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The mechanical properties of natural rubber (NR) composites depend on many factors, including the filler loading, filler size, filler dispersion, and filler-rubber interfacial interactions. Thus, NR composites with nano-sized fillers have attracted a great deal of attention for improving properties such as stiffness, chemical resistance, and high wear resistance. Here, a coarse-grained (CG) model based on the MARTINI force field version 2.1 has been developed and deployed for simulations of cis-1,4-polyisoprene (cis-PI). The model shows qualitative and quantitative agreement with the experiments and atomistic simulations. Interestingly, only a 0.5% difference with respect to the experimental result of the glass transition temperature (Tg) of the cis-PI in the melts was observed. In addition, the mechanical and thermodynamical properties of the cis-PI-fullerene(C60) composites were investigated. Coarse-grained molecular dynamics (MD) simulations of cis-PI-C60 composites with varying fullerene concentrations (0–32 parts per hundred of rubber; phr) were performed over 200 microseconds. The structural, mechanical, and thermal properties of the composites were determined. The density, bulk modulus, thermal expansion, heat capacity, and Tg of the NR composites were found to increase with increasing C60 concentration. The presence of C60 resulted in a slight increasing of the end-to-end distance and radius of the gyration of the cis-PI chains. The contribution of C60 and cis-PI interfacial interactions led to an enhancement of the bulk moduli of the composites. This model should be helpful in the investigations and design of effective fillers of NR-C60 composites for improving their properties.

Macroscopic and microscopic properties of fullerene (C60)–cis-polyisoprene (cis-PI) composites at varying fullerene concentrations were investigated using atomistic molecular dynamics (MD) simulations over microsecond time scales. Results show that the introduction of fullerenes into a polymer matrix increases density, bulk modulus and heat capacity while thermal expansivity decreases. The presence of fullerenes slowed the diffusion of both C60 and cis-PI. Moreover, increasing fullerene concentration results in ordering of the cis-PI chains at the cis-PI–fullerene interfaces and shrinking of bulk PI regions. Free energy calculations of fullerene dimerization suggest that fullerenes disperse at low and aggregate at high fullerene concentrations. Our multi-scaled analysis approach demonstrates the role of ‘ordered’ regions adjacent to the interface between cis-PI and fullerene in controlling the level of order and mobility of the cis-PI chains. The relationship between the microscopic behavior and the changes in mechanical and thermal properties are discussed. Our study is beneficial for further studies and development of advanced rubber technology for novel, cost-effective, material with very high stiffness and thermal endurance with optimizing conditions of filler contents.

Natural rubber (NR) foam can be prepared by the Dunlop method using concentrated natural latex with chemical agents. Most previous studies have focused on the thermodynamic parameters of solid rubber in extension. The main objective of this study is to investigate the effect of the NR matrix concentration on the static and dynamic properties of NR foams, especially the new approach of considering the thermodynamic aspects of NR foam in compression. We found that the density and compression strength of NR foams increased with increasing NR matrix concentration. The mechanical properties of NR foam were in agreement with computational modelling. Moreover, thermodynamic aspects showed that the ratio of internal energy force to the compression force, Fu/F, and the entropy, S, increased with increasing matrix concentration. The activation enthalpy, ∆Ha, also increased with increasing matrix concentration in the NR foam, indicating the greater relaxation time of the backbone of the rubber molecules. New scientific concepts of thermodynamic parameters of the crosslinked NR foam in compression mode are proposed and discussed. Our results will improve both the knowledge and the development of rubber foams based on the structure–properties relationship, especially the new scientific concept of the thermodynamical parameters under compression.

Concentrated natural latex was used to produce a rubber foam that is porous, elastic and well ventilated. The mechanical properties can be either soft or firm, depending on the formulation of the latex used. Briefly, concentrated natural latex was mixed with chemical agents to make the rubber foam on a laboratory scale using the Dunlop process. In this work, we changed the concentration of the chemical blowing agent in the latex. The morphological properties of the rubber foam were characterised using scanning electron microscopy, and the mechanical properties, or elasticity, were studied using compression experiments and the Mooney–Rivlin calculation. The results show that the concentration of the chemical blowing agent affects the morphological properties of the rubber foam but not the mechanical properties, indicating the heterogeneous structure of the rubber foam. The thermodynamic parameters (∆G and ∆S) and the internal energy force per compression force (Fu/F) of the rubber foam with various amounts of chemical blowing agent were also investigated. This study could be applied in the foam industry, particularly for pillow, mattress and insulation materials, as the present work shows the possible novel control of the morphological structure of the rubber foam without changing its mechanical properties. The difference in cell sizes could affect the airflow in rubber foam.

