arXiv subjects

Jin Dai

Publications and source records attributed to Jin Dai.

At least 37 records · Page 2Linked to original sources

arXiv2019

Can all-atom protein dynamics be reconstructed from the knowledge of C-alpha time evolution?

We inquire to what extent protein peptide plane and side chain dynamics can be reconstructed from knowledge of C-alpha dynamics. Due to lack of experimental data we analyze all atom molecular dynamics trajectories from Anton supercomputer, and for clarity we limit our attention to the peptide plane O atoms and side chain C-beta atoms. We try and reconstruct their dynamics using four different approaches. Three of these are the publicly available reconstruction programs Pulchra, Remo Scwrl4. The fourth, Statistical Method, builds entirely on statistical analysis of Protein Data Bank (PDB) structures. All four methods place the O and C-beta atoms accurately along the Anton trajectories. However, the Statistical Method performs best. The results suggest that under physiological conditions, the all atom dynamics is slaved to that of C-alpha atoms. The results can help improve all atom force fields, and advance reconstruction and refinement methods for reduced protein structures. The results provide impetus for development of effective coarse grained force fields in terms of reduced coordinates.

q-bio.BM↗

arXiv2018

Coordination and Control of Distributed Discrete Event Systems under Actuator and Sensor Faults

We investigate the coordination and control problems of distributed discrete event systems that are composed of multiple subsystems subject to potential actuator and/or sensor faults. We model actuator faults as local controllability loss of certain actuator events and sensor faults as observability failure of certain sensor readings, respectively. Starting from automata-theoretic models that characterize behaviors of the subsystems in the presence of faulty actuators and/or sensors, we establish necessary and sufficient conditions for the existence of actuator and sensor fault tolerant supervisors, respectively, and synthesize appropriate local post-fault supervisors to prevent the post-fault subsystems from jeopardizing local safety requirements. Furthermore, we apply an assume-guarantee coordination scheme to the controlled subsystems for both the nominal and faulty subsystems so as to achieve the desired specifications of the system. A multi-robot coordination example is used to illustrate the proposed coordination and control architecture.

eess.SY↗

arXiv2018

Distributed Communication-aware Motion Planning for Networked Mobile Robots under Formal Specifications

Control and communication are often tightly coupled in motion planning of networked mobile robots, due to the fact that robotic motions will affect the overall communication quality, and the quality of service (QoS) of the communication among the robots will in turn affect their coordination performance. In this paper, we propose a control theoretical motion planning framework for a team of networked mobile robots in order to accomplish high-level spatial and temporal motion objectives while optimizing communication QoS. Desired motion specifications are formulated as Signal Temporal Logic (STL), whereas the communication performances to be optimized are captured by recently proposed Spatial Temporal Reach and Escape Logic (STREL) formulas. Both the STL and STREL specifications are encoded as mixed integer linear constraints posed on the system and/or environment state variables of the mobile robot network, where satisfactory control strategies can be computed by exploiting a distributed model predictive control (MPC) approach. To the best of the authors' knowledge, we are the first to study controller synthesis for STREL specifications. A two-layer hierarchical MPC procedure is proposed to efficiently solve the problem, whose soundness and completeness are formally ensured. The effectiveness of the proposed framework is validated by simulation examples.

eess.SY↗

arXiv2018

Dual-Band Quasi-Coherent Radiative Thermal Source

Thermal radiation from an unpatterned object is similar to that of a gray body. The thermal emission is insensitive to polarization, shows only Lambertian angular dependence, and is well modeled as the product of the blackbody distribution and a scalar emissivity over large frequency bands. Here, we design, fabricate and experimentally characterize the spectral, polarization, angular and temperature dependence of a microstructured SiC dual band thermal infrared source, achieving independent control of the frequency and polarization of thermal radiation in two spectral bands. The measured emission of the device in the Reststrahlen band (10.3-12.7 um) selectively approaches that of a blackbody, peaking at an emissivity of 0.85 at Lx=11.75 um and 0.81 at Ly=12.25 um. This effect arises due to the thermally excited phonon polaritons in silicon carbide. The control of thermal emission properties exhibited by the design is well suited for applications requiring infrared sources, gas or temperature sensors and nanoscale heat transfer. Our work paves the way for future silicon carbide based thermal metasurfaces.

physics.optics↗

arXiv2018

Synthesis of Insertion Functions to Enforce Decentralized and Joint Opacity Properties of Discrete-event Systems

