical analysis of the Redox potential shift of cytochrome c complexed with a cardiolipin-containing lipid membrane of varied composition Liu Li (刘丽), Wu Lie (武烈), Zeng Li (曾丽), Jiang Xiu-E (姜秀娥) Chin. Phys. B, 2015, 24 (12): 128201.   DOI: 10.1088/1674-1056/24/12/128201 Abstract （459）   HTML    PDF （1195KB）（257）       Knowledge map    In this study, a lipid membrane was fabricated by fusing cardiolipin-phosphatidylcholine (CL_PC, 1:4) vesicles onto a hydrophobic surface of 1-dodecanethiol (DT) preadsorbed on a nanostructured gold film. By changing the concentration of the DT adsorption solution, we constructed a series of CL_PC-DT bilayers with different hydrophobicity to study the effects of lipid membrane characteristics on the adsorption conformation of cytochrome c (Cyt c). Electrochemical analysis showed that the formal potential is 0.24 V for Cyt c-CL_PC-DT(10), 0.2 V for Cyt c-CL_PC-DT(20), and 0.16 V for Cyt c-CL_PC-DT(40)–a gradual positive shift with the decreasing DT concentration–relative to the potential of native cyt c (0.02 V). Potential-induced surface-enhanced infrared adsorption difference spectroscopy revealed that the gradual positive shift of the formal potential of CL-bound cyt c is determined by the environment with the gradually lowered dielectric constant for the heme cofactor in CL-bound cyt c (Fe3+). Select Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58 Yu Jia-Feng (于家峰), Sui Tian-Xiang (隋天翔), Wang Hong-Mei (王红梅), Wang Chun-Ling (王春玲), Jing Li (荆莉), Wang Ji-Hua (王吉华) Chin. Phys. B, 2015, 24 (12): 128202.   DOI: 10.1088/1674-1056/24/12/128202 Abstract （593）   HTML    PDF （468KB）（293）       Knowledge map    Agrobacterium tumefaciens strain C58 is a type of pathogen that can cause tumors in some dicotyledonous plants. Ever since the genome of A. tumefaciens strain C58 was sequenced, the quality of annotation of its protein-coding genes has been queried continually, because the annotation varies greatly among different databases. In this paper, the questionable hypothetical genes were re-predicted by integrating the TN curve and Z curve methods. As a result, 30 genes originally annotated as “hypothetical” were discriminated as being non-coding sequences. By testing the re-prediction program 10 times on data sets composed of the function-known genes, the mean accuracy of 99.99% and mean Matthews correlation coefficient value of 0.9999 were obtained. Further sequence analysis and COG analysis showed that the re-annotation results were very reliable. This work can provide an efficient tool and data resources for future studies of A. tumefaciens strain C58. Select Catch-bond behavior of DNA condensate under tension Li Wei (李伟), Wong Wei-Juan, Lim Ci-Ji, Ju Hai-Peng (车海鹏), Li Ming (李明), Yan Jie (严洁), Wang Peng-Ye (王鹏业) Chin. Phys. B, 2015, 24 (12): 128704.   DOI: 10.1088/1674-1056/24/12/128704 Abstract （634）   HTML    PDF （1587KB）（323）       Knowledge map    Toroid formation is an important mechanism underlying DNA condensation, which has been investigated extensively by single-molecule experiments in vitro. Here, the de-condensation dynamics of DNA condensates were studied using magnetic tweezers combined with Brownian dynamics simulations. The experimental results revealed a surprising non-monotonic dependence of the unfolding rate on the force applied under strong adhesion conditions, resembling the catch-bond behavior reported in the field of ligand-receptor interactions. Simulation results showed that the different unfolding pathways of DNA condensate under large forces derive from the force-dependent deformation of the DNA toroid, which explains the catch-bond behavior of DNA condensate in the magnetic tweezers experiments. These results challenge the universality of the regular toroidal DNA unwrapping mechanism and provide the most complete description to date of multivalent cation-dependent DNA unwrapping under tension. Select Comparison of ligand migration and binding in heme proteins of the globin family Karin Nienhaus, G. Ulrich Nienhaus Chin. Phys. B, 2015, 24 (12): 128705.   DOI: 10.1088/1674-1056/24/12/128705 Abstract （484）   HTML    PDF （1569KB）（268）       Knowledge map    The binding of small diatomic ligands such as carbon monoxide or dioxygen to heme proteins is among the simplest biological processes known. Still, it has taken many decades to understand the mechanistic aspects of this process in full detail. Here, we compare ligand binding in three heme proteins of the globin family, myoglobin, a dimeric hemoglobin, and neuroglobin. The combination of structural, spectroscopic, and kinetic experiments over many years by many laboratories has revealed common properties of globins and a clear mechanistic picture of ligand binding at the molecular level. In addition to the ligand binding site at the heme iron, a primary ligand docking site exists that ensures efficient ligand binding to and release from the heme iron. Additional, secondary docking sites can greatly facilitate ligand escape after its dissociation from the heme. Although there is only indirect evidence at present, a preformed histidine gate appears to exist that allows ligand entry to and exit from the active site. The importance of these features can be assessed by studies involving modified proteins (via site-directed mutagenesis) and comparison with heme proteins not belonging to the globin family. Select One-dimensional chain of quantum molecule motors as a mathematical physics model for muscle fibers Si Tie-Yan (司铁岩) Chin. Phys. B, 2015, 24 (12): 128708.   DOI: 10.1088/1674-1056/24/12/128708 Abstract （517）   HTML    PDF （615KB）（311）       Knowledge map    A quantum chain model of multiple molecule motors is proposed as a mathematical physics theory for the microscopic modeling of classical force-velocity relation and tension transients in muscle fibers. The proposed model was a quantum many-particle Hamiltonian to predict the force-velocity relation for the slow release of muscle fibers, which has not yet been empirically defined and was much more complicated than the hyperbolic relationships. Using the same Hamiltonian model, a mathematical force-velocity relationship was proposed to explain the tension observed when the muscle was stimulated with an alternative electric current. The discrepancy between input electric frequency and the muscle oscillation frequency could be explained physically by the Doppler effect in this quantum chain model. Further more, quantum physics phenomena were applied to explore the tension time course of cardiac muscle and insect flight muscle. Most of the experimental tension transient curves were found to correspond to the theoretical output of quantum two- and three-level models. Mathematical modeling electric stimulus as photons exciting a quantum three-level particle reproduced most of the tension transient curves of water bug Lethocerus maximus.