Calcium carbonate (CaCO3) is one of the most important inorganic powders and is widely used as filler in order to reduce costs in the rubber industry. Nanocalcium carbonate reduces costs and acts as a semireinforcing filler that improves the mechanical properties of rubber composites. The objective of this study was to investigate the effect of nano-CaCO3 (NCC) and micro-CaCO3 (MCC) on the properties of natural rubber composites, in particular, new results of structure&ndash, properties relationship. The effects of NCC/MCC on the properties of rubber composites, such as Mooney viscosity, bound rubber, Mullins effect, and Payne effect, were investigated. The result of the Mullins effect of rubber composites filled with NCC was in good agreement with the results of Mooney viscosity and bound rubber, with higher Mooney viscosity and bound rubber leading to higher stress to pull the rubber composites. The Payne effect showed that the value of different storage moduli (&Delta, G&rsquo, ) of rubber composites filled with 25 parts per hundred rubber (phr) NCC was the lowest due to weaker filler network, while the rubber supplemented with 100 phr NCC had more significant &Delta, values with increase in strain. The results of rubber composites filled with MCC showed the same tendency as those of rubber composites filled with NCC. However, the effect of specific surface area of NCC on the properties of rubber composites was more pronounced than those of rubber composites filled with MCC. Finite element analysis of the mechanical property of rubber composites was in good agreement with the result from the experiment. The master curves of time&ndash, temperature superposition presented lower free volume in the composites for higher loading of filler, which would require more relaxation time of rubber molecules. This type of nanocalcium carbonate material can be applied to tailor the properties and processability of rubber products.

The specific adsorption of alkali ions, Li + , Na + , K + , and Cs + , in electrolyte solutions on Prussian blue (PB) is investigated by using the three-dimensional (3D) reference interaction site-model (RISM) theory. The results from 3D-RISM show dramatically different adsorption sites between large ions (K + and Cs + ) and small ions (Li + and Na + ). The small ions are adsorbed at the channel entrance sites without the water–ion exchange mechanism. In contrast, the large ions are adsorbed in PB by the water–ion exchange mechanism, and the adsorption site of large ions is located at the center of the cage or at the interstitial site.

Ferric hexacyanoferrate (FeHCF) or Prussian blue (PB) exhibits selective alkali ion adsorption and has great potential for use in various applications. In the present work, alkali ion (Li+, Na+, K+, and Cs+) and water configurations in defective PB (d-PB) were studied by using the statistical mechanics of molecular liquids. The three-dimensional (3D) distribution functions of the ions and water were determined by solving the 3D-reference interaction site model (RISM) equation of systems of a unit lattice of d-PB in electrolyte solutions, i.e., LiCl, NaCl, KCl, and CsCl. The results show the difference in the ion-water configurations and distributions between small (Li+ and Na+) and large ions (K+ and Cs+). The adsorption sites of Li+ and Na+ are located off-center and lie on the diagonal axis. By contrast, the larger ions, K+ and Cs+, are adsorbed at the center of the unit cell. The degree of dehydration due to the adsorption of alkali ions indicates that there was no water exchange during Li+ and Na+ adsorption, whereas two and three water molecules were removed after adsorption of K+ or Cs+ in the unit cell.

In this study, we investigated the intercalation of water and K+ to interlayer of Montmorillonite (MMT) nanoclay by using the statistical mechanics theory of molecular liquids or three-dimensional reference interaction site model (3D-RISM). The results from 3D-RISM show that the distribution of water and K+ bound to the MMT’s surfaces with different sites. Moreover, the results from 3D-RISM show the amount of water corresponds to the d-basal spacing of the clay, which are in good agreements with other simulation methods as well as experimental.

