No description available.

The protein side chain prediction is an essential issue, in protein structure prediction, protein design, and protein docking problems. The protein side chain packing problem has been proved to be NP-hard. Our method for solving this problem is first to reduce it to the clique finding problem, and then we can apply the Ant Colony Optimization (ACO) algorithm to solve it. In knowledge-based methods, the rotamers are chosen from the rotamer library, which are based on the pair of dihedral angles, £r and £p, of backbones. We take the coordinate rotamer library as the template, so we do not need the complicated energy function to calculate the bond length and bond angle. We use a simple score function to evaluate the goodness of a solution of the ACO algorithm. The score function combines some factors, such as charge-charge interaction, intermolecular hydrogen bonds, disulfide bonds and van der Waals interactions. The experimental results show that our score function is biologically sensible. We compare our computational results with the results of SCWRL 3.0 and the residue-rotamer-reduction (R3) algorithm. The accuracy of our method outperforms both SCWRL 3.0 and R3 methods.

In this research,we observed PAMA(poly(n-alkyl methacrylate)) and PAA(poly(n-alkyl acrylate)¡^side chain crystalline.We find side chain is longer and crystalize more easily,melting point is higher.In the result of DSC thermograms,the length of side chain is 6 carbons,we can't find any thermal transition.But the length of side chain is 12¡B18 carbons,we only found Tm.In PLM observation,we only get side chain crystalline's picture,and can't see any liquid crystalline yet. Although in X-ray's illustrative can find layer structure's diffraction peak,but i think this evidence can't prove the system that is liquid crystalline.It just can be said that the layed structure was formed by side chain crystallization.

The polyglutamate which grafts with flexible alkyl side-chain by ester exchange reaction is like rod-hairy molecule. The numbers of methylene group of side-chain and the graft-density affect the molecular packing of poly(gama-alkyl-L-glutamate)s. To be sure the correct chemical structure of poly(gama-alkyl-L-glutamate)s by Fourier transform infrared spectrometer (FTIR), and find out the graft-density of each sample by proton nuclear resonance spectrometer (1H-NMR). Phase behavior of poly(gama-alkyl-L-glutamate)s were studied via differential scanning calorimetry (DSC) and variable temperature x-ray diffraction (XRD).We combine the results from C. C. Hsu(24). When the side-chain length is long enough (m>10), side-chains will crystallize into a 3D hexagonal lattice. The results of DSC and XRD analyses show that the side-chain crystalline phase will melt at Tm1, where as a liquid crystalline (LC) phase transition exists at Tm2. Poly(gama-alkyl-L-glutamate)s with shorter side-chain (m<8) tend to form 2D hexagonal LC structure. On the other hand, longer side-chains (m>10) tend to give lamellar structure. The critical number of methylene group of side-chain between hexagonal and lamellar structure is between 8 and 10.

P3DDT (3-dodecylthiophene-2,5-diyl) and PCBM( [6,6]-phenyl C61-butyric acid methyl ester) were fabricated to the active layer of Bulk Heterojunction Organic Solar Cells .We obtained the device efficiency was 0.64 % by evaporating solvent at room temperature. We measured Thermal decomposition Temperature (Td) of P3DDT was 487¢J. But operational temperature was over 90¢J, it could affect the roughness of thin film and make efficiency to be 4¡Ñ10-3(%). For results of experiments, we know that roughness changed by the crystallization of side chain and exciton dissociation modified by the morphology between P3DDT and PCBM. Thin film solar cell has a large effect on the formation of active layer, such as heat treatment, choices of solvents, composition ratio, and speed of spin coating. The efficiency of solar cell has been shown to be highly sensitive to the size, composition and crystallization of the formed domains. We studied two kinds of conjugated polythiophenes with the same main chain but different side chain. When the number of carbon atoms of alkyl side chains is more than 10, some orderly arrangements will occur for side chains between the layers. We tried to explain the crystallization caused by long alkyl side chains determined which intrinsic phenomena are the most evident for altering the PCE of solar cell. After recrystallization, the layered structures of P3DDT can be improved, but those orderly degrees of the arrangements with PCBM are further aggregated. The main point for low PEC and Jsc by heat treatment is the unfavorable and roughened morphology. Charge transfer only occurs at the boundary ,which is interfacial area between donor and acceptor materials, hence, the low Jsc could be caused by poor charge transfer between P3DDT and PCBM. The redistributed arrangement of P3DDT domains exclude PCBM from original space, and it makes PCBM to aggregate large particles, from nanophase to mesophase scales, which reduce mutual solubility to be the source of PCE and Jsc reduction.

