arXiv subjects

Bo Sun

Publications and source records attributed to Bo Sun.

At least 127 records · Page 7Linked to original sources

arXiv2016

Temperature dependence of anisotropic thermal conductivity tensor of bulk black phosphorus

To date, the intrinsic thermal conductivity tensor of bulk black phosphorus (BP), an important 2D material, is still unknown, since recent studies focus on BP flakes not on bulk BP. Here we report the anisotropic thermal conductivity tensor of bulk BP, for temperature range 80 - 300 K. Our measurements are similar to prior measurements on submicron BP flakes along zigzag and armchair axes, but are >25% higher in the through-plane axis, suggesting that phonon mean-free-paths are substantially longer in the through-plane direction. We find that despite the anisotropy in thermal conductivity, phonons are predominantly scattered by the same Umklapp processes in all directions. We also find that the phonon relaxation time is rather isotropic in the basal planes, but is highly anisotropic in the through-plane direction. Our work advances fundamental knowledge of anisotropic scattering of phonons in BP and is an important benchmark for future studies on thermal properties of BP nanostructures.

cond-mat.mtrl-sci↗

arXiv2016

Probing Three-dimensional Collective Cancer Invasion with DIGME

Multicellular migration and pattern formation play important roles in developmental biology, cancer metastasis and wound healing. To understand the collective cell dynamics in three dimensional extracellular matrix (ECM), we have developed a simple and mechanical-based strategy, Diskoid In Geometrically Micropatterned ECM (DIGME). DIGME allows easy engineering of the shape of 3-D tissue organoid, the mesoscale ECM heterogeneity, and the fiber alignment of collagen-based ECM all at the same time. We have employed DIGME to study the collective cancer invasion and find that DIGME provides a powerful tool to probe three dimensional dynamics of tumor organoid in patterned microenvironment.

q-bio.TO↗

arXiv2016

Dynamic sampling and information encoding in biochemical networks

Cells use biochemical networks to translate environmental information into intracellular responses. These responses can be highly dynamic, but how the information is encoded in these dynamics remains poorly understood. Here we investigate the dynamic encoding of information in the ATP-induced calcium responses of fibroblast cells, using a vectorial, or multi-time-point, measure from information theory. We find that the amount of extracted information depends on physiological constraints such as the sampling rate and memory capacity of the downstream network, and is affected differentially by intrinsic vs. extrinsic noise. By comparing to a minimal physical model, we find, surprisingly, that the information is often insensitive to the detailed structure of the underlying dynamics, and instead the decoding mechanism acts as a simple low-pass filter. These results demonstrate the mechanisms and limitations of dynamic information storage in cells.

q-bio.CB↗

arXiv2016

Communication shapes sensory response in multicellular networks

Collective sensing by interacting cells is observed in a variety of biological systems, and yet a quantitative understanding of how sensory information is collectively encoded is lacking. Here we investigate the ATP-induced calcium dynamics of monolayers of fibroblast cells that communicate via gap junctions. Combining experiments and stochastic modeling, we find that increasing the ATP stimulus increases the propensity for calcium oscillations despite large cell-to-cell variability. The model further predicts that the oscillation propensity increases not only with the stimulus, but also with the cell density due to increased communication. Experiments confirm this prediction, showing that cell density modulates the collective sensory response. We further implicate cell-cell communication by coculturing the fibroblasts with cancer cells, which we show act as "defects" in the communication network, thereby reducing the oscillation propensity. These results suggest that multicellular networks sit at a point in parameter space where cell-cell communication has a significant effect on the sensory response, allowing cells to simultaneously respond to a sensory input and to the presence of neighbors.

q-bio.CB↗

arXiv2016

An interacting replica approach applied to the traveling salesman problem

We present a physics inspired heuristic method for solving combinatorial optimization problems. Our approach is specifically motivated by the desire to avoid trapping in metastable local minima- a common occurrence in hard problems with multiple extrema. Our method involves (i) coupling otherwise independent simulations of a system ("replicas") via geometrical distances as well as (ii) probabilistic inference applied to the solutions found by individual replicas. The {\it ensemble} of replicas evolves as to maximize the inter-replica correlation while simultaneously minimize the local intra-replica cost function (e.g., the total path length in the Traveling Salesman Problem within each replica). We demonstrate how our method improves the performance of rudimentary local optimization schemes long applied to the NP hard Traveling Salesman Problem. In particular, we apply our method to the well-known "$k$-opt" algorithm and examine two particular cases- $k=2$ and $k=3$. With the aid of geometrical coupling alone, we are able to determine for the optimum tour length on systems up to $280$ cities (an order of magnitude larger than the largest systems typically solved by the bare $k=3$ opt). The probabilistic replica-based inference approach improves $k-opt$ even further and determines the optimal solution of a problem with $318$ cities and find tours whose total length is close to that of the optimal solutions for other systems with a larger number of cities.

