Chemical compositional changes in fault zones are dealt with in this paper from a dynamic point of view. In fault zones consisted of silicates, relative accumulation of Si and Fe is noticed in response to the leaching...Chemical compositional changes in fault zones are dealt with in this paper from a dynamic point of view. In fault zones consisted of silicates, relative accumulation of Si and Fe is noticed in response to the leaching of K, Na, and to a lesser extent, Mg,Ca and Ah The order of pctrogenetic elements from stable to mobile is tentatively suggested as follows: Si, Fe, Mg, Ca, Al, K and Na. The difference in ionic radius of these chemical elements is thought; to be the major factor controlling this dynamic differentiation. For fault zones along which one side is silicates and the other is carbonates, new mincrals are recognized in tectonite. On the silicate side Ca and Mg increase but Si and Al decrease; and the reverse is true on the carbonate side. This phenomenon indicates that the migration of elements in fault; zones is accelerated by dynamic cffect.展开更多
Molecular dynamics simulations on octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) at 303-383 K and atmospheric pressure are carried out under NPT ensemble and COMPASS force field, the equilibrium structures a...Molecular dynamics simulations on octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) at 303-383 K and atmospheric pressure are carried out under NPT ensemble and COMPASS force field, the equilibrium structures at elevated temperatures were obtained and showed that the stacking style of molecules don't change. The coefficient of thermal expansion (CTE) values were calculated by linear fitting method. The results show that the CTE values are close to the experimental results and show anisotropy. The total energies of HMX cells with separately increasing expansion rates (100%-105%) along each crystallographic axis was calculated by periodic density functional theory method, the results of the energy change rates are anisotropic, and the correlation equations of energy change-CTE values are established. Thus the hypostasis of the anisotropy of HMX crystal's thermal expansion, the determinate molecular packing style, is elucidated.展开更多
AIM: To analyze the hemodynamic and respiratory effects of propofol on patients undergoing gastroscopy and colonoscopy. METHODS: In this prospective study, conducted over a period of three years, 1,104 patients refe...AIM: To analyze the hemodynamic and respiratory effects of propofol on patients undergoing gastroscopy and colonoscopy. METHODS: In this prospective study, conducted over a period of three years, 1,104 patients referred for a same day GI endoscopy procedure were analyzed. All patients were given a propofol bolus (0.5-1.5 mg/kg). Arterial blood pressure (BP) was monitored at 3 rain intervals and heart rate and oxygen saturation (SpO2) were recorded continuously by pulse oximetry. Analyzed data acquisition was carried out before, during, and after the procedure. RESULTS: A statistically significant reduction in mean arterial pressure was demonstrated (P〈0.001) when compared to pre-intervention values, but severe hypotension, defined as a systolic blood pressure below 60mmHg, was noted in only 5 patients (0.5%). Oxygen saturation decreased from 96.5% to 94.4 % (P〈0.001). A critical decrease in oxygen saturation (〈90%) was documented in 27 patients (2.4%). CONCLUSION: Our results showed that propofol provided good sedation with excellent pain control, a short recovery time and no significant hemodynamic side effelts if carefully titrated. All the patients (and especially ASA Ⅲ group) require monitoring and care of an anesthesiologist.展开更多
Based on molecular dynamics(MD)simulation,the mechanisms of plastic anisotropy in nanotwinned polycrystalline copper with{111}texture during tensile deformation were systematically studied from the aspects of Schmid f...Based on molecular dynamics(MD)simulation,the mechanisms of plastic anisotropy in nanotwinned polycrystalline copper with{111}texture during tensile deformation were systematically studied from the aspects of Schmid factor of the dominant slip system and the dislocation mechanism.The results show that the Schmid factor of dominated slip system is altered by changing the inclining angle of the twin boundaries(TBs),while the yield stress or flow stress does not strictly follow the Schmid law.There exist hard and soft orientations involving different dislocation mechanisms during the tensile deformation.The strengthening mechanism of hard orientation lies in the fact that there exist interactions between the dislocations and the TBs during plastic deformation,which leads to the dislocation blocking and reactions.The softening mechanism of soft orientation lies in the fact that there is no interaction between the dislocations and the TBs because only the slip systems parallel to the TBs are activated and the dislocations slip on the planes parallel to the TBs.It is concluded that the plastic anisotropy in the nanotwinned polycrystalline copper with{111}texture is aroused by the combination effect of the Schmid factor of dominated slip system and the dislocation mechanism.展开更多