Yes / Current drugs against human African trypanosomiasis (HAT) suffer from several serious drawbacks. The search for novel, effective, brain permeable, safe, and inexpensive antitrypanosomal compounds is therefore an urgent need. We have recently reported that the 4-aminoquinoline derivative huprine Y, developed in our group as an anticholinesterasic agent, exhibits a submicromolar potency against Trypanosoma brucei and that its homo- and hetero-dimerization can result in to up to three-fold increased potency and selectivity. As an alternative strategy towards more potent smaller molecule anti-HAT agents, we have explored the introduction of ω-cyanoalkyl, ω-aminoalkyl, or ω-guanidinoalkyl chains at the primary amino group of huprine or the simplified 4-aminoquinoline analogue tacrine. Here, we describe the evaluation of a small in-house library and a second generation of newly synthesized derivatives, which has led to the identification of 13 side chain modified 4-aminoquinoline derivatives with submicromolar potencies against T. brucei. Among these compounds, the guanidinononyltacrine analogue 15e exhibits a 5-fold increased antitrypanosomal potency, 10-fold increased selectivity, and 100-fold decreased anticholinesterasic activity relative to the parent huprine Y. Its biological profile, lower molecular weight relative to dimeric compounds, reduced lipophilicity, and ease of synthesis, make it an interesting anti-HAT lead, amenable to further optimization to eliminate its remaining anticholinesterasic activity. / Wellcome Trust

No description available.

In many studies of the side-chain liquid crystalline polymers (SCLCPs) bearing azobenzene mesogens as pendant groups, obtaining the orientation of azobenzene mesogens at a macroscopic scale as well as its control is important, because it impacts many properties related to the cooperative motion characteristic of liquid crystals and the trans-cis photoisomerization of the azobenzene molecules. Various means can be used to align the mesogens in the polymers, including rubbed surface, mechanical stretching or shearing, and electric or magnetic field. In the case of azobenzene-containing SCLCPs, another method consists in using linearly polarized light (LPL) to induce orientation of azobenzene mesogens perpendicular to the polarization direction of the excitation light, and such photoinduced orientation has been the subject of numerous studies. In the first study realized in this thesis (Chapter 1), we carried out the first systematic investigation on the interplay of the mechanically and optically induced orientation of azobenzene mesogens as well as the effect of thermal annealing in a SCLCP and a diblock copolymer comprising two SCLCPs bearing azobenzene and biphenyl mesogens, respectively. Using a supporting-film approach previously developed by our group, a given polymer film can be first stretched in either the nematic or smectic phase to yield orientation of azobenzene mesogens either parallel or perpendicular to the strain direction, then exposed to unpolarized UV light to erase the mechanically induced orientation upon the trans–cis isomerization, followed by linearly polarized visible light for photoinduced reorientation as a result of the cis–trans backisomerization, and finally heated to different LC phases for thermal annealing. Using infrared dichroism to monitor the change in orientation degree, the results of this study have unveiled complex and different orientational behavior and coupling effects for the homopolymer of poly{6-[4-(4-methoxyphenylazo)phenoxy]hexyl methacrylate} (PAzMA) and the diblock copolymer of PAzMA-block- poly{6-[4-(4-cyanophenyl) phenoxy]hexyl methacrylate} (PAzMA-PBiPh). Most notably for the homopolymer, the stretching-induced orientation exerts no memory effect on the photoinduced reorientation, the direction of which is determined by the polarization of the visible light regardless of the mechanically induced orientation direction in the stretched film. Moreover, subsequent thermal annealing in the nematic phase leads to parallel orientation independently of the initial mechanically or photoinduced orientation direction. By contrast, the diblock copolymer displays a strong orientation memory effect. Regardless of the condition used, either for photoinduced reorientation or thermal annealing in the liquid crystalline phase, only the initial stretching-induced perpendicular orientation of azobenzene mesogens can be recovered. The reported findings provide new insight into the different orientation mechanisms, and help understand the important issue of orientation induction and control in azobenzene-containing SCLCPs. The second study presented in this thesis (Chapter 2) deals with supramolecular side-chain liquid crystalline polymers (S-SCLCPs), in which side-group mesogens are linked to the chain backbone through non-covalent interactions such as hydrogen bonding. Little is known about the mechanically induced orientation of mesogens in S-SCLCPs. In contrast to covalent SCLCPs, free-standing, solution-cast thin films of a S-SCLCP, built up with 4-(4’-heptylphenyl) azophenol (7PAP) H-bonded to poly(4-vinyl pyridine) (P4VP), display excellent stretchability. Taking advantage of this finding, we investigated the stretching-induced orientation and the viscoelastic behavior of this S-SCLCP, and the results revealed major differences between supramolecular and covalent SCLCPs. For covalent SCLCPs, the strong coupling between chain backbone and side-group mesogens means that the two constituents can mutually influence each other; the lack of chain entanglements is a manifestation of this coupling effect, which accounts for the difficulty in obtaining freestanding and mechanically stretchable films. Upon elongation of a covalent SCLCP film cast on a supporting film, the mechanical force acts on the coupled polymer backbone and mesogenic side groups, and the latter orients cooperatively and efficiently (high orientation degree), which, in turn, imposes an anisotropic conformation of the chain backbone (low orientation degree). In the case of the S-SCLCP of P4VP-7PAP, the coupling between the side-group mesogens and the chain backbone is much weakened owing to the dynamic dissociation/association of the H-bonds linking the two constituents. The consequence of this decoupling is readily observable from the viscoelastic behavior. The average molecular weight between entanglements is basically unchanged in both the smectic and isotropic phase, and is similar to non-liquid crystalline samples. As a result, the S-SCLCP can easily form freestanding and stretchable films. Furthermore, the stretching induced orientation behavior of P4VP-7PAP is totally different. Stretching in the smectic phase results in a very low degree of orientation of the side-group mesogens even at a large strain (500%), while the orientation of the main chain backbone develops steadily with increasing the strain, much the same way as amorphous polymers. The results imply that upon stretching, the mechanical force is mostly coupled to the polymer backbone and leads to its orientation, while the main chain orientation exerts little effect on orienting the H-bonded mesogenic side groups. This surprising finding is explained by the likelihood that during stretching in the smectic phase (at relatively higher temperatures) the dynamic dissociation of the H-bonds allow the side-group mesogens to be decoupled from the chain backbone and relax quickly. In the third project (Chapter 3), we investigated the shape memory properties of a S-SCLCP prepared by tethering two azobenzene mesogens, namely, 7PAP and 4-(4'-ethoxyphenyl) azophenol (2OPAP), to P4VP through H-bonding. The results revealed that, despite the dynamic nature of the linking H-bonds, the supramolecular SCLCP behaves similarly to covalent SCLCP by exhibiting a two-stage thermally triggered shape recovery process governed by both the glass transition and the LC-isotropic phase transition. The ability for the supramolecular SCLCP to store part of the strain energy above T[subscript g] in the LC phase enables the triple-shape memory property. Moreover, thanks to the azobenzene mesogens used, which can undergo trans-cis photoisomerization, exposure the supramolecular SCLCP to UV light can also trigger the shape recovery process, thus enabling the remote activation and the spatiotemporal control of the shape memory. By measuring the generated contractile force and its removal upon turning on and off the UV light, respectively, on an elongated film under constant strain, it seems that the optically triggered shape recovery stems from a combination of a photothermal effect and an effect of photoplasticization or of an order-disorder phase transition resulting from the trans-cis photoisomerization of azobenzene mesogens.

