Nanoscale spatial heterogeneity in ionic liquids is formed by the aggregation of cationic tail groups. The electrostatic interactions between polar groups and the collective van der Waals interactions between nonpolar...Nanoscale spatial heterogeneity in ionic liquids is formed by the aggregation of cationic tail groups. The electrostatic interactions between polar groups and the collective van der Waals interactions between nonpolar tail groups both contribute to the formation of tail domains, but the degrees of their contributions were unknown. In this work, by applying a strong external electric field to effectively overpower the electrostatic interactions between polar groups, we have determined that the tail aggregation is majorly attributed to the electrostatic interactions and the van der Waals interactions only have minor influence on the spatial heterogeneity phenomenon of ionic liquids.展开更多
It is very important to determine the phase transition temperature,such as the water/ice coexistence temperature in various water models,via molecular simulations.We show that a single individual direct simulation is ...It is very important to determine the phase transition temperature,such as the water/ice coexistence temperature in various water models,via molecular simulations.We show that a single individual direct simulation is sufficient to get the temperature with high accuracy and small computational cost based on the generalized canonical ensemble(GCE).Lennard–Jones fluids,the atomic water models,such as TIP4P/2005,TIP4P/ICE,and the mW water models are applied to illustrate the method.We start from the coexistent system of the two phases with a plane interface,then equilibrate the system under the GCE,which can stabilize the coexistence of the phases,to directly derive the phase transition temperature without sensitive dependence on the applied parameters of the GCE and the size of the simulation systems.The obtained result is in excellent agreement with that in literatures.These features make the GCE approach in determining the phase transition temperature of systems be robust,easy to use,and particularly good at working on computationally expensive systems.展开更多
This works examine the responses of housing prices to the monetary policies in various Chinese cities. Thirty-five large and medium sized Chinese cities are classified into six clusters applying the minimum variance c...This works examine the responses of housing prices to the monetary policies in various Chinese cities. Thirty-five large and medium sized Chinese cities are classified into six clusters applying the minimum variance clustering method according to the calculated correlation coefficients between the housing price indices of every two cities.Time difference correlation analysis is then employed to quantify the relations between the housing price indices of the six clusters and the monetary policies.It is suggested that the housing prices of various cities evolved at different paces and their responses to the monetary policies are heterogeneous,and local economic features are more important than geographic distances in determining the housing price trends.展开更多
Formation and dissociation mechanisms of C-C＋ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environmen...Formation and dissociation mechanisms of C-C＋ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C-C＋ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C-C＋ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.展开更多
A non-equilibrium steady state can be characterized by a nonzero but stationary flux driven by a static external force. Under a weak external force, the drift velocity is difficult to detect because the drift motion i...A non-equilibrium steady state can be characterized by a nonzero but stationary flux driven by a static external force. Under a weak external force, the drift velocity is difficult to detect because the drift motion is feeble and submerged in the intense thermal diffusion. In this article, we employ an accurate method in molecular dynamics simulation to determine the drift velocity of a particle driven by a weak external force in a one-dimensional periodic potential. With the calculated drift velocity, we found that the mobility and diffusion of the particle obey the Einstein relation, whereas their temperature dependences deviate from the Arrhenius law. A microscopic hopping mechanism was proposed to explain the non-Arrhenius behavior. Moreover, the position distribution of the particle in the potential well was found to deviate from the Boltzmann equation in a non-equilibrium steady state. The non-Boltzmann behavior may be attributed to the thermostat which introduces an effective "viscous" drag opposite to the drift direction of the particle.展开更多
Diffusion-limited aggregation （DLA） assumes that particles perform pure random walk at a finite tem- perature and aggregate when they come close enough and stick together. Although it is well known that DLA in two d...Diffusion-limited aggregation （DLA） assumes that particles perform pure random walk at a finite tem- perature and aggregate when they come close enough and stick together. Although it is well known that DLA in two dimensions results in a ramified fractal structure, how the particle shape influences the formed morphology is still un- clear. In this work, we perform the off-lattice two-dimensional DLA simulations with different particle shapes of triangle, quadrangle, pentagon, hexagon, and octagon, respectively, and compare with the results for circular particles. Our results indicate that different particle shapes only change the local structure, but have no effects on the global structure of the formed fractal duster. The local compactness decreases as the number of polygon edges increases.展开更多