Fillers have been widely used in the rubber industry for many applications such as tile floor, vehicle tire, etc. Calcium carbonate (CaCO3) is one of the important inorganic powders and it is widely used as filler in order to reduce the cost in rubber industry. The objective of this study is to investigate physical and mechanical properties of the rubber composites with CaCO3 powder. We studied the CaCO3 additive in natural rubber (NR) with 25, 50, 75 and 100 parts per hundred rubber (phr). The effect of CaCO3 on the properties of rubber composite, such as Mooney viscosity, bound rubber, Mullins effect and Payne effect, was investigated. The result of Mullins effect of rubber composite filled with CaCO3 is in good agreement with the result of bound rubber: higher bound rubber leads to higher stress to pull the rubber composites. The Payne effect shows that the value of different storage moduli (ΔG’) of rubber compound filled with 25 phr CaCO3 is the lowest due to weaker filler network. While, the NR supplemented with 100 phr CaCO3 represents more significant ΔG’ with the strain increasing. This type of material could be applied for tailoring the properties of rubber products.

Conductive polymer nanocomposites material (PNCs) is one type of alternative polymeric materials to replace high-cost intrinsically conductive polymers (ICPs). PNC is a composite of electrical insulative polymer matrix and electrically conductive filler in which it is made by less complicated synthesis protocols but has similar quantitative conductive properties to existing conducting polymers. Therefore, PNC is a candidate for many applications, such as, light-emitting diodes, flexible electrodes, batteries and strain sensors [1]. In this study, an in-house Monte-Carlo simulation was used to investigate the percolation paths of the 3D model of nanorod filler network in the polymer lattice and estimate the nanorod concentration at percolation threshold [2]. The model also includes the nanorod filler orientation angles. We then focused on the effects of stretching lattice on the percolation threshold. The dimension of lattice length was varied with constant volume for each simulation system (incompressible material). Results of simulations showed that the percolation thresholds decreased when increasing the lattice stretching and the nanorod orientation angles have been confined by finite lattice dimension which shows there is the effect of orientations angle on the percolation threshold. Our finding will be a useful guideline for designing polymer nanocomposite as a switching sensor.

The binding affinity of oseltamivir to the influenza B neuraminidase and to its variants with three single substitutions, E119G, R152K, and D198N, is investigated by the MM/3D-RISM method. The binding affinity or the binding free energy of ligand to receptor was found to be determined by a subtle balance of two major contributions that largely cancel out each other: the ligand-receptor interactions and the dehydration free energy. The theoretical results of the binding affinity of the drug to the mutants reproduced the observed trend in the resistivity, measured by IC50 ; the high-level resistance of E119G and R152K, and the low-level resistance of D198N. For E119G and R152K, reduction of the direct drug-target interaction, especially at the mutated residue, is the main source of high-level oseltamivir resistance. This phenomenon, however, is not found in the D198N strain, which is located in the framework of the active-site.

The potassium channel is highly selective for K + over other monovalent cations, and the narrow pore structure with 3 A in diameter named the selectivity filter (SF) is responsible for the selective permeation. Here we applied the statistical mechanics of liquids called three-dimensional reference interaction site model (3D-RISM) theory, and the binding configurations of the monovalent cations, Li + , Na + and K + , with special attention on the contribution of water in the KcsA potassium channel were examined. All the three types of cations are bound in the open SF with high affinity, but with different binding coordinations: the in-cage configuration by eight carbonyl oxygens for K + , and the in-plane configuration by four carbonyl oxygens for Li + , whereas both configurations are allowed for Na + . In each case, water contributes an integral part of the ion coordination. In the case of Li + , a linear water-Li + -water complex is settled into two adjacent cages with the Li + centered at the in-plane site. Positions of water around Na + are more flexible, which may allow a transition between in-plane and in-cage configurations. K + stably occupied in-cage configuration, and water occupies adjacent cages. The results provide the distinct configuration of ion and water in the SF, and serves clues for elementary process of selectivity.