β-glucan is a major component of the fungal cell wall consisting of (1→3)-β linked glucose polymers with (1→6)-β linked side chains. The published classical isolation procedure of β-glucan from Saccharomyces cerevisiae is expensive and time-consuming. Thus, the aim of this research was to develop an effective procedure for the extraction of glucans. We have developed a new method for glucan extraction that will be cost effective and will maintain the native structure of the glucan. The method that we developed is 80% faster and utilizes 1/3 of the reagents compared to the published classical method. Further, the method developed increases the yield from 2.9 % to 10.3 %. Our new process has a branching frequency of 18.4 down from 197 and a side chain of 5.1 up from 2.5. The data indicate a more preserved native structure of isolated glucans.

The prediction of energetically favorable side-chain conformations is a fundamental element in homology modeling of proteins and the design of novel protein sequences. The space of side-chain conformations can be approximated by a discrete space of probabilistically representative side-chain conformations (called rotamers). The problem is, then, to find a rotamer selection for each amino acid that minimizes a potential energy function. This is called the Global Minimum Energy Conformation (GMEC) problem. This problem is an NP-hard optimization problem. The Dead-End Elimination theorem together with the A* algorithm (DEE/A*) has been successfully applied to this problem. However, DEE fails to converge for some complex instances. In this paper, we explore two alternatives to DEE/A* in solving the GMEC problem. We use a probabilistic inference method, the max-product (MP) belief-propagation algorithm, to estimate (often exactly) the GMEC. We also investigate integer programming formulations to obtain the exact solution. There are known ILP formulations that can be directly applied to the GMEC problem. We review these formulations and compare their effectiveness using CPLEX optimizers. We also present preliminary work towards applying the branch-and-price approach to the GMEC problem. The preliminary results suggest that the max-product algorithm is very effective for the GMEC problem. Though the max-product algorithm is an approximate method, its speed and accuracy are comparable to those of DEE/A* in large side-chain placement problems and may be superior in sequence design. / Singapore-MIT Alliance (SMA)