Agonist binding of A2A adenosine receptor (A2AAR) shows protective effects against inflammatory and immune. Efforts are exerted in understanding the general mechanism and developing A2AAR selectively binding agonist...Agonist binding of A2A adenosine receptor (A2AAR) shows protective effects against inflammatory and immune. Efforts are exerted in understanding the general mechanism and developing A2AAR selectively binding agonists. Using molecular dynamics (MD) simula- tions, we have studied the interactions between A2AAR and its agonist (adenosine), and analyzed the induced dynamic behaviors of the receptor. Key residues interacting with adenosine are identified: A63^2.61,I66^2.64,V84^3.32,L85^3.33,T88^3.36,F168^5.29,M177^5.38,L249^6.51,H250^6.52 and N253^6.55 interacting with adenosine with affinities larger than 0.5 kcal/mol. Moreover, no interaction between adenosine and L167^5.28 is observed, which supports our previous findings that L1675^5.28 is an antagonist specific binding reside. The dynamic be- haviors of agonist bound A2AAR are found to be different from apo-A2AAR in three typical functional switches: (i) tight "ionic lock" forms in adenosine-A2AAR, but it is in equilibrium between formation and breakage in apo-A2AAR; (ii) the "rotamer toggle switch", T88^3.36/F242^6.44/W246^6.48, adopted different rotameric conformations in adenosin-A2AAR and apo-A2AAR; (iii) adenosine-A2AAR has a flexible intracellular loop 2 (IC2) and s-helical IC3, while apo-A2AAR preferred s-helical IC2 and flexible IC3. Our results indicate that agonist binding induced different conformational rearrangements of these characteristic functional switches in adenosine-A2AAR and apo-A2AAR.展开更多
The complex model of Thermus thermophilus xylose isomerase (TtXI) with D-xylose was constructed, and molecular dynamics (MD) simulations were carried out at 300 and 360 K for 10 ns by NAMD2.5. The radius of gyrati...The complex model of Thermus thermophilus xylose isomerase (TtXI) with D-xylose was constructed, and molecular dynamics (MD) simulations were carried out at 300 and 360 K for 10 ns by NAMD2.5. The radius of gyration (Rg), subunit interactions, and residue flexibility were analyzed. The results show that residues 60-69, 142-148, 169-172, and 332-340 have high flexibility at 300 and 360 K. Residues with higher flexibility at 360 K than that at 300 K can mainly be divided into two groups: one locates in the helix-loophelix region consisting of residues 55-80 in catalytic domain; the other at subunit interfaces. The Rg of catalytic domain at 360 K shows 0.16 A higher than that at 300 K, but Rg of small C-terminal domain has no obvious difference. The results indicate that enhanced Rg of catalytic domain may lead to the intense motion of the active site of TtXI and promote the D-xylose isomization reaction. Eight hydrogen bonds and five ion pairs are reduced at subunit interfaces at 360 K compared with 300 K, that may be the main reason for the decrease in rigidity and increase in activity at high temperature of TtXI. This result also help to explain the cold-adaption phenomenon of TtXI E372G mutant reported previously. Our results reveal the relationship between temperature and structure flexibility of TtXI, and play an important role in understanding the thermostability of thermophile protein with multiple subunits.展开更多
In this paper we have investigated the reflection and the transmission of a system of two symmetric circular-arc-shaped thin porous plates submerged in deep water within the context of linear theory. The hypersingular...In this paper we have investigated the reflection and the transmission of a system of two symmetric circular-arc-shaped thin porous plates submerged in deep water within the context of linear theory. The hypersingular integral equation technique has been used to analyze the problem mathematically. The integral equations are formulated by applying Green's integral theorem to the fundamental potential function and the scattered potential function into a suitable fluid region, and then using the boundary condition on the porous plate surface. These are solved approximately using an expansion-cure-collocation method where the behaviour of the potential functions at the tips of the plates have been used. This method ultimately produces a very good numerical approximation for the reflection and the transmission coefficients and hydrodynamic force components. The numerical results are depicted graphically against the wave number for a variety of layouts of the arc. Some results are compared with known results for similar configurations of dual rigid plate systems available in the literature with good agreement.展开更多