The behavior of saturated aqueous Na Cl solutions under a constant external electric field（E） was studied by molecular dynamics（MD） simulation. Our dynamic MD simulations indicated that the irreversible nucleation...The behavior of saturated aqueous Na Cl 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.展开更多
Flocking and vortical are two typical motion modes in active matter.Although it is known that the two modes can spontaneously switch between each other in a finite-size system,the switching dynamics remain elusive.In ...Flocking and vortical are two typical motion modes in active matter.Although it is known that the two modes can spontaneously switch between each other in a finite-size system,the switching dynamics remain elusive.In this work,by computer simulation of a two-dimensional Vicsek-like system with 1000 particles,we find from the perspective of the classical nucleation theory that the forward and backward switching dynamics are asymmetric:going from flocking to vortical is a one-step nucleation process,while the opposite is a two-step nucleation process,with the system staying in a metastable state before reaching the final flocking state.展开更多
To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics （MD） simulation in aqueous solution four fragments cut out of a protein G, including one a...To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics （MD） simulation in aqueous solution four fragments cut out of a protein G, including one a-helix （seqB： KVFKQYAN）, two -turns （seqA： LNGKTLKG and seqC： YDDATKTF）, and one -strand （seqD： DGEWTYDD）. The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-#s equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics.展开更多
Various soft materials share some common features, such as significant entropic effect, large fluctuations, sensitivity to thermodynamic conditions, and mesoscopic characteristic spatial and temporal scales. However, ...Various soft materials share some common features, such as significant entropic effect, large fluctuations, sensitivity to thermodynamic conditions, and mesoscopic characteristic spatial and temporal scales. However, no quantitative defini- tions have yet been provided for soft matter, and the intrinsic mechanisms leading to their common features are unclear. In this work, from the viewpoint of statistical mechanics, we show that soft matter works in the vicinity of a specific thermo- dynamic state named moderate point, at which entropy and enthalpy contributions among substates along a certain order parameter are well balanced or have a minimal difference. Around the moderate point, the order parameter fluctuation, the associated response function, and the spatial correlation length maximize, which explains the large fluctuation, the sensitivity to thermodynamic conditions, and mesoscopic spatial and temporal scales of soft matter, respectively. Possible applications to switching chemical bonds or allosteric biomachines determining their best working temperatures are also briefly discussed.展开更多
We study the behaviors of mean end-to-end distance and specific heat of a two-dimensional intrinsically curved semiflexible biopolymer with a hard-core excluded volume interaction. We find the mean square end-to-end d...We study the behaviors of mean end-to-end distance and specific heat of a two-dimensional intrinsically curved semiflexible biopolymer with a hard-core excluded volume interaction. We find the mean square end-to-end distance R2 N∝ Nβ at large N, with N being the number of monomers. Bothβ and proportional constant are dependent on the reduced bending rigidity κ and intrinsic curvature c. The larger the c, the smaller the proportional constant, and 1.5 ≥β ≥ 1. Up to a moderate κ = κc, or down to a moderate temperature T = Tc, β = 1.5, the same as that of a self-avoiding random walk, and the larger the intrinsic curvature, the smaller the κc. However, at a large κ or a low temperature,β is close to 1, and the conformation of the biopolymer can be more compact than that of a random walk. There is an intermediate regime with 1.5 〉β 〉 1 and the transition fromβ = 1.5 toβ= 1 is smooth. The specific heat of the system increases smoothly with increasing κ or there is no peak in the specific heat. Therefore, a nonvanishing intrinsic curvature seriously affects the thermal properties of a semiflexible biopolymer, but there is no phase transition in the system.展开更多