The potassium channel is highly selective for K+ over Na+, and the mechanism underlying this selectivity remains unclear. We show the three-dimensional distribution functions (3D-DFs) of small cations (Li+, Na+, and K+) and the free energy profile of ions inside the open selectivity filter (SF) of the KcsA channel. Our previous results [S. Phongphanphanee, N. Yoshida, S. Oiki, F. Hirata. Abstract Book of 5th International Symposium on Molecular Science of Fluctuations toward Biological Functions, P062 (2012)] indicate that the 3D-DF for K+ exhibits distinct peaks at the sites formed by the eight carbonyl oxygen atoms belonging to the surrounding peptide-backbone and residues (the cage site). Li+ has sharp distributions in the 3D-DF at the center of a quadruplex composed of four carbonyl oxygen atoms (the plane site). Na+ has a rather diffuse distribution throughout the SF region with peaks both in the plane and in cage sites. The results provide microscopic evidence of the phenomenological findings that Li+ and Na+ are not excluded from the SF region and that the binding affinity alone does not cause the ion selectivity of KcsA. In the present study, with an ion placed explicitly along the pore axis, the free energy profiles of the ions inside the SF were calculated; from these profiles we suggest a new mechanism for selective K+ permeation. According to the model, a K+ ion must overcome a free energy barrier that is approximately half that of Na+ to exit from either of the SF mouths due to the existence of an intermediate local minimum along the route for climbing the barriers.

Conductive polymer (CP) is a special class of polymeric materials with conductive property which possesses high potential for the fabrication of future advanced electronic devices. To design a higher conductivity polymer, composite polymer material with conductive nanorod filler is one of alternative ideas to replace the high-cost intrinsically conductive polymeric materials. In this study, our in-house Monte-Carlo simulation was performed to generate a number of randomly-positioned nanorods within a 3D confined-space box and to assess percolation paths formed by nanorods that connected two electrodes for each configuration. The results showed that the probability of finding connection path was related to the concentrations of nanorod filler in 3D confined-space box. The increasing probability to find connection paths when adding more filler concentrations was found to be a logistic growth, in which growth rate and threshold concentration depended on soft-shell filler radius. Our finding will be beneficial for designing composite conductive polymer for switching sensor.

Prussian Blue (PB) or ferric hexacyanoferrate (II) is one of the most attractive materials in green battery industry. It has defective structure (d-PB), Fe 4 III [ Fe II ( CN ) 6 ] 3 ⋅ xH 2 O ( x ≈ 14 − 16 ) , that one of [Fe(CN)6]4− group is missing, and hydrated with water molecules at the 24e empty nitrogen site. In this study, we investigated the distributions of water and Li+ in d-PB by using three-dimensional reference interaction site-model (3D-RISM) theory, which is a statistical mechanics theory of molecular liquids. The theory can examine the selective ion adsorption in solvated molecular materials. The results from 3D-RISM show that there are 14 water molecules located in different positions inside the d-PB lattice, which are in good agreement with experiment. Moreover, we also found the Li+ distributed at inside d-PB lattice positioned closely to the 32f spherical cavity of d-PB.

Molecular recognition (MR) is an essential elementary process allowing biomolecules to perform their function. MR can be defined as a molecular process in which one or several guest molecules are bound with a high probability at a particular site such as a cleft or a cavity, of a host molecule in a particular orientation. It is a thermodynamic process which is characterised by the difference of the free energies between two states of a host–guest system, bound and unbound. The process features an extremely heterogeneous atomic-environment around binding sites, which has turned away challenges by the conventional statistical mechanics of liquids, e.g. a mean field theory. We have been developing a new theory for MR in biomolecular systems, based on the statistical mechanics of liquids, or the 3D-reference interaction site model (RISM)/RISM theory. The theory has demonstrated its amazing capability of predicting the process from the first principle. In this article, we review our recent works on MR concerni...

Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the 3D-RISM/RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as “recognized” by the protein. 3D-distribution functions can be obtained by means of 3D-RISM/RISM theory. Some biochemical processes are investigated, which are intimately related to the molecular recognition of small ligands such as water, ions, and carbon monoxide by a protein.