cond-mat.stat-mech↗

arXiv2016

Inference of hidden structures in complex physical systems by multi-scale clustering

We survey the application of a relatively new branch of statistical physics--"community detection"-- to data mining. In particular, we focus on the diagnosis of materials and automated image segmentation. Community detection describes the quest of partitioning a complex system involving many elements into optimally decoupled subsets or communities of such elements. We review a multiresolution variant which is used to ascertain structures at different spatial and temporal scales. Significant patterns are obtained by examining the correlations between different independent solvers. Similar to other combinatorial optimization problems in the NP complexity class, community detection exhibits several phases. Typically, illuminating orders are revealed by choosing parameters that lead to extremal information theory correlations.

cond-mat.mtrl-sci↗

arXiv2015

Heterogeneous Force Chains in Cellularized Biopolymer Network

Biopolymer Networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the mechanical response of a model biopolymer network due to the active contraction of embedded cells. Specifically, a graph (bond-node) model derived from confocal microscopy data is used to represent the network microstructure, and cell contraction is modeled by applying correlated displacements at specific nodes, representing the focal adhesion sites. A force-based stochastic relaxation method is employed to obtain force-balanced network under cell contraction. We find that the majority of the forces are carried by a small number of heterogeneous force chains emitted from the contracting cells. The force chains consist of fiber segments that either possess a high degree of alignment before cell contraction or are aligned due to the reorientation induced by cell contraction. Large fluctuations of the forces along different force chains are observed. Importantly, the decay of the forces along the force chains is significantly slower than the decay of radially averaged forces in the system. These results suggest that the fibrous nature of biopolymer network structure can support long-range force transmission and thus, long-range mechanical signaling between cells.

cond-mat.soft↗

arXiv2014

The different roles of Pu-oxide overlayers in the hydrogenation of Pu-metal: An ab initio molecular dynamics study based on vdW-DFT+U

Based on the van der Waals density functional theory (vdW-DFT)+U scheme, we carry out the ab initio molecular dynamics (AIMD) study of the interaction dynamics for H$_{2}$ impingement against the stoichiometric PuO$_{2}$(111), the reduced PuO$_{2}$(111), and the stoichiometric $α$-Pu$_{2}$O$_{3}$(111) surfaces. The hydrogen molecular physisorption states, which can not be captured by pure DFT+\textit{U} method, are obtained by employing the vdW-DFT+\textit{U} scheme. We show that except for the weak physisorption, PuO$_{2}$(111) surfaces are so difficult of access that almost all of the H$_{2}$ molecules will bounce back to the vacuum when their initial kinetic energies are not sufficient. Although the dissociative adsorption of H$_{2}$ on PuO$_{2}$(111) surfaces is found to be very exothermic, the collision-induced dissociation barriers of H$_{2}$ are calculated to be as high as $3.2$ eV and $2.0$ eV for stoichiometric and reduced PuO$_{2}$ surfaces, respectively. Unlike PuO$_{2}$, our AIMD study directly reveals that the hydrogen molecules can penetrate into $α$-Pu$_{2}$O$_{3}$(111) surface and diffuse easily due to the $25$\ native O vacancies located along the $\langle $111$\rangle $ diagonals of $α$-Pu$_{2}$O$_{3}$ matrix. By examining the temperature effect and the internal vibrational excitations of H$_{2}$, we provide a detailed insight into the interaction dynamics of H$_{2}$ in $α$-Pu$_{2}$O$_{3}$. The optimum pathways for hydrogen penetration and diffusion, the corresponding energy barriers ($1.0$ eV and $0.53$ eV, respectively) and rate constants are systematically calculated. Overall, our study fairly reveals the different interaction mechanisms between H$_{2}$ and Pu-oxide surfaces, which have strong implications to the interpretation of experimental observations.

cond-mat.mtrl-sci↗

arXiv2014

Flight trajectory recreation and playback system of aerial mission based on ossimplanet