Besides our previous experimental discovery （Zhao Y R, et al. 2015 Langmuir, 31, 12975） that acetonitrile （ACN） can tune the morphological features of nanostructures self-assembled by short peptides KIIIIK （KI4K...Besides our previous experimental discovery （Zhao Y R, et al. 2015 Langmuir, 31, 12975） that acetonitrile （ACN） can tune the morphological features of nanostructures self-assembled by short peptides KIIIIK （KI4K） in aqueous solution, further experiments reported in this work demonstrate that ACN can also tune the mass of the self-assembled nanostructures. To understand the microscopic mechanism how ACN molecules interfere peptide self-assembly process, we conducted a series of molecular dynamics simulations on a monomer, a cross-β sheet structure, and a proto-fibril of KI4K in pure water, pure ACN, and ACN-water mixtures, respectively. The simulation results indicate that ACN enhances the intra-sheet interaction dominated by the hydrogen bonding （H-bonding） interactions between peptide backbones, but weakens the inter-sheet interaction dominated by the interactions between hydrophobic side chains. Through analyzing the correlations between different groups of solvent and peptides and the solvent behaviors around the proto-fibril, we have found that both the polar and nonpolar groups of ACN play significant roles in causing the opposite effects on intermolecular interactions among peptides. The weaker correlation of the polar group of ACN than water molecule with the peptide backbone enhances H-bonding interactions between peptides in the proto-fibril. The stronger correlation of the nonpolar group of ACN than water molecule with the peptide side chain leads to the accumulation of ACN molecules around the proto-fibril with their hydrophilic groups exposed to water, which in turn allows more water molecules close to the proto-fibril surface and weakens the inter-sheet interactions. The two opposite effects caused by ACN form a microscopic mechanism clearly explaining our experimental observations.展开更多
Nanostructures self-assembled by cross-β peptides with ordered structures and advantageous mechanical properties have many potential applications in biomaterials and nanotechnologies. Quantifying the intra-and inter-...Nanostructures self-assembled by cross-β peptides with ordered structures and advantageous mechanical properties have many potential applications in biomaterials and nanotechnologies. Quantifying the intra-and inter-molecular driving forces for peptide self-assembly at the atomistic level is essential for understanding the formation mechanism and nanomechanics of various morphologies of self-assembled peptides. We investigate the thermodynamics of the intra-and inter-sheet structure formations in the self-assembly process of cross-β peptide KⅢIK by means of steered molecular dynamics simulation combined with umbrella sampling. It is found that the mechanical properties of the intra-and inter-sheet structures are highly anisotropic with their intermolecular bond stiffness at the temperature of 300 K being 5.58 N/m and 0.32 N/m, respectively. This mechanical anisotropy comes from the fact that the intra-sheet structure is stabilized by enthalpy but the inter-sheet structure is stabilized by entropy. Moreover, the formation process of KⅢIK intra-sheet structure is cooperatively driven by the van der Waals （VDW） interaction between the hydrophobic side chains and the electrostatic interaction between the hydrophilic backbones, but that of the inter-sheet structure is primarily driven by the VDW interaction between the hydrophobic side chains. Although only peptide KⅢIK is studied, the qualitative conclusions on the formation mechanism should also apply to other cross-β peptides.展开更多
A classical particle system coupled with a thermostat driven by an external constant force reaches its steady state when the ensemble-averaged drift velocity does not vary with time.In this work,the statistical mechan...A classical particle system coupled with a thermostat driven by an external constant force reaches its steady state when the ensemble-averaged drift velocity does not vary with time.In this work,the statistical mechanics of such a system is derived solely based on the equiprobability and ergodicity principles,free from any conclusions drawn on equilibrium statistical mechanics or local equilibrium hypothesis.The momentum space distribution is determined by a random walk argument,and the position space distribution is determined by employing the equiprobability and ergodicity principles.The expressions for energy,entropy,free energy,and pressures are then deduced,and the relation among external force,drift velocity,and temperature is also established.Moreover,the relaxation towards its equilibrium is found to be an exponentially decaying process obeying the minimum entropy production theorem.展开更多
The Poisson–Boltzmann(PB)theory is one of the most important theoretical models describing charged systems continuously.However,it suffers from neglecting ion correlations,which hinders its applicability to more gene...The Poisson–Boltzmann(PB)theory is one of the most important theoretical models describing charged systems continuously.However,it suffers from neglecting ion correlations,which hinders its applicability to more general charged systems other than extremely dilute ones.Therefore,some modified versions of the PB theory are developed to effectively include ion correlations.Focused on their applications to ionic solutions,the original PB theory and its variances,including the field-theoretic approach,the correlation-enhanced PB model,the Outhwaite–Bhuiyan modified PB theory and the mean field theories,are briefly reviewed in this paper with the diagnosis of their advantages and limitations.展开更多
