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Search Results: 1 - 10 of 120121 matches for " Zhisong Wang "
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Synergic mechanism and fabrication target for bipedal nanomotors
Zhisong Wang
Physics , 2009, DOI: 10.1073/pnas.0703639104
Abstract: Inspired by dimeric motor proteins capable of undergoing transportation in living cells, significant efforts have been expended to the fabrication of track-walking nanomotors possessing two foot-like components that each can bind or detach from an array of anchorage groups on the track in response to local events of reagent consumption. The central problem in fabricating bipedal nanomotors is how the motor as a whole can gain the synergic capacity of directional track-walking, given the fact that each pedal component alone often is incapable of any directional drift. Implemented bipedal motors to date solve this thermodynamically intricate problem by an intuitive strategy that requires a hetero-pedal motor, multiple anchorage species for the track, and multiple reagent species for motor operation. Here we presented a detailed molecular mechanism by which motor-level directionality arises from a homo-pedal motor along a minimally heterogeneous track. Optimally, the operation may be reduced to a random supply of a single species of reagents to allow the motor's autonomous functioning. The mechanism suggests a distinct class of fabrication targets of drastically reduced system requirements. Intriguingly, a defective form of the mechanism falls into the realm of the well known Brownian motor mechanism, yet distinct features emerge from the normal working of the mechanism.
An Improved Kriging Interpolation Technique Based on SVM and Its Recovery Experiment in Oceanic Missing Data  [PDF]
Zhisong Huang, Huizan Wang, Ren Zhang
American Journal of Computational Mathematics (AJCM) , 2012, DOI: 10.4236/ajcm.2012.21007
Abstract: In Kriging interpolation, the types of variogram model are very finite, which make the variogram very difficult to describe the spatial distributional characteristics of true data. In order to overcome its shortage, an improved interpolation called Support Vector Machine-Kriging interpolation (SVM-Kriging) was proposed in this paper. The SVM-Kriging uses Least Square Support Vector Machine (LS-SVM) to fit the variogram, which needn’t select the basic variogram model and can directly get the optimal variogram of real interpolated field by using SVM to fit the variogram curve automatically. Based on GODAS data, by using the proposed SVM-Kriging and the general Kriging based on other traditional variogram models, the interpolation test was carried out and the interpolated results were analyzed contrastively. The test show that the variogram of SVM-Kriging can avoid the subjectivity of selecting the type of variogram models and the SVM-Kriging is better than the general Kriging based on other variogram model as a whole. Therefore, the SVM-Kriging is a good and adaptive interpolation method.
Role of directional fidelity in multiple extreme performance of F1-ATPase motor
Ruizheng Hou,Zhisong Wang
Physics , 2013, DOI: 10.1103/PhysRevE.88.022703
Abstract: Quantitative understanding of the best possible performance of nanomotors allowed by physical laws pertains to study of nanomotors from biology as well as nanotechnology. Biological nanomotor F1-ATPase is the best available model system as it is the only nanomotor known for extreme energy conversion near the limit of energy conservation. Using a unified theoretical framework centred on a concept called directional fidelity, we analyze recent experiments in which F1-motor's performance was measured for controlled chemical potentials, and expose from the experiments quantitative evidence for the motor's multiple extreme performance in directional fidelity, speed and catalytic capability close to physical limits. Specifically, the motor nearly exhausts available energy from the fuel to retain the highest possible directional fidelity for arbitrary load, encompassing the motor's extreme energy conversion and beyond. The theory-experiment comparison implies a tight chemomechanical coupling up to stalemate as futile steps occur but unlikely involve fuel consumption. The F1-motor data also helps clarify relation between directional fidelity and experimentally measured stepping ratio.
Directional fidelity of nanoscale motors and particles is limited by the second law of thermodynamics via a universal equality
Zhisong Wang,Ruizheng Hou,Artem Efremov
Physics , 2013, DOI: 10.1063/1.4813626
Abstract: Directional motion of nanoscale motors and driven particles in an isothermal environment costs a finite amount of energy despite zero work as decreed by the 2nd law, but quantifying this general limit remains difficult. Here we derive a universal equality linking directional fidelity of an arbitrary nanoscale object to the least possible energy driving it. The fidelity-energy equality depends on the environmental temperature alone; any lower energy would violate the 2nd law in a thought experiment. Real experimental proof for the equality comes from force-induced motion of biological nanomotors by three independent groups for translational as well as rotational motion. Interestingly, the natural self-propelled motion of a biological nanomotor (F1-ATPase) known to have nearly 100% energy efficiency evidently pays the 2nd-law decreed least energy cost for direction production.