Recreation of flight trajectory is important among research areas. The design of a flight trajectory recreation and playback system is presented in this paper. Rather than transferring the flight data to diagram, graph and table, flight data is visualized on the 3D global of ossimPlanet. ossimPlanet is an open-source 3D global geo-spatial viewer and the system realization is based on analysis it. Users are allowed to choose their interested flight of aerial mission. The aerial photographs and corresponding configuration files in which flight data is included would be read in. And the flight statuses would be stored. The flight trajectory is then recreated. Users can view the photographs and flight trajectory marks on the correct positions of 3D global. The scene along flight trajectory is also simulated at the plane's eye point. This paper provides a more intuitive way for recreation of flight trajectory. The cost is decreased remarkably and security is ensured by secondary development on open-source platform.

cs.HC↗

arXiv2012

First-principles study of surface properties of PuO2: Effects of thickness and O-vacancy on surface stability and chemical activity

The (111), (110), and (001) surfaces properties of PuO2 are studied by using density-functional theory+U method. The total-energy static calculations determine the relative order of stability for low-index PuO2 surfaces, namely, O-terminated (111) > (110) > defective (001) > polar (001). The effect of thickness is shown to modestly modulate the surface stability and chemical activity of the (110) surface. The high work function of 6.19 eV indicates the chemical inertia of the most stable (111) surface, and the surface O-vacancy with concentration C_V=25% can efficiently lower the work function to 4.35 eV, which is a crucial indicator of the difference in the surface chemical activities between PuO2 and α-Pu2O3. For the polar (001) surface, 50% on-surface O-vacancy can effectively quench the dipole moment and stabilize the surface structure, where the residual surface oxygen atoms are arranged in a zigzag manner along the <100> direction. We also investigate the relative stability of PuO2 surfaces in an oxygen environment. Under oxygen-rich conditions, the stoichiometric O-terminated (111) is found to be the most stable surface. Whereas under O-reducing conditions, the on-surface O-vacancy of C_V = 1/9 is stable, and for high reducing conditions, the (111) surface with nearly one monolayer subsurface oxygen removed (C_V = 8/9) becomes most stable.

cond-mat.mtrl-sci↗

arXiv2012

The environmental dependence of redox energetics of PuO2 and α-Pu2O3: A quantitative solution from DFT+U calculations

We report a comprehensive density functional theory (DFT) + $U$ study of the energetics of charged and neutral oxygen defects in both PuO$_{2}$ and $α$-Pu$_{2}$O$_{3}$, and present a quantitative determination of the equilibrium compositions of reduced PuO$_{2}$ (PuO$_{2-x}$) as functions of environmental temperature and partial pressure of oxygen, which shows fairly agreement with corresponding high-temperature experiments. Under ambient conditions, the endothermic reduction of PuO$_{2}$ to $α$-Pu$_{2}$O$_{3} $ is found to be facilitated by accompanying volume expansion of PuO$_{2-x}$ and the possible migration of O-vacancy, whereas further reduction of $α$-Pu$_{2}$O$_{3}$ is predicted to be much more difficult. In contrast to the endothermic oxidation of PuO$_{2}$,\ the oxidation of $α$-Pu$_{2} $O$_{3}$ is a stable exothermic process.

cond-mat.mtrl-sci↗

arXiv2012

Persistent narrowing of nuclear-spin fluctuations in InAs quantum dots using laser excitation

We demonstrate the suppression of nuclear spin fluctuations in an InAs quantum dot and measure the timescales of the spin narrowing effect. By initializing for tens of milliseconds with two continuous wave diode lasers, fluctuations of the nuclear spins are suppressed via the hole assisted dynamic nuclear polarization feedback mechanism. The fluctuation narrowed state persists in the dark (absent light illumination) for well over one second even in the presence of a varying electron charge and spin polarization. Enhancement of the electron spin coherence time (T2*) is directly measured using coherent dark state spectroscopy. By separating the calming of the nuclear spins in time from the spin qubit operations, this method is much simpler than the spin echo coherence recovery or dynamic decoupling schemes.

cond-mat.mes-hall↗

arXiv2011

Dissociation of hydrogen molecules on the clean and hydrogen-preadsorbed Be(0001) surface

Using first-principles calculations, we systematically study the potential energy surfaces and dissociation processes for hydrogen molecules on the clean and hydrogen-preadsorbed Be(0001) surfaces. It is found that the most energetically favored dissociation channel for H2 molecules on the clean Be surface is at the surface top site, with the minimum energy barrier of 0.75 eV. It is further found that after dissociation, hydrogen atoms do not like to cluster with each other, as well as to penetrate into subsurface sites. For the hydrogen-preadsorbed Be(0001) surface, the smallest dissociation energy barrier for H2 molecules is found to be 0.50 eV, which is smaller than the dissociation energy barrier on a clean Be(0001) surface. The critical dependence of the dissociation energy barriers for H2 molecules on their horizontal distances from the preadsorbed hydrogen atom is revealed. Our studies well describe the adsorption behaviors of hydrogen on the Be(0001) surface.