Ionic liquids(ILs),also known as room-temperature molten salts,are solely composed of ions with melting points usually below 100℃.Because of their low volatility and vast amounts of species,ILs can serve as’green so...Ionic liquids(ILs),also known as room-temperature molten salts,are solely composed of ions with melting points usually below 100℃.Because of their low volatility and vast amounts of species,ILs can serve as’green solvents’and’designer solvents’to meet the requirements of various applications by fine-tuning their molecular structures.A good understanding of the phase behaviors of ILs is certainly fundamentally important in terms of their wide applications.This review intends to summarize the major conclusions so far drawn on phase behaviors of ILs by computational,theoretical,and experimental studies,illustrating the intrinsic relationship between their dual ionic and organic nature and the crystalline phases,nanoscale segregation liquid phase,IL crystal phases,as well as phase behaviors of their mixture with small organic molecules.展开更多
The folding of many small proteins is kinetically a two-state process with one major free-energy barrier to overcome,which can be roughly regarded as the inverse process of unfolding.In this work,we first use a Gaussi...The folding of many small proteins is kinetically a two-state process with one major free-energy barrier to overcome,which can be roughly regarded as the inverse process of unfolding.In this work,we first use a Gaussian network model to predict the folding nucleus corresponding to the major free-energy barrier of protein 2 GB1,and find that the folding nucleus is located in theβ-sheet domain.High-temperature molecular dynamics simulations are then used to investigate the unfolding process of 2 GB1.We draw free-energy surface from unfolding simulations,taking RMSD and contact number as reaction coordinates,which confirms that the folding of 2 GB1 is kinetically a two-state process.The comparison of the contact maps before and after the free energy barrier indicates that the transition from native to non-native structure of the protein is kinetically caused by the destruction of theβ-sheet domain,which manifests that the folding nucleus is indeed located in theβ-sheet domain.Moreover,the constrained MD simulation further confirms that the destruction of the secondary structures does not alter the topology of the protein retained by the folding nucleus.These results provide vital information for upcoming researchers to further understand protein folding in similar systems.展开更多
基金Supported by the Hundred Talent Program of the Chinese Academy of Sciencesthe General Program of the National Natural Science Foundation of China under Grant No. 10974208
文摘Nanoscale spatial heterogeneity in ionic liquids is formed by the aggregation of cationic tail groups. The electrostatic interactions between polar groups and the collective van der Waals interactions between nonpolar tail groups both contribute to the formation of tail domains, but the degrees of their contributions were unknown. In this work, by applying a strong external electric field to effectively overpower the electrostatic interactions between polar groups, we have determined that the tail aggregation is majorly attributed to the electrostatic interactions and the van der Waals interactions only have minor influence on the spatial heterogeneity phenomenon of ionic liquids.
基金the National Natural Science Foundation of China(Grant Nos.11574310,11674345,and 21733010)Beijing National Laboratory for Molecular Sciences,China(Grant No.BNLMS201835).
文摘It is very important to determine the phase transition temperature,such as the water/ice coexistence temperature in various water models,via molecular simulations.We show that a single individual direct simulation is sufficient to get the temperature with high accuracy and small computational cost based on the generalized canonical ensemble(GCE).Lennard–Jones fluids,the atomic water models,such as TIP4P/2005,TIP4P/ICE,and the mW water models are applied to illustrate the method.We start from the coexistent system of the two phases with a plane interface,then equilibrate the system under the GCE,which can stabilize the coexistence of the phases,to directly derive the phase transition temperature without sensitive dependence on the applied parameters of the GCE and the size of the simulation systems.The obtained result is in excellent agreement with that in literatures.These features make the GCE approach in determining the phase transition temperature of systems be robust,easy to use,and particularly good at working on computationally expensive systems.
基金Supported by the Hundred Talent Program of the Chinese Academy of Sciences,the National Natural Science Foundation of China under Grant Nos.71103179 and 71102129Program for Young Innovative Research Team in China University of Political Science and Law, 2010 Fund Project under the Ministry of Education of China for Youth Who are Devoted to Humanities and Social Sciences Research 10YJC630425
文摘This works examine the responses of housing prices to the monetary policies in various Chinese cities. Thirty-five large and medium sized Chinese cities are classified into six clusters applying the minimum variance clustering method according to the calculated correlation coefficients between the housing price indices of every two cities.Time difference correlation analysis is then employed to quantify the relations between the housing price indices of the six clusters and the monetary policies.It is suggested that the housing prices of various cities evolved at different paces and their responses to the monetary policies are heterogeneous,and local economic features are more important than geographic distances in determining the housing price trends.