Molecular dynamics(MD)simulations and anisotropic thermal diffusion dynamics(ATD)simulations were performed on the wild TrpR and its 75 residue mutant(mTrpR)to investigate TrpR longrange effects.The ATD result shows t...Molecular dynamics(MD)simulations and anisotropic thermal diffusion dynamics(ATD)simulations were performed on the wild TrpR and its 75 residue mutant(mTrpR)to investigate TrpR longrange effects.The ATD result shows that the mTrpR has higher fluctuation than the wild TrpR,and its helix chainⅡF has particular disorder.It is obvious that the 75 residue of wild TrpR and mTrpR affects the protein dynamics flexibilities by the long-range effects.The ATD and MD both confirm that the differences in the size of side-chain and three-dimensional structures of two different 75 residues in the wild TrpR and mTrpR will spread to the entire protein by way of the long-range effects.Long-range effect affects the protein side chain interaction,conformational changes,flexibilities and secondary structures.Further,the ATD result also shows that each 75 residue of the symmetric homodimer has the same effect,and the two 75 residues have a positive correlation in long-range regulating processes.The residues 48,50,71,79 in chainⅠof wild TrpR and residues 45,72,80 in chainⅡof mTrpR play important roles in long-range interaction processes.展开更多
In this mini-review we summarize the progress of modeling, simulation and analysis of shock responses of heterogeneous materials in our group in recent years. The basic methodology is as below. We first decompose the ...In this mini-review we summarize the progress of modeling, simulation and analysis of shock responses of heterogeneous materials in our group in recent years. The basic methodology is as below. We first decompose the problem into different scales. Construct/Choose a model according to the scale and main mechanisms working at that scale. Perform numerical simulations using the relatively mature schemes. The physical information is transferred between neighboring scales in such a way: The statistical information of results in smaller scale contributes to establishing the constitutive equation in larger one. Except for the microscopic Molecular Dynamics(MD) model, both the mesoscopic and macroscopic models can be further classified into two categories,solidic and fluidic models, respectively. The basic ideas and key techniques of the MD, material point method and discrete Boltzmann method are briefly reviewed. Among various schemes used in analyzing the complex fields and structures, the morphological analysis and the home-built software, GISO, are briefly introduced. New observations are summarized for scales from the larger to the smaller.展开更多
Ion specificity of Na+ and C1- ions for NaCI solution confined in silicon nanochannels is investigated with molecular dynamics (MD) simulations. The MD simulation results demonstrate that ion specificity for Na+ a...Ion specificity of Na+ and C1- ions for NaCI solution confined in silicon nanochannels is investigated with molecular dynamics (MD) simulations. The MD simulation results demonstrate that ion specificity for Na+ and C1- ions exhibits clearly in na- nochannels with high surface charge density. The two types of ions show different density distributions perpendicular to the channel surface due to the ion specificity when they act as countefions near negatively and positively charged surfaces, respec- tively. Both the two counterion distributions cannot be predicted by Poisson-Boltzmann equation within 0.75 nm near the sur- face. In addition, the ion specificity is also demonstrated through affecting the water density distributions. In the nanochannel with negatively charged surfaces, the presence of the Na+ ions reduces the number of water peaks in water density distribution profile. In comparison, when the C1- ions act as counterions near positively charged surfaces, they do not affect the number of the water peaks. Besides the influence on the water density distribution, ion specificity also exhibits through affecting the wa- ter molecule orientation in the adsorbed layer. It is found that C1- ions make the water molecules in the adsorbed layer align more orderly than Na~ ions do when the two types of ions act as the counterions near the positively and negatively charged surfaces with the same surface charge density.展开更多
文摘Chemical compositional changes in fault zones are dealt with in this paper from a dynamic point of view. In fault zones consisted of silicates, relative accumulation of Si and Fe is noticed in response to the leaching of K, Na, and to a lesser extent, Mg,Ca and Ah The order of pctrogenetic elements from stable to mobile is tentatively suggested as follows: Si, Fe, Mg, Ca, Al, K and Na. The difference in ionic radius of these chemical elements is thought; to be the major factor controlling this dynamic differentiation. For fault zones along which one side is silicates and the other is carbonates, new mincrals are recognized in tectonite. On the silicate side Ca and Mg increase but Si and Al decrease; and the reverse is true on the carbonate side. This phenomenon indicates that the migration of elements in fault; zones is accelerated by dynamic cffect.