Opacity is a confidentiality property that characterizes the non-disclosure of specified secret information of a system to an outside observer. In this paper, we consider the enforcement of opacity within the discrete-event system formalism in the presence of multiple intruders. We study two cases, one without coordination among the intruders and the other with coordination. We propose appropriate notions of opacity corresponding to the two cases, respectively, and propose enforcement mechanisms for these opacity properties based on the implementation of insertion functions, which manipulates the output of the system by inserting fictitious observable events whenever necessary. The insertion mechanism is adapted to the decentralized framework to enforce opacity when no coordination exists. Furthermore, we present a coordination and refinement procedure to synthesize appropriate insertion functions to enforce opacity when intruders may coordinate with each other by following an intersection-based coordination protocol. The effectiveness of the proposed opacity-enforcement approaches is validated through illustrative examples.

cs.CR↗

arXiv2017

Virtual reality analysis of intrinsic protein geometry with applications to cis peptide planes

A protein is traditionally visualised as a piecewise linear discrete curve, and its geometry is conventionally characterised by the extrinsically determined Ramachandran angles. However, a protein backbone has also two independent intrinsic geometric structures, due to the peptide planes and the side chains. Here we adapt and develop modern 3D virtual reality techniques to scrutinize the atomic geometry along a protein backbone, in the vicinity of a peptide plane. For this we compare backbone geometry-based (extrinsic) and structure-based (intrinsic) coordinate systems, and as an example we inspect the trans and cis peptide planes. We reveal systematics in the way how a cis peptide plane deforms the neighbouring atomic geometry, and we develop a virtual reality based visual methodology that can identify the presence of a cis peptide plane from the arrangement of atoms in its vicinity. Our approach can easily detect exceptionally placed atoms in crystallographic structures. Thus it can be employed as a powerful visual refinement tool which is applicable also in the case when resolution of the protein structure is limited and whenever refinement is needed. As concrete examples we identify a number of crystallographic protein structures in Protein Data Bank (PDB) that display exceptional atomic positions around their cis peptide planes.

q-bio.BM↗

arXiv2017

Learning-based Formal Synthesis of Cooperative Multi-agent Systems

We propose a formal design framework for synthesizing coordination and control policies for cooperative multi-agent systems to accomplish a global mission. The global performance requirements are specified as regular languages while dynamics of each agent as well as the shared environment are characterized by finite automata, upon on which a formal design approach is carried out via divide-and-conquer. Specifically, the global mission is decomposed into local tasks; and local mission supervisors are designed to accomplish these local tasks while maintaining the multi-agent performance by integrating supervisor synthesis with compositional verification techniques; finally, motion plans are automatically synthesized based on the obtained mission plans. We present three modifications of the L* learning algorithm such that they are adapted for the synthesis of the local mission supervisors, the compositional verification and the synthesis of local motion plans, to guarantee that the collective behavior of the agents will ensure the satisfaction of the global specification. Furthermore, the effectiveness of the proposed framework is demonstrated by a detailed experimental study based on the implementation of a multi-robot coordination scenario. The proposed hardware-software architecture, with each robot's communication and localization capabilities, is exploited to examine the automatic supervisor synthesis with inter-robot communication.

eess.SY↗

arXiv2017

Communication-aware Motion Planning for Multi-agent Systems from Signal Temporal Logic Specifications

We propose a mathematical framework for synthesizing motion plans for multi-agent systems that fulfill complex, high-level and formal local specifications in the presence of inter-agent communication. The proposed synthesis framework consists of desired motion specifications in temporal logic (STL) formulas and a local motion controller that ensures the underlying agent not only to accomplish the local specifications but also to avoid collisions with other agents or possible obstacles, while maintaining an optimized communication quality of service (QoS) among the agents. Utilizing a Gaussian fading model for wireless communication channels, the framework synthesizes the desired motion controller by solving a joint optimization problem on motion planning and wireless communication, in which both the STL specifications and the wireless communication conditions are encoded as mixed integer-linear constraints on the variables of the agents' dynamical states and communication channel status. The overall framework is demonstrated by a case study of communication-aware multi-robot motion planning and the effectiveness of the framework is validated by simulation results.

eess.SY↗

arXiv2017

Distributed Communication-aware Motion Planning for Multi-agent Systems from STL and SpaTeL Specifications

In future intelligent transportation systems, networked vehicles coordinate with each other to achieve safe operations based on an assumption that communications among vehicles and infrastructure are reliable. Traditional methods usually deal with the design of control systems and communication networks in a separated manner. However, control and communication systems are tightly coupled as the motions of vehicles will affect the overall communication quality. Hence, we are motivated to study the co-design of both control and communication systems. In particular, we propose a control theoretical framework for distributed motion planning for multi-agent systems which satisfies complex and high-level spatial and temporal specifications while accounting for communication quality at the same time. Towards this end, desired motion specifications and communication performances are formulated as signal temporal logic (STL) and spatial-temporal logic (SpaTeL) formulas, respectively. The specifications are encoded as constraints on system and environment state variables of mixed integer linear programs (MILP), and upon which control strategies satisfying both STL and SpaTeL specifications are generated for each agent by employing a distributed model predictive control (MPC) framework. Effectiveness of the proposed framework is validated by a simulation of distributed communication-aware motion planning for multi-agent systems.