Single-Trial Decoding of Bistable Perception Based on Sparse Nonnegative Tensor Decomposition
Zhisong Wang,Alexander Maier,Nikos K. Logothetis,Hualou Liang
Computational Intelligence and Neuroscience , 2008, DOI: 10.1155/2008/642387
Abstract: The study of the neuronal correlates of the spontaneous alternation in perception elicited by bistable visual stimuli is promising for understanding the mechanism of neural information processing and the neural basis of visual perception and perceptual decision-making. In this paper, we develop a sparse nonnegative tensor factorization-(NTF)-based method to extract features from the local field potential (LFP), collected from the middle temporal (MT) visual cortex in a macaque monkey, for decoding its bistable structure-from-motion (SFM) perception. We apply the feature extraction approach to the multichannel time-frequency representation of the intracortical LFP data. The advantages of the sparse NTF-based feature extraction approach lies in its capability to yield components common across the space, time, and frequency domains yet discriminative across different conditions without prior knowledge of the discriminating frequency bands and temporal windows for a specific subject. We employ the support vector machines (SVMs) classifier based on the features of the NTF components for single-trial decoding the reported perception. Our results suggest that although other bands also have certain discriminability, the gamma band feature carries the most discriminative information for bistable perception, and that imposing the sparseness constraints on the nonnegative tensor factorization improves extraction of this feature.
Single-Trial Classification of Bistable Perception by Integrating Empirical Mode Decomposition, Clustering, and Support Vector Machine
Zhisong Wang,Alexander Maier,Nikos K. Logothetis,Hualou Liang
EURASIP Journal on Advances in Signal Processing , 2008, DOI: 10.1155/2008/592742
Abstract: We propose an empirical mode decomposition (EMD-) based method to extract features from the multichannel recordings of local field potential (LFP), collected from the middle temporal (MT) visual cortex in a macaque monkey, for decoding its bistable structure-from-motion (SFM) perception. The feature extraction approach consists of three stages. First, we employ EMD to decompose nonstationary single-trial time series into narrowband components called intrinsic mode functions (IMFs) with time scales dependent on the data. Second, we adopt unsupervised K-means clustering to group the IMFs and residues into several clusters across all trials and channels. Third, we use the supervised common spatial patterns (CSP) approach to design spatial filters for the clustered spatiotemporal signals. We exploit the support vector machine (SVM) classifier on the extracted features to decode the reported perception on a single-trial basis. We demonstrate that the CSP feature of the cluster in the gamma frequency band outperforms the features in other frequency bands and leads to the best decoding performance. We also show that the EMD-based feature extraction can be useful for evoked potential estimation. Our proposed feature extraction approach may have potential for many applications involving nonstationary multivariable time series such as brain-computer interfaces (BCI).
Nonadiabatic simulation study of photoisomerization of azobenzene: Detailed mechanism and load-resisting capacity
Junfeng Shao,Yibo Lei,Zhenyi Wen,Yusheng Dou,Zhisong Wang
Physics , 2009, DOI: 10.1063/1.3000008
Abstract: Nonadiabatic dynamical simulations were carried out to study cis-to-trans isomerization of azobenzene under laser irradiation and/or external mechanical loads. We used a semiclassical electron-radiation-ion dynamics method that is able to describe the coevolution of the structural dynamics and the underlying electronic dynamics in a real-time manner. It is found that azobenzene photoisomerization occurs predominantly by an out-of-plane rotation mechanism even under a nontrivial resisting force of several tens of piconewtons. We have repeated the simulations systematically for a broad range of parameters for laser pulses, but could not find any photoisomerization event by a previously suggested in-plane inversion mechanism. The simulations found that the photoisomerization process can be held back by an external resisting force of 90 - 200 pN depending on the frequency and intensity of the lasers. This study also found that a pure mechanical isomerization is possible from the cis state if the azobenzene molecule is stretched by an external force of 1250 -1650 pN. Remarkably, the mechanical isomerization first proceeds through a mechanically activated inversion, and then is diverted to an ultrafast downhill rotation that accomplishes the isomerization. Implications of these findings to azobenzene-based nanomechanical devices are discussed.