文摘Molecular dynamics simulations on octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) at 303-383 K and atmospheric pressure are carried out under NPT ensemble and COMPASS force field, the equilibrium structures at elevated temperatures were obtained and showed that the stacking style of molecules don't change. The coefficient of thermal expansion (CTE) values were calculated by linear fitting method. The results show that the CTE values are close to the experimental results and show anisotropy. The total energies of HMX cells with separately increasing expansion rates (100%-105%) along each crystallographic axis was calculated by periodic density functional theory method, the results of the energy change rates are anisotropic, and the correlation equations of energy change-CTE values are established. Thus the hypostasis of the anisotropy of HMX crystal's thermal expansion, the determinate molecular packing style, is elucidated.
基金Supported by "Bates" Clinic, Svetice 15, Zagreb, Croatia, in the form of grant, equipment and drugs
文摘AIM: To analyze the hemodynamic and respiratory effects of propofol on patients undergoing gastroscopy and colonoscopy. METHODS: In this prospective study, conducted over a period of three years, 1,104 patients referred for a same day GI endoscopy procedure were analyzed. All patients were given a propofol bolus (0.5-1.5 mg/kg). Arterial blood pressure (BP) was monitored at 3 rain intervals and heart rate and oxygen saturation (SpO2) were recorded continuously by pulse oximetry. Analyzed data acquisition was carried out before, during, and after the procedure. RESULTS: A statistically significant reduction in mean arterial pressure was demonstrated (P〈0.001) when compared to pre-intervention values, but severe hypotension, defined as a systolic blood pressure below 60mmHg, was noted in only 5 patients (0.5%). Oxygen saturation decreased from 96.5% to 94.4 % (P〈0.001). A critical decrease in oxygen saturation (〈90%) was documented in 27 patients (2.4%). CONCLUSION: Our results showed that propofol provided good sedation with excellent pain control, a short recovery time and no significant hemodynamic side effelts if carefully titrated. All the patients (and especially ASA Ⅲ group) require monitoring and care of an anesthesiologist.
基金the National Natural Science Foundation of China(No.51871070).
文摘Based on molecular dynamics(MD)simulation,the mechanisms of plastic anisotropy in nanotwinned polycrystalline copper with{111}texture during tensile deformation were systematically studied from the aspects of Schmid factor of the dominant slip system and the dislocation mechanism.The results show that the Schmid factor of dominated slip system is altered by changing the inclining angle of the twin boundaries(TBs),while the yield stress or flow stress does not strictly follow the Schmid law.There exist hard and soft orientations involving different dislocation mechanisms during the tensile deformation.The strengthening mechanism of hard orientation lies in the fact that there exist interactions between the dislocations and the TBs during plastic deformation,which leads to the dislocation blocking and reactions.The softening mechanism of soft orientation lies in the fact that there is no interaction between the dislocations and the TBs because only the slip systems parallel to the TBs are activated and the dislocations slip on the planes parallel to the TBs.It is concluded that the plastic anisotropy in the nanotwinned polycrystalline copper with{111}texture is aroused by the combination effect of the Schmid factor of dominated slip system and the dislocation mechanism.