cs.MA↗

arXiv2017

Ultra-Broadband Super-Planckian Radiative Heat Transfer with Artificial Continuum Cavity States in Patterned Hyperbolic Metamaterial

Localized cavity resonances due to nanostructures at material surfaces can greatly enhance radiative heat transfer (RHT) between two closely placed bodies owing to stretching of cavity states in momentum space beyond light line. Based on such understanding, we numerically demonstrate the possibility of ultra-broadband super-Planckian RHT between two plates patterned with trapezoidal-shaped hyperbolic metamaterial (HMM) arrays. The phenomenon is rooted not only in HMM's high effective index for creating sub-wavelength resonators, but also its extremely anisotropic isofrequency contour. The two properties enable one to create photonic bands with a high spectral density to populate a desired thermal radiation window. At sub-micron gap sizes between such two plates, the artificial continuum states extend outside light cone, tremendously increasing overall RHT. Our study reveals that structured HMM offers unprecedented potential in achieving a controllable super-Planckian radiative heat transfer for thermal management at nanoscale.

physics.optics↗

arXiv2016

Combined Top-Down and Bottom-Up Approaches to Performance-guaranteed Integrated Task and Motion Planning of Cooperative Multi-agent Systems

We propose a hierarchical design framework to automatically synthesize coordination schemes and control policies for cooperative multi-agent systems to fulfill formal performance requirements, by associating a bottom-up reactive motion controller with a top-down mission plan. On one hand, starting from a global mission that is specified as a regular language over all the agents' mission capabilities, a mission planning layer sits on the top of the proposed framework, decomposing the global mission into local tasks that are in consistency with each agent's individual capabilities, and compositionally justifying whether the achievement of local tasks implies the satisfaction of the global mission via an assume-guarantee paradigm. On the other hand, bottom-up motion plans associated with each agent are synthesized corresponding to the obtained local missions by composing basic motion primitives, which are verified safe by differential dynamic logic (d$\mathcal{L}$), through a Satisfiability Modulo Theories (SMT) solver that searches feasible solutions in face of constraints imposed by local task requirements and the environment description. It is shown that the proposed framework can handle dynamical environments as the motion primitives possess reactive features, making the motion plans adaptive to local environmental changes. Furthermore, on-line mission reconfiguration can be triggered by the motion planning layer once no feasible solutions can be found through the SMT solver. The effectiveness of the overall design framework is validated by an automated warehouse case study.

cs.RO↗

arXiv2016

Towards multistage modelling of protein dynamics with monomeric Myc oncoprotein as an example

We propose to combine a mean field approach with all atom molecular dynamics into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic level precision. As an example we investigate an isolated monomeric Myc oncoprotein that has been implicated in carcinomas including those in colon, breast and lungs. Under physiological conditions a monomeric Myc is presumed to be an example of intrinsically disordered proteins, that pose a serious challenge to existing modelling techniques. We argue that a room temperature monomeric Myc is in a dynamical state, it oscillates between different conformations that we identify. For this we adopt the C-alpha backbone of Myc in a crystallographic heteromer as an initial Ansatz for the monomeric structure. We construct a multisoliton of the pertinent Landau free energy, to describe the C-alpha profile with ultra high precision. We use Glauber dynamics to resolve how the multisoliton responds to repeated increases and decreases in ambient temperature. We confirm that the initial structure is unstable in isolation. We reveal a highly degenerate ground state landscape, an attractive set towards which Glauber dynamics converges in the limit of vanishing ambient temperature. We analyse the thermal stability of this Glauber attractor using room temperature molecular dynamics. We identify and scrutinise a particularly stable subset in which the two helical segments of the original multisoliton align in parallel, next to each other. During the MD time evolution of a representative structure from this subset, we observe intermittent quasiparticle oscillations along the C-terminal alpha-helix, some of which resemble a translating Davydov's Amide-I soliton. We propose that the presence of oscillatory motion is in line with the expected intrinsically disordered character of Myc.

q-bio.BM↗

arXiv2016

Near-Field Radiative Heat Transfer Between Metasurfaces: A Full-Wave Study Based on 2D Grooved Metal Plates