Influence of Local and Residual Structures on the Scaling Behavior and Dimensions of Unfolded Proteins
Zhisong Wang,Kevin W. Plaxco,Dmitrii E. Makarov
Physics , 2009,
Abstract: Although recent spectroscopic studies of chemically denatured proteins hint at significant nonrandom residual structure, the results of extensive small angle X-ray scattering studies suggest random coil behavior, calling for a coherent understanding of these seemingly contradicting observations. Here, we report the results of a Monte Carlo study of the effects of two types of local structures, a helix and Polyproline II (PPII) helix, on the dimensions of random coil polyalanine chains viewed as a model of highly denatured proteins. With an alpha helix content of 20%, corresponding to the Ramachandran probability of being in the helical basin, experimentally observed radii of gyration are recovered. Experimental radii are similarly recovered at an a helix content of 87%, providing an explanation for the previously puzzling experimental finding that the dimensions of the highly helical methanol-induced unfolded state are experimentally indistinguishable from those of the helix-poor urea-unfolded state. In contrast, the radius of gyration increases monotonically with increasing PPII content, and is always more expanded than the dimensions observed experimentally. These results suggest that PPII is unlikely the sole, dominant preferred conformation for unfolded proteins.
Kinesin Is an Evolutionarily Fine-Tuned Molecular Ratchet-and-Pawl Device of Decisively Locked Direction
Zhisong Wang,Min Feng,Wenwei Zheng,Dagong Fan
Physics , 2009, DOI: 10.1529/biophysj.107.108233
Abstract: Conventional kinesin is a dimeric motor protein that transports membranous organelles toward the plus-end of microtubules (MTs). Individual kinesin dimers show steadfast directionality and hundreds of consecutive steps, yetthe detailed physical mechanism remains unclear. Here we compute free energies for the entire dimer-MT system for all possible interacting configurations by taking full account of molecular details. Employing merely first principles and several measured binding and barrier energies, the system-level analysis reveals insurmountable energy gaps between configurations, asymmetric ground state caused by mechanically lifted configurational degeneracy, and forbidden transitions ensuring coordination between both motor domains for alternating catalysis. This wealth of physical effects converts a kinesin dimer into a molecular ratchet-and-pawl device, which determinedly locks the dimer's movement into the MT plus-end and ensures consecutive steps in hand-over-hand gait.Under a certain range of extreme loads, however, the ratchet-and-pawl device becomes defective but not entirely abolished to allow consecutive back-steps. This study yielded quantitative evidence that kinesin's multiple molecular properties have been evolutionarily adapted to fine-tune the ratchet-and-pawl device so as to ensure the motor's distinguished performance.
Modeling Motility of the Kinesin Dimer from Molecular Properties of Individual Monomers
Dagong Fan,Wenwei Zheng,Ruizheng Hou,Fuli Li,Zhisong Wang
Physics , 2009,
Abstract: Conventional kinesin is a homodimeric motor protein that unidirectionally transports organelles along filamentous microtubule (MT) by hydrolyzing ATP molecules. This study shows that the load modulations of ATP turnover and head diffusion are both essential in determining the performance of the dimer under loads. It is found that the consecutive run length of the dimer critically depends upon a few pathways, leading to the detachment of individual heads from MT. Modifying rates for these detachment pathways changes the run length but not the velocity of the dimer, consistent with mutant experiments. The run length may increase with or without the ATP concentration, depending upon a single rate for pure mechanical detachment. This finding provides an explanation to a previous controversy concerning ATP dependence of the run length, and related quantitative predictions of this study can be tested by a future experiment. This study also finds that the experimental observations for assisting loads can be quantitatively explained by load-biased head diffusion. We thus conclude that the dimer motility under resisting as well as assisting loads is governed by essentially the same mechanisms.
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