文摘Agonist binding of A2A adenosine receptor (A2AAR) shows protective effects against inflammatory and immune. Efforts are exerted in understanding the general mechanism and developing A2AAR selectively binding agonists. Using molecular dynamics (MD) simula- tions, we have studied the interactions between A2AAR and its agonist (adenosine), and analyzed the induced dynamic behaviors of the receptor. Key residues interacting with adenosine are identified: A63^2.61,I66^2.64,V84^3.32,L85^3.33,T88^3.36,F168^5.29,M177^5.38,L249^6.51,H250^6.52 and N253^6.55 interacting with adenosine with affinities larger than 0.5 kcal/mol. Moreover, no interaction between adenosine and L167^5.28 is observed, which supports our previous findings that L1675^5.28 is an antagonist specific binding reside. The dynamic be- haviors of agonist bound A2AAR are found to be different from apo-A2AAR in three typical functional switches: (i) tight "ionic lock" forms in adenosine-A2AAR, but it is in equilibrium between formation and breakage in apo-A2AAR; (ii) the "rotamer toggle switch", T88^3.36/F242^6.44/W246^6.48, adopted different rotameric conformations in adenosin-A2AAR and apo-A2AAR; (iii) adenosine-A2AAR has a flexible intracellular loop 2 (IC2) and s-helical IC3, while apo-A2AAR preferred s-helical IC2 and flexible IC3. Our results indicate that agonist binding induced different conformational rearrangements of these characteristic functional switches in adenosine-A2AAR and apo-A2AAR.
基金This work was supported by the National Natural Science Foundation of China (No.20336010) and the State Key Basic Research and Development Plan of China (No.2003CB716000).
文摘The complex model of Thermus thermophilus xylose isomerase (TtXI) with D-xylose was constructed, and molecular dynamics (MD) simulations were carried out at 300 and 360 K for 10 ns by NAMD2.5. The radius of gyration (Rg), subunit interactions, and residue flexibility were analyzed. The results show that residues 60-69, 142-148, 169-172, and 332-340 have high flexibility at 300 and 360 K. Residues with higher flexibility at 360 K than that at 300 K can mainly be divided into two groups: one locates in the helix-loophelix region consisting of residues 55-80 in catalytic domain; the other at subunit interfaces. The Rg of catalytic domain at 360 K shows 0.16 A higher than that at 300 K, but Rg of small C-terminal domain has no obvious difference. The results indicate that enhanced Rg of catalytic domain may lead to the intense motion of the active site of TtXI and promote the D-xylose isomization reaction. Eight hydrogen bonds and five ion pairs are reduced at subunit interfaces at 360 K compared with 300 K, that may be the main reason for the decrease in rigidity and increase in activity at high temperature of TtXI. This result also help to explain the cold-adaption phenomenon of TtXI E372G mutant reported previously. Our results reveal the relationship between temperature and structure flexibility of TtXI, and play an important role in understanding the thermostability of thermophile protein with multiple subunits.
基金Partially Supported by the Department of Science and Technology Through a Research Grant to RG(No.SR/FTP/MS-020/2010)
文摘In this paper we have investigated the reflection and the transmission of a system of two symmetric circular-arc-shaped thin porous plates submerged in deep water within the context of linear theory. The hypersingular integral equation technique has been used to analyze the problem mathematically. The integral equations are formulated by applying Green's integral theorem to the fundamental potential function and the scattered potential function into a suitable fluid region, and then using the boundary condition on the porous plate surface. These are solved approximately using an expansion-cure-collocation method where the behaviour of the potential functions at the tips of the plates have been used. This method ultimately produces a very good numerical approximation for the reflection and the transmission coefficients and hydrodynamic force components. The numerical results are depicted graphically against the wave number for a variety of layouts of the arc. Some results are compared with known results for similar configurations of dual rigid plate systems available in the literature with good agreement.