Metamaterials possess artificial bulk and surface electromagnetic states. Tamed dispersion properties of surface waves allow one to achieve controllable super-Planckian radiative heat transfer (RHT) process between two closely spaced objects. We numerically demonstrate enhanced RHT between two 2D grooved metal plates by a full-wave scattering approach. The enhancement originates from both transverse magnetic spoof surface plasmon polaritons and a series of transverse electric bonding- and anti-bonding waveguide modes at surfaces. The RHT spectrum is frequency-selective, and highly geometrically tailorable. Our simulation also reveals thermally excited non-resonant surface waves in constituent materials can play a prevailing role for RHT at an extremely small separation between two plates, rendering metamaterial modes insignificant for the energy transfer process.

physics.optics↗

arXiv2015

Bloch spin waves and emergent structure in protein folding with HIV envelope glycoprotein as an example

We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques, in combination with analytic tools that we deduce from the concept of integrable models and structure of discrete nonlinear Schroedinger equation. The example we consider is an alpha-helical subunit of the HIV envelope glycoprotein gp41. The helical structure is stable when the subunit is part of the biological oligomer. But in isolation the helix becomes unstable, and the monomer starts deforming. We follow the process computationally. We interpret the evolving structure both in terms of a backbone based Heisenberg spin chain and in terms of a side chain based XY spin chain. We find that in both cases the formation of protein super-secondary structure is akin the formation of a topological Bloch domain wall along a spin chain. During the process we identify three individual Bloch walls and we show that each of them can be modelled with a very high precision in terms of a soliton solution to a discrete nonlinear Schroedinger equation.

q-bio.BM↗

arXiv2015

Design of a 325MHz Half Wave Resonator prototype at IHEP

A 325MHz beta=0.14 superconducting half wave resonator(HWR) prototype has been developed at the Institute of High Energy Physics(IHEP), which can be applied in continuous wave (CW) high beam proton accelerators. In this paper, the electromagnetic (EM) design, multipacting simulation, mechanical optimization, and fabrication are introduced in details. In vertical test at 4.2K, the cavity reached Eacc=7MV/m with Q0=1.4*10^9 and Eacc=15.9MV/m with Q0=4.3*10^8.

physics.acc-ph↗

arXiv2015

Thermal self-oscillations in radiative heat exchange

We report the effect of relaxation-type self-induced temperature oscillations in the system of two parallel plates of SiO$_2$ and VO$_2$ which exchange heat by thermal radiation in vacuum. The non-linear feedback in the self-oscillating system is provided by metal-insulator transition in VO$_2$. Using the method of fluctuational electrodynamics we show that under the action of an external laser of a constant power, the temperature of VO$_2$ plate oscillates around its phase transition value. The period and amplitude of oscillations depend on the geometry of the structure. We found that at 500\,nm vacuum gap separating bulk SiO$_2$ plate and 50 nm thick VO$_2$ plate, the period of self-oscillations is 2 s and the amplitude is 4 K which is determined by phase switching at threshold temperatures of phase transition.

physics.optics↗

arXiv2014

Aspects of structural landscape of human islet amyloid polypeptide

The human islet amyloid polypeptide (hIAPP) co-operates with insulin to maintain glycemic balance. It also constitutes the amyloid plaques that aggregate in the pancreas of type-II diabetic patients. We have performed extensive in silico investigations to analyse the structural landscape of monomeric hIAPP, which is presumed to be intrinsically disordered. For this we construct from first principles a highly predictive energy function that describes a monomeric hIAPP observed in a NMR experiment, as a local energy minimum. We subject our theoretical model of hIAPP to repeated heating and cooling simulations, back and forth between a high temperature regime where the conformation resembles a random walker and a low temperature limit where no thermal motions prevail. We find that the final low temperature conformations display a high level of degeneracy, in a manner which is fully in line with the presumed intrinsically disordered character of hIAPP. In particular, we identify an isolated family of alpha-helical conformations that might cause the transition to amyloidosis, by nucleation.

q-bio.BM↗

arXiv1995

Flavor Symmetry Breaking in the 1/N Expansion

The breaking of flavor SU(3) symmetry in the axial couplings and magnetic moments of baryons is analyzed in the $1/N_c$ expansion. A simple meson loop graph which is known to be of order $\sqrt{m_s}$ and leading order in $1/N_c$ correctly predicts the pattern of symmetry breaking in the magnetic moments. It is, however, not possible to use this graph to predict the magnitude of the breaking. The situation with the axial couplings is less clear. In this case the breakings are relatively small and do not appear to follow an obvious pattern. Nevertheless there is a clear indication that, with symmetry breaking taken into account, the F/D ratio (defined in the presence of SU(3) breaking) is considerably less than the SU(6) value of 2/3. With sizeable uncertainty, we find F/D \approx 0.44. The quantity 3F-D which is relevant for the analysis of spin-dependent deep inelastic scattering is considerably smaller than the SU(6) value of unity. The new value, 3F-D=0.27+-0.09, is consistent with vanishing strange-quark spin in the nucleon.

hep-ph↗