The three-deimensional distribution functions (3D-DFs) and potentials of mean force (PMFs) of small neutral molecules inside the two aquaporin channels, AQP1 and GlpF, are calculated based on the 3D-RISM theory, the statistical mechanics theory of molecular liquids, in order to investigate the permeability of those ligands through the channels. The ligands investigated are neon (Ne), carbon dioxide (CO(2)), nitric oxide (NO), ammonia (NH(3)), urea, and glycerol. Neon shows continuous distribution throughout the channel pore in AQP1 as is the case of water, although the PMF of Ne at the selective filter (SF) region is higher than that of water, indicating that the stability of molecules in the channel is determined not only by their size, but also by the charge distribution. The ligand molecules, CO(2), NO, urea, and glycerol, have a large barrier in PMF at the SF region in AQP1, indicating that the channel is not permeable by those ligands. On the other hand, NH(3) has only a small activation barrier, approximately 2.5 kJ/mol, to be overcome. Therefore, our theory predicts that a NH(3) molecule can be permeated through the AQP1 channel. In GlpF, all the ligands have negative PMF throughout the channel pore except for glycerol, which has a small barrier at the SF area, approximately 2.1 kJ/mol. The barrier can be readily overcome by the thermal motion. So, our results are quite consistent with the experiments for urea and glycerol, for which the corresponding data are available. The results obtained by the 3D-RISM theory show striking differences from those obtained by the MD simulations, especially in the case of GlpF. Possible causes of the difference in the results between the two methods are discussed.

The three dimensional (3D) distributions of sodium, chloride, and hydronium ions along with water, in two aquaporin channels, AQP1 and GlpF, were calculated using the three dimensional reference interaction site model (3D-RISM) theory. It was found from the potential of mean force (PMF) obtained from the 3D-distribution that water inside the both channels is slightly more stable than bulk, and that PMF does not have high barriers for a water molecule to cross. The results are completely in harmony with the experimental observations, while they are in accord with none of the molecular simulation studies. All the ions studied are hard to permeate through either of the channels. However, the reasons why the permeability is so low are different depending on the channels and the ions. In the AQP1 channel, the cations, or Na + and H 3 O + , are largely excluded from the channel essentially by the electrostatic repulsion due to the positively charged residues, while the Cl − ion is blocked by a high steric barrier at the selective filter (SF) region. In the GlpF, the PMFs of Na + and H 3 O + inside the channel are mostly positive, and they have three large barriers to cross, which may be preventing the ions from permeation. On the other hand, the PMF of Cl − is largely negative, but it has wide and deep well which likely prevents the ion from permeating through the channel by “trapping” mechanism.

The equilibrium distribution function of water in the aquaporin-Z is calculated based on the three-dimensional reference interaction site model theory. It is found that water in aquaporin-Z distributes continuously throughout the channel with the open structure, while the distribution has a conspicuous gap around the R189 side chain in the closed form. The gating mechanism of the channel is inferred from the water distribution. The method also provides information with respect to the distribution of hydrogen atoms of water inside the channel, which is important to investigate the conduction mechanism of molecules including protons in the channel.

Selective ion binding by human lysozyme and its mutants is probed with the three-dimensional interaction site model theory which is the statistical mechanical integral equation theory. Preliminary and partial results of the study have been already published (Yoshida, N. et al. J. Am. Chem. Soc. 2006, 128, 12042-12043). The calculation was carried out for aqueous solutions of three different electrolytes, CaCl2, NaCl, and KCl, and for four different mutants of the human lysozyme: wild type, Q86D, A92D, and Q86D/A92D, which have been studied experimentally. The discussion of this article focuses on the cleft that consists of amino acid residues from Q86 to A92. For the wild type of protein in the aqueous solutions of all the electrolytes studied, there are no distributions observed for the ions inside the cleft. The Q86D mutant shows essentially the same behavior with that of the wild type. The A92D mutant shows strong binding ability to Na+ in the recognition site, which is in accord with the experimental results. There are two isomers of the Q86D/A92D mutant, e.g., apo-Q86D/A92D and holo-Q86D/A92D. Although both isomers exhibit the binding ability to the Na+ and Ca2+ ions, the holo isomer shows much greater affinity compared with the apo isomer. Regarding the selective ion binding of the holo-Q86D/A92D mutant, it shows greater affinity to Ca2+ than to Na+, which is also consistent with the experimental observation.