基金Project supported by the National Basic Research Program of China (973 Program,Grant No.2013CB932804)the National Natural Science Foundation of China (Grant Nos.91227115 and 11121403)the Hundred Talent Program of the Chinese Academy of Sciences (CAS)
文摘Formation and dissociation mechanisms of C-C＋ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C-C＋ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C-C＋ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.
基金Supported by the National Basic Research Program of China 973 Program,under Grant No.2013CB932804the National Natural Science Foundation of China under Nos.11274319 and 11121403
文摘A non-equilibrium steady state can be characterized by a nonzero but stationary flux driven by a static external force. Under a weak external force, the drift velocity is difficult to detect because the drift motion is feeble and submerged in the intense thermal diffusion. In this article, we employ an accurate method in molecular dynamics simulation to determine the drift velocity of a particle driven by a weak external force in a one-dimensional periodic potential. With the calculated drift velocity, we found that the mobility and diffusion of the particle obey the Einstein relation, whereas their temperature dependences deviate from the Arrhenius law. A microscopic hopping mechanism was proposed to explain the non-Arrhenius behavior. Moreover, the position distribution of the particle in the potential well was found to deviate from the Boltzmann equation in a non-equilibrium steady state. The non-Boltzmann behavior may be attributed to the thermostat which introduces an effective "viscous" drag opposite to the drift direction of the particle.
基金Supported by the Hundred Talent Program of the Chinese Academy of Sciences (CAS)the National Natural Science Foundation of China under Grant Nos. 10974208, 11121403, 1083401401, and 91027045
文摘Diffusion-limited aggregation （DLA） assumes that particles perform pure random walk at a finite tem- perature and aggregate when they come close enough and stick together. Although it is well known that DLA in two dimensions results in a ramified fractal structure, how the particle shape influences the formed morphology is still un- clear. In this work, we perform the off-lattice two-dimensional DLA simulations with different particle shapes of triangle, quadrangle, pentagon, hexagon, and octagon, respectively, and compare with the results for circular particles. Our results indicate that different particle shapes only change the local structure, but have no effects on the global structure of the formed fractal duster. The local compactness decreases as the number of polygon edges increases.
基金Project supported by the National Basic Research Program of China(Grant No.2013CB932804)the National Natural Science Foundation of China(Grant Nos.91227115+1 种基金11274319and 11421063)
文摘The behavior of saturated aqueous Na Cl 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.
基金supported by the National Natural Science Foundation of China (No. 11947302)
文摘Flocking and vortical are two typical motion modes in active matter.Although it is known that the two modes can spontaneously switch between each other in a finite-size system,the switching dynamics remain elusive.In this work,by computer simulation of a two-dimensional Vicsek-like system with 1000 particles,we find from the perspective of the classical nucleation theory that the forward and backward switching dynamics are asymmetric:going from flocking to vortical is a one-step nucleation process,while the opposite is a two-step nucleation process,with the system staying in a metastable state before reaching the final flocking state.
基金Supported by the National Basic Research Program of China under Grant No.2013CB932804the National Natural Science Foundation of China under Grant No.11421063the CAS Biophysics Interdisciplinary Innovation Team Project
文摘To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics （MD） simulation in aqueous solution four fragments cut out of a protein G, including one a-helix （seqB： KVFKQYAN）, two -turns （seqA： LNGKTLKG and seqC： YDDATKTF）, and one -strand （seqD： DGEWTYDD）. The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-#s equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics.
基金Project supported by the National Basic Research Program of China(Grant No.2013CB932804)the National Natural Science Foundation of China(Grant Nos.11274319 and 11421063)
文摘Various soft materials share some common features, such as significant entropic effect, large fluctuations, sensitivity to thermodynamic conditions, and mesoscopic characteristic spatial and temporal scales. However, no quantitative defini- tions have yet been provided for soft matter, and the intrinsic mechanisms leading to their common features are unclear. In this work, from the viewpoint of statistical mechanics, we show that soft matter works in the vicinity of a specific thermo- dynamic state named moderate point, at which entropy and enthalpy contributions among substates along a certain order parameter are well balanced or have a minimal difference. Around the moderate point, the order parameter fluctuation, the associated response function, and the spatial correlation length maximize, which explains the large fluctuation, the sensitivity to thermodynamic conditions, and mesoscopic spatial and temporal scales of soft matter, respectively. Possible applications to switching chemical bonds or allosteric biomachines determining their best working temperatures are also briefly discussed.