基金supported by the Innovation project of Henan Agricultural University(No.30600982)PhD Start-up Foundation of Henan Agricultural University(30600780)2023 Instrument Operator Capability lmprovement Project(SYS2023T04)
文摘Molecular dynamics(MD)simulations and anisotropic thermal diffusion dynamics(ATD)simulations were performed on the wild TrpR and its 75 residue mutant(mTrpR)to investigate TrpR longrange effects.The ATD result shows that the mTrpR has higher fluctuation than the wild TrpR,and its helix chainⅡF has particular disorder.It is obvious that the 75 residue of wild TrpR and mTrpR affects the protein dynamics flexibilities by the long-range effects.The ATD and MD both confirm that the differences in the size of side-chain and three-dimensional structures of two different 75 residues in the wild TrpR and mTrpR will spread to the entire protein by way of the long-range effects.Long-range effect affects the protein side chain interaction,conformational changes,flexibilities and secondary structures.Further,the ATD result also shows that each 75 residue of the symmetric homodimer has the same effect,and the two 75 residues have a positive correlation in long-range regulating processes.The residues 48,50,71,79 in chainⅠof wild TrpR and residues 45,72,80 in chainⅡof mTrpR play important roles in long-range interaction processes.
基金supported by the Science Foundation of LCPNational Natural Science Foundation of China(Grant Nos.11475028 and 11325209)+4 种基金the Opening Project of State Key Laboratory of Explosion Science and Technology(Beijing Institute of TechnologyGrant No.KFJJ14-1M)the Open Project Program of State Key Laboratory of Theoretical Physics,Institute of Theoretical PhysicsChinese Academy of SciencesChina(Grant No.Y4KF151CJ1)
文摘In this mini-review we summarize the progress of modeling, simulation and analysis of shock responses of heterogeneous materials in our group in recent years. The basic methodology is as below. We first decompose the problem into different scales. Construct/Choose a model according to the scale and main mechanisms working at that scale. Perform numerical simulations using the relatively mature schemes. The physical information is transferred between neighboring scales in such a way: The statistical information of results in smaller scale contributes to establishing the constitutive equation in larger one. Except for the microscopic Molecular Dynamics(MD) model, both the mesoscopic and macroscopic models can be further classified into two categories,solidic and fluidic models, respectively. The basic ideas and key techniques of the MD, material point method and discrete Boltzmann method are briefly reviewed. Among various schemes used in analyzing the complex fields and structures, the morphological analysis and the home-built software, GISO, are briefly introduced. New observations are summarized for scales from the larger to the smaller.
基金supported by the National Basic Research Program of Chi-na(Grant Nos.2011CB707601,2011CB707605)the National Natural Science Foundation of China(Grant No.50925519)+3 种基金the Research Funding for the Doctor Program from China Educational Ministry(Grant No.20100092110051)the Innovative Project for Graduate Students of Jiangsu Province(Grant No.CXZZ13_0087)the Scientific Research Founda-tion of Graduate School of Southeast University(Grant No.YBJJ1322)The calculations were performed on Tianhe-1A at National Supercomputing Center in Tianjin,China
文摘Ion specificity of Na+ and C1- ions for NaCI solution confined in silicon nanochannels is investigated with molecular dynamics (MD) simulations. The MD simulation results demonstrate that ion specificity for Na+ and C1- ions exhibits clearly in na- nochannels with high surface charge density. The two types of ions show different density distributions perpendicular to the channel surface due to the ion specificity when they act as countefions near negatively and positively charged surfaces, respec- tively. Both the two counterion distributions cannot be predicted by Poisson-Boltzmann equation within 0.75 nm near the sur- face. In addition, the ion specificity is also demonstrated through affecting the water density distributions. In the nanochannel with negatively charged surfaces, the presence of the Na+ ions reduces the number of water peaks in water density distribution profile. In comparison, when the C1- ions act as counterions near positively charged surfaces, they do not affect the number of the water peaks. Besides the influence on the water density distribution, ion specificity also exhibits through affecting the wa- ter molecule orientation in the adsorbed layer. It is found that C1- ions make the water molecules in the adsorbed layer align more orderly than Na~ ions do when the two types of ions act as the counterions near the positively and negatively charged surfaces with the same surface charge density.