In this study, we have successfully parameterized the coarse-grained (CG) model of cis-1,4-polyisoprene (main component of natural rubber) based on the MARTINI force field. An isoprene monomer is mapped into one bead of CG model. The structure, bulk and thermodynamics properties of cis-1,4-polyisoprene with new CG model are well comparable to the atomistic simulation model and experiment. Our CG model of cis-1,4-polyisoprene will be helpful to study in the advanced rubber nanocomposite materials.

“Molecular recognition” is one of the most important molecular processes for living systems in order to maintain their life, since most of the biological functions are initiated with the process. Understanding of the process is also important for designing a new drug. Firstly, it is important to find a target of a drug, which is in many cases a function of protein or DNA to be inhibited. Secondly, binding a drug molecule to the active site of a biomolecule itself is a “molecular recognition process. In the present article, we review our recent studies on the molecular recognition process, carried out by means of the 3D-RISM theory, a statistical mechanics theory of liquids. Studies on the conduction mechanisms in two types of molecular channels, aquaporin and the M2 channels, are reviewed.

The three-dimensional distribution function (DF) and the potential of mean force (PMF) of water and hydronium ions in five protonated states of the influenza A M2 channel are calculated by means of the three-dimensional reference interaction site model (3D-RISM) theory in order to clarify the proton conduction mechanism of the channel. Each protonated state, denoted as iH, where i = 0-4, has a different number of protonated histidines, from 0 to 4. The DF of water in each state exhibits closed structures of 0H, 1H, and 2H and open structures in 3H and 4H. In the closed form, the DF and PMF indicate that hydronium ions are excluded from the channel. In contrast, the ion can distribute throughout the opened channel. The barrier in PMF of 3H, approximately 3-5 kJ/mol, is lower than that of 4H, 5-7 kJ/mol, indicating that 3H has higher permeability to protons. On the basis of the radial DFs of water and hydronium ions around the imidazole rings of His37, we propose a new mechanism of proton transfer through the gating region of the channel. In this process, a hydronium ion hands a proton to a non-protonated histidine through a hydrogen bond between them, and then the other protonated histidine releases a proton to a water molecule via a hydrogen bond. The process transfers a proton effectively from one water molecule to another.

Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the RISM/3D-RISM theory during the last five years in the authors' group. The method requires just the structure of protein and the potential energy parameters for the biomolecules and solutions as inputs. The calculation is carried out in two steps. The first step is to obtain the pair correlation functions for solutions consisting of water and ligands based on the RISM theory. Then, given the pair correlation functions prepared in the first step, we calculate the 3D-distribution functions of water and ligands around and inside protein based on the 3D-RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as "recognized" by the protein. Some biochemical processes are investigated, which are intimately related to the molecular recognition of small ligands including water, noble gases, and ions by a protein.

Cations (Ca2+, Na+, K+) selectively bound by human lysozyme and its mutants are probed by the 3D-RISM theory, a statistical mechanics theory of liquids.

Water and hydronium ion distribution inside aquaporin channels are probed by the 3D-RISM theory, a statistical mechanics theory of liquids.