基金Project supported by the Minister of Science and Technology of China
文摘We study the behaviors of mean end-to-end distance and specific heat of a two-dimensional intrinsically curved semiflexible biopolymer with a hard-core excluded volume interaction. We find the mean square end-to-end distance R2 N∝ Nβ at large N, with N being the number of monomers. Bothβ and proportional constant are dependent on the reduced bending rigidity κ and intrinsic curvature c. The larger the c, the smaller the proportional constant, and 1.5 ≥β ≥ 1. Up to a moderate κ = κc, or down to a moderate temperature T = Tc, β = 1.5, the same as that of a self-avoiding random walk, and the larger the intrinsic curvature, the smaller the κc. However, at a large κ or a low temperature,β is close to 1, and the conformation of the biopolymer can be more compact than that of a random walk. There is an intermediate regime with 1.5 〉β 〉 1 and the transition fromβ = 1.5 toβ= 1 is smooth. The specific heat of the system increases smoothly with increasing κ or there is no peak in the specific heat. Therefore, a nonvanishing intrinsic curvature seriously affects the thermal properties of a semiflexible biopolymer, but there is no phase transition in the system.
基金Project supported by the National Basic Research Program of China(Grant No.2013CB932804)the National Natural Science Foundation of China(Grant Nos.91227115,11421063,11504431,and 21503275)+1 种基金the Fundamental Research Funds for Central Universities of China(Grant No.15CX02025A)the Application Research Foundation for Post-doctoral Scientists of Qingdao City,China(Grant No.T1404096)
文摘Besides our previous experimental discovery （Zhao Y R, et al. 2015 Langmuir, 31, 12975） that acetonitrile （ACN） can tune the morphological features of nanostructures self-assembled by short peptides KIIIIK （KI4K） in aqueous solution, further experiments reported in this work demonstrate that ACN can also tune the mass of the self-assembled nanostructures. To understand the microscopic mechanism how ACN molecules interfere peptide self-assembly process, we conducted a series of molecular dynamics simulations on a monomer, a cross-β sheet structure, and a proto-fibril of KI4K in pure water, pure ACN, and ACN-water mixtures, respectively. The simulation results indicate that ACN enhances the intra-sheet interaction dominated by the hydrogen bonding （H-bonding） interactions between peptide backbones, but weakens the inter-sheet interaction dominated by the interactions between hydrophobic side chains. Through analyzing the correlations between different groups of solvent and peptides and the solvent behaviors around the proto-fibril, we have found that both the polar and nonpolar groups of ACN play significant roles in causing the opposite effects on intermolecular interactions among peptides. The weaker correlation of the polar group of ACN than water molecule with the peptide backbone enhances H-bonding interactions between peptides in the proto-fibril. The stronger correlation of the nonpolar group of ACN than water molecule with the peptide side chain leads to the accumulation of ACN molecules around the proto-fibril with their hydrophilic groups exposed to water, which in turn allows more water molecules close to the proto-fibril surface and weakens the inter-sheet interactions. The two opposite effects caused by ACN form a microscopic mechanism clearly explaining our experimental observations.
基金Project supported by the National Basic Research Program of China(Grant No.2013CB932804)the National Natural Science Foundation of China(Grant Nos.11421063,11647601,11504431,and 21503275)+1 种基金the Scientific Research Foundation of China University of Petroleum(East China)for Young Scholar(Grant Y1304073)financial support through the CAS Biophysics Interdisciplinary Innovation Team Project(Grant No.2060299)
文摘Nanostructures self-assembled by cross-β peptides with ordered structures and advantageous mechanical properties have many potential applications in biomaterials and nanotechnologies. Quantifying the intra-and inter-molecular driving forces for peptide self-assembly at the atomistic level is essential for understanding the formation mechanism and nanomechanics of various morphologies of self-assembled peptides. We investigate the thermodynamics of the intra-and inter-sheet structure formations in the self-assembly process of cross-β peptide KⅢIK by means of steered molecular dynamics simulation combined with umbrella sampling. It is found that the mechanical properties of the intra-and inter-sheet structures are highly anisotropic with their intermolecular bond stiffness at the temperature of 300 K being 5.58 N/m and 0.32 N/m, respectively. This mechanical anisotropy comes from the fact that the intra-sheet structure is stabilized by enthalpy but the inter-sheet structure is stabilized by entropy. Moreover, the formation process of KⅢIK intra-sheet structure is cooperatively driven by the van der Waals （VDW） interaction between the hydrophobic side chains and the electrostatic interaction between the hydrophilic backbones, but that of the inter-sheet structure is primarily driven by the VDW interaction between the hydrophobic side chains. Although only peptide KⅢIK is studied, the qualitative conclusions on the formation mechanism should also apply to other cross-β peptides.
