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Nonequilibrium Dynamics of Chemically Active Particles

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Chinese Journal of Chemistry 2022年第3期40卷 419-429页

作者： Huijun Jiang zhonghuai hou Hefei National Laboratory for Physical Sciences ot the Microscale&Technology of China HefeiAnhui 230026China

Chemically active motion is ubiquitous in many nature and artificial systems where each unit can move directionally by converting chemical energy into kinetic *** the systems are driven by activity far from equilibrium,many dynamical behaviors forbidden in equilibrium systems may be *** dynamics of such systems is then a hot multidisciplinary topic with great ***,we review our recent theoretical advances in some fundamental problems at the single active particle level,the collective behavior level,as well as in systems where active particles act as baths.

关键词： Statistical mechanics Nonequilibrium processes Kinetics Chemically active particle Multiscale modeling

On the study of nonlinear dynamics of complex chemical reaction systems

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Science China Chemistry 2006年第1期49卷 1-11页

作者： XIN houwen hou zhonghuai Department of chemical physics University of Science and Technology of China Hefei 230026 China Department of chemical physics University of Science and Technology of China Hefei 230026 China

With ever-increasing attentions being paid to complex systems such as the life system, soft matter, and nano-systems, theoretical studies of non-equilibrium nonlinear problems involved in chemical dynamics are now of general interest. In this mini-review, we mainly give a brief introduction to some frontier topics in this field, namely, nonlinear state-state dynamics, nonlinear chemical dynamics on complex networks, and nonlinear dynamics in mesoscopic chemical reaction systems. Deep study of these topics will make great contribution to discovering new laws of chemical dynamics, to exploring new control methods of complex chemical processes, to figuring out the very roles of chemical proc-esses in the life system, and to crosslinking the scientific study of chemistry, physics and biology.

关键词： complex chemical reaction systems, nonlinear dynamics.

Fluctuation theorem for entropy production in a chemical reaction channel

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Science China Chemistry 2010年第2期53卷 396-401页

作者： XIAO TieJun hou zhonghuai Hefei National Laboratory for Physical Sciences at the Microscale Department of Chemical PhysicsUniversity of Science and Technology of ChinaHefei 230026China

Fluctuation theorem for entropy production in a mesoscopic chemical reaction network is discussed. When the system size is sufficiently large, it is found that, by defining a kind of coarse-grained dissipation function, the entropy production in a reversible reaction channel can be approximately described by a type of detailed fluctuation theorem. Such a fluctuation relation has been successfully tested by direct simulations in a linear reaction model consisting of two reversible channels and in an oscillatory model wherein only one channel is reversible.

关键词： nonequilibrium thermodynamics chemical reaction network entropy production fluctuation theorem

Internal signal stochastic resonance of a synthetic gene network

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Science China Chemistry 2005年第3期48卷 189-194页

作者： WANG Zhiwei hou zhonghuai XIN houwen Department of Chemical Physics University of Science and Technology of China Hefei 230026 China Department of Chemical Physics University of Science and Technology of China Hefei 230026 China Department of Chemical Physics University of Science and Technology of China Hefei 230026 China

The dynamics behavior of a synthetic gene network controlled by random noise is investigated using a model proposed recently. The phenomena of noise induced oscillation (NIO) of the protein concentrations and internal signal stochastic resonance (SR) are studied by com-puter simulation. We also find that there exists an optimal noise intensity that can most favor the occurrence of effective oscillation (EO). Finally we discuss the potential constructive roles of SR on gene expression systems.

关键词： noise, noise-induced oscillation, stochastic resonance, gene expression, synthetic gene network.

An efficient self-optimized sampling method for rare events in nonequilibrium systems

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Science China Chemistry 2014年第1期57卷 165-171页

作者： JIANG HuiJun PU MingFeng hou zhonghuai Hefei National Laboratory for Physical Sciences at Microscales Department of Chemical Physics University of Science and Technology of China

Rare events such as nucleation processes are of ubiquitous importance in real *** most popular method for nonequilibrium systems,forward flux sampling(FFS),samples rare events by using interfaces to partition the whole transition process into sequence of steps along an order parameter connecting the initial and final *** usually suffers from two main difficulties:low computational efficiency due to bad interface locations and even being not applicable when trapping into unknown intermediate metastable *** the present work,we propose an approach to overcome these difficulties,by self-adaptively locating the interfaces on the fly in an optimized *** to the conventional FFS which set the interfaces with equal distance of the order parameter,our approach determines the interfaces with equal transition probability which is shown to satisfy the optimization *** is done by firstly running long local trajectories starting from the current interface i to get the conditional probability distribution Pc(>i|i),and then determining i+1by equaling Pc(i+1|i)to a give value *** these optimized interfaces,FFS can be run in a much more efficient *** addition,our approach can conveniently find the intermediate metastable states by monitoring some special long trajectories that neither end at the initial state nor reach the next interface,the number of which will increase sharply from zero if such metastable states are *** apply our approach to a two-state model system and a two-dimensional lattice gas Ising *** approach is shown to be much more efficient than the conventional FFS method without losing accuracy,and it can also well reproduce the two-step nucleation scenario of the Ising model with easy identification of the intermediate metastable state.