cond-mat.mtrl-sci↗

arXiv2011

Quantum oscillations in adsorption energetics of atomic oxygen on Pb(111) ultrathin films: A density-functional theory study

Using first-principles calculations, we have systematically studied the quantum size effects of ultrathin Pb(111) films on the adsorption energies and diffusion energy barriers of oxygen atoms. For the on-surface adsorption of oxygen atoms at different coverages, all the adsorption energies are found to show bilayer oscillation behaviors. It is also found that the work function of Pb(111) films still keeps the bilayer-oscillation behavior after the adsorption of oxygen atoms, with the values being enlarged by 2.10 to 2.62 eV. For the diffusion and penetration of the adsorbed oxygen atoms, it is found that the most energetically favored paths are the same on different Pb(111) films. And because of the modulation of quantum size effects, the corresponding energy barriers are all oscillating with a bilayer period on different Pb(111) films. Our studies indicate that the quantum size effect in ultrathin metal films can modulate a lot of processes during surface oxidation.

physics.chem-ph↗

arXiv2011

Rotation of hydrogen molecules during the dissociative adsorption on the Mg(0001) surface: A first-principles study

Using first-principles calculations, we systematically study the potential energy surfaces and dissociation processes of the hydrogen molecule on the Mg(0001) surface. It is found that during the dissociative adsorption process with the minimum energy barrier, the hydrogen molecule firstly orients perpendicular, and then rotates to be parallel to the surface. It is also found that the orientation of the hydrogen molecule at the transition state is neither perpendicular nor parallel to the surface. Most importantly, we find that the rotation causes a reduction of the calculated dissociation energy barrier for the hydrogen molecule. The underlying electronic reasons for the rotation of the hydrogen molecule is also discussed in our paper.

cond-mat.mtrl-sci↗

arXiv2011

QoS Provisioning for Multimedia Transmission in Cognitive Radio Networks

In cognitive radio (CR) networks, the perceived reduction of application layer quality of service (QoS), such as multimedia distortion, by secondary users may impede the success of CR technologies. Most previous work in CR networks ignores application layer QoS. In this paper we take an integrated design approach to jointly optimize multimedia intra refreshing rate, an application layer parameter, together with access strategy, and spectrum sensing for multimedia transmission in a CR system with time varying wireless channels. Primary network usage and channel gain are modeled as a finite state Markov process. With channel sensing and channel state information errors, the system state cannot be directly observed. We formulate the QoS optimization problem as a partially observable Markov decision process (POMDP). A low complexity dynamic programming framework is presented to obtain the optimal policy. Simulation results show the effectiveness of the proposed scheme.

cs.IT↗

arXiv2011

The sky brightness and transparency in i-band at Dome A, Antarctica

The i-band observing conditions at Dome A on the Antarctic plateau have been investigated using data acquired during 2008 with the Chinese Small Telescope ARray. The sky brightness, variations in atmospheric transparency, cloud cover, and the presence of aurorae are obtained from these images. The median sky brightness of moonless clear nights is 20.5 mag arcsec^{-2} in the SDSS $i$ band at the South Celestial Pole (which includes a contribution of about 0.06 mag from diffuse Galactic light). The median over all Moon phases in the Antarctic winter is about 19.8 mag arcsec^{-2}. There were no thick clouds in 2008. We model contributions of the Sun and the Moon to the sky background to obtain the relationship between the sky brightness and transparency. Aurorae are identified by comparing the observed sky brightness to the sky brightness expected from this model. About 2% of the images are affected by relatively strong aurorae.

astro-ph.IM↗

arXiv2010

Localization of spin mixing dynamics in a spin-1 Bose-Einstein condensate

We propose to localize spin mixing dynamics in a spin-1 Bose-Einstein condensate by a temporal modulation of spin exchange interaction, which is tunable with optical Feshbach resonance. Adopting techniques from coherent control, we demonstrate the localization/freezing of spin mixing dynamics, and the suppression of the intrinsic dynamic instability and spontaneous spin domain formation in a ferromagnetically interacting condensate of $^{87}$Rb atoms. This work points to a promising scheme for investigating the weak magnetic spin dipole interaction, which is usually masked by the more dominant spin exchange interaction.

cond-mat.quant-gas↗