基金funded by the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDA17010504)the National Natural Science Foundation of China(Nos.11774357,11947302)。
文摘A classical particle system coupled with a thermostat driven by an external constant force reaches its steady state when the ensemble-averaged drift velocity does not vary with time.In this work,the statistical mechanics of such a system is derived solely based on the equiprobability and ergodicity principles,free from any conclusions drawn on equilibrium statistical mechanics or local equilibrium hypothesis.The momentum space distribution is determined by a random walk argument,and the position space distribution is determined by employing the equiprobability and ergodicity principles.The expressions for energy,entropy,free energy,and pressures are then deduced,and the relation among external force,drift velocity,and temperature is also established.Moreover,the relaxation towards its equilibrium is found to be an exponentially decaying process obeying the minimum entropy production theorem.
基金supported by the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDA17010504)the National Natural Science Foundation of China(Nos.11774357 and 11947302)the CAS Biophysics Interdisciplinary Innovation Team Project(No.2060299)。
文摘The Poisson–Boltzmann(PB)theory is one of the most important theoretical models describing charged systems continuously.However,it suffers from neglecting ion correlations,which hinders its applicability to more general charged systems other than extremely dilute ones.Therefore,some modified versions of the PB theory are developed to effectively include ion correlations.Focused on their applications to ionic solutions,the original PB theory and its variances,including the field-theoretic approach,the correlation-enhanced PB model,the Outhwaite–Bhuiyan modified PB theory and the mean field theories,are briefly reviewed in this paper with the diagnosis of their advantages and limitations.
基金supported by the National Natural Science Foundation of China(Nos.11774357,22011530390,12047503)the Chinese Academy of Sciences(No.QYZDJ-SSWSYS01)
文摘Ionic liquids(ILs),also known as room-temperature molten salts,are solely composed of ions with melting points usually below 100℃.Because of their low volatility and vast amounts of species,ILs can serve as’green solvents’and’designer solvents’to meet the requirements of various applications by fine-tuning their molecular structures.A good understanding of the phase behaviors of ILs is certainly fundamentally important in terms of their wide applications.This review intends to summarize the major conclusions so far drawn on phase behaviors of ILs by computational,theoretical,and experimental studies,illustrating the intrinsic relationship between their dual ionic and organic nature and the crystalline phases,nanoscale segregation liquid phase,IL crystal phases,as well as phase behaviors of their mixture with small organic molecules.
基金Project supported by the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDA17010504)the National Natural Science Foundation of China(Grant No.11947302)。
文摘The folding of many small proteins is kinetically a two-state process with one major free-energy barrier to overcome,which can be roughly regarded as the inverse process of unfolding.In this work,we first use a Gaussian network model to predict the folding nucleus corresponding to the major free-energy barrier of protein 2 GB1,and find that the folding nucleus is located in theβ-sheet domain.High-temperature molecular dynamics simulations are then used to investigate the unfolding process of 2 GB1.We draw free-energy surface from unfolding simulations,taking RMSD and contact number as reaction coordinates,which confirms that the folding of 2 GB1 is kinetically a two-state process.The comparison of the contact maps before and after the free energy barrier indicates that the transition from native to non-native structure of the protein is kinetically caused by the destruction of theβ-sheet domain,which manifests that the folding nucleus is indeed located in theβ-sheet domain.Moreover,the constrained MD simulation further confirms that the destruction of the secondary structures does not alter the topology of the protein retained by the folding nucleus.These results provide vital information for upcoming researchers to further understand protein folding in similar systems.