Aquaporins (AQPs), known as the water channel, are membrane proteins that can conduct water across cell membrane. Then they play an important role to maintain the homeostasis of a cell AQPs function not only as a water channel, but several members in the aquaporin family are also permeable by glycerol, urea ammonia and other molecules. In spite that intensive efforts have been devoted to clarify the molecular mechanism of the aquaporin functions, there are many questions remained unanswered. Among the questions, the followings are most sharply focused in the experimental and as well as theoretical studies: 1) what is the role of R189 in the gating mechanism of aquaporins? 2) Why protons do not permeate through the channels, while water does? 3) Why both cations and anions are prohibited to transmit through the channels? And 4) Do small molecules other than water, such as, CO2 and NH3, permeate through AQP1? In the thesis work, he studied the molecular mechanism of aquaporin functions based on the RISM and 3D-RISM theories, and tied to answer the questions with respect to the molecular mechanism of aquaporins listed above. The RISM and 3D-RISM theories are the statistical mechanical integral equation theories of molecular liquids which have been developed by Hirata's group. The theories enable one to calculate the three dimensional distribution of water as well as other solute molecules around and inside a protein in aqueous solution. For study the gating mechanism, he had calculated the distribution of water in AQPZ by using the RISM/3DRISM method. The positions of the water molecules inside some cavities of the protein, which have not been identified by the experiments, are also reported. The density profiles of water inside the channels with four different conformations, one open and three closed, have demonstrated good agreement with the experimental data. The water molecures distribute continuously along the channel in the open conformation, whereas the distributions in the closed conformations are interrupted by the gap at the location of the side chain R189. The results indicate that water cannot pass through the AQPZ channel in its close conformation. The results confirm the experimental postulate for the role of R189 in the gating mechanism of AQPZ. The mechanism underlying the proton exclusion from AQP1 and GlpF has also elucidated in this work. It is found that the mechanisms to exclude the proton transport through AQP1 and GlpF are different. In AQP1 the hydronium ion is banned in a wide area from the NPA regron to the SF region, which is equivalent with the existence of the high positive barrier in the potential mean of force (PMF) along the entire channel. The proton cannot transport across this barrier. The high positive electrostatic potential is the primary cause to the high positive barrier in PMF. In GlpF, the electrostatic potential inside the channel is not as high as in AQP1. Hydronium ions can be distributed almost throughout the channel except the SF region; there is a small gap of distribution of hydronium ion at this region. The electrostatic potential itself cannot completely prevent protons from transportation because a proton may jump across the gap of distribution around SF area due to the Grotthuss mechanism. His analysis of the distribution functions has clarified that the hydrogen-bonded chain of water in the channel was disrupted due to the bipolar coordination of water molecules to the atoms in the side chains, which in turn interrupts the Grothuss mechanism to take place. It was concluded that the two mechanisms, electrostatic repulsion and bipolar coordination of orientation of water, are the causes to prevent the proton from transporting in GlpF. In order to clarify the mechanism of ion exclusions from AQP1 and GlpF, he has calculated the distribution functions and PMF of ions, including cations, sodium and hydronium ions, and anion, chloride ion, in both channels. The distributions and PMF of both cations are similar. The results indicate that different mechanisms are working on the exclusion of cations and anion. In AQP1, there is a large gap in the distribution of each cation, spanning from SF to NPA regions. The gap in the distribution is equivalent to the high positive potential in PMF. The cations are excluded from the channel due to this high potential barrier. The essential cause of the barrier is the electrostatic field produced by protein. For the case of anion, the gap in the distribution is much narrower than the cations, which is limited at the SF region. This gap in the distribution corresponds to a high positive potential in PMF. Unlike the case of cations, the barrier is created by the steric effect due to the bulkiness of the ion, not by the electrostatic repulsion between the ion and channel atoms. Unlike AQP1, the distribution of cations in GlpF has three large minimums, corresponding to the three positive barriers in PMF. The height of the barriers is lower than those in AQP1 due to weaker electrostatic potential inside the channel. These barriers prevent the cations from transmitting across the channel. On the other hand, PMF of the anion is negative throughout the channel, and it has a deep well at the SF region. This result suggests another mechanism for the exclusion of ion transport through the channel. The anion is trapped at the SF region due to the strong electrostatic "attraction," which prevents the ion from permeating across the channel. To know whether the gas molecules can permeate through AQP or not, he has presented the results of the distribution and PMF of CO2 and NH3 in both central channel and water channel of AQP1. The results show that CO2 and NH3 cannot permeate through the central channel of the tetramer. In the water channel, the distribution function of CO2 is discontinuous; it is interrupted by a gap. The corresponding PMF show a very high positive potential barrier at the gap area. The results suggest that CO2 is prevented from transporting through the water channel. The distributions of NH3 is similar to that of water, however the PMFs of both are different at R197 area. At this area PMF of NH3 rises up to the peak whereas that of water falls down to the minimum. The height of the peak of PMF of NH3, ～2.5 kJ/mol, is simlar to the thermal energy. It suggests that NH3 has possibility to transport though the channel, although its permeability is lower than water. In conclusion, he has applied the statistical mechanics theories of liquid to explore the mechanism of transportation of solute through the AQPs. The result of distribution of water in AQPZ give a good agreement with experimental data and confirm the role R189 side chain on opening and closing channel. He also clarified the mechanism of proton and ions exclusion in AQPs, and proposes the new mechanism to prevent anion to transport through GlpF. Furthermore, he also showed that NH3 can permeate through AQP1 but CO2 can not.