关键词： sampling method,rare events,nonequilibrium systems

Canard explosion and internal signal stochastic bi-resonance in the CO oxidation on platinum surface

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Science China Chemistry 2006年第2期49卷 133-139页

作者： ZHAO Gang hou zhonghuai XIN houwen Department of Chemical Physics University of Science and Technology of China Hefei 230026 China Department of Chemical Physics University of Science and Technology of China Hefei 230026 China Department of Chemical Physics University of Science and Technology of China Hefei 230026 China

Canard explosion is a kind of complex temporal behavior and is ubiquitous in excitable systems. It is associated with an abrupt change of amplitude and period of an oscillatory trajectory in a very narrow interval of a control parameter. We have analyzed in the present paper the behavior of canard explosion that is near a supercritical Hopf bifurcation and its response to white noise in a temporal model of CO oxidation on platinum surface. We have found that the presence of canard explosion gives rise to internal signal stochastic bi-resonance, thus demonstrating a novel functional feature of noise: selective amplifying signals with different periods.

关键词： internal signal stochastic bi-resonance, canard explosion, CO oxidation on platinum surface, excitable system, nullcline.

Theoretical modelling of liquid–liquid phase separation: from particle-based to field-based simulation

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Biophysics Reports 2022年第2期8卷 55-67页

作者： Lin-ge Li zhonghuai hou Hefei National Laboratory for Physical Sciences at the Microscale & Department of Chemical Physics University of Science and Technology of China

Liquid–liquid phase separation(LLPS) has proved to be ubiquitous in living cells, forming membraneless organelles(MLOs) and dynamic condensations essential in physiological processes. However,some underlying mechanisms remain challenging to unravel experimentally, making theoretical modeling an indispensable aspect. Here we present a protocol for understanding LLPS from fundamental physics to detailed modeling procedures. The protocol involves a comprehensive physical picture on selecting suitable theoretical approaches, as well as how and what to interpret and resolve from the results. On the particle-based level, we elaborate on coarse-grained simulation procedures from building up models, identifying crucial interactions to running simulations to obtain phase diagrams and other concerned properties. We also outline field-based theories which give the system's density profile to determine phase diagrams and provide dynamic properties by studying the time evolution of density field, enabling us to characterize LLPS systems with larger time and length scales and to further include other nonequilibrium factors such as chemical reactions.

关键词： Liquid–liquid phase separation Theoretical modelling Coarse-grained simulation

Lattice Mismatch Induced Tunable Dimensionality of Transition Metal Dichalcogenides

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Chinese Journal of Chemical Physics 2022年第6期35卷 853-859,I0001-I0004,I0072页

作者： Hanxiao Dong Huijun Jiang zhonghuai hou Department of Chemical Physics Hefei National Research Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaHefei 230026China

Low-dimensional materials have excellent properties which are closely related to their ***,the growth mechanism underlying tunable dimensionality from 2D triangles to 1D ribbons of such materials is still ***,we establish a general kinetic Monte Carlo model for transition metal dichalcogenides(TMDs) growth to address such an *** model is able to reproduce several key findings in experiments,and reveals that the dimensionality is determined by the lattice mismatch and the interaction strength between TMDs and the *** predict that the dimensionality can be well tuned by the interaction strength and the geometry of the *** work deepens the understanding of tunable dimensionality of low-dimensional materials and may inspire new concepts for the design of such materials with expected dimensionality.

关键词： Transition metal dichalcogenide Dimensionality Low-dimensional material Lattice mismatch Kinetic Monte Carlo simulation

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介观化学体系中的动力学尺度效应

化学进展 2006年第2期18卷 142-158页

作者：侯中怀辛厚文中国科学技术大学化学物理系合肥230026

以生命和表面催化体系为对象,研究了介观化学体系中内涨落对体系非线性动力学行为的调控作用。内涨落可以诱导随机振荡,其强度在体系处于最佳尺度时会出现一个甚至多个极大值,并且在耦合体系中会得到进一步增强,表现为尺度共振效应、尺... 详细信息

以生命和表面催化体系为对象,研究了介观化学体系中内涨落对体系非线性动力学行为的调控作用。内涨落可以诱导随机振荡,其强度在体系处于最佳尺度时会出现一个甚至多个极大值,并且在耦合体系中会得到进一步增强,表现为尺度共振效应、尺度选择效应和双重尺度效应,揭示了介观化学体系中尺度效应的新机制。

关键词：介观化学非线性化学动力学内涨落尺度效应