The non-ideal solvation of NaCl in solvent: a simulation study

The non-ideality of the solvation of NaCl in a family of modified hybrid water solvent environments with varying local structural order is investigated using intensive molecular dynamics simulations. The results show that there are ion clusters of different size in all environments studied. The size distribution of the ion clusters is sensitive to the local structure of the solvent, which is determined by the hydrogen bonding strength. The ions are inclined to be in contact in solvents with high translational order, for competition between structure breaking among solvent molecules and structure formation around hydrated ions.     

活细胞内单个大分子的行为

以往细胞内大分子活动的研究,多数是许多分子活动的一个平均结果,即一种集群平均（ensemble averaging）的结果,随着各种技术,特别是光学及荧光检测技术的成熟,实时视见活细胞内单个大分子的时代已经到来.在现时条件下,有许多方法可供选择,如荧光共振能量转移、原子力显微镜、全内反射显微技术、荧光相关光谱法等等.“活细胞内单个大分子的行为”的研究有可能为了解活细胞内单个分子的活动带来完全新的认识,但目前还存在不少方法学上的局限性,有待进一步提高,如有效的特异标记物、细胞深部荧光的检测、新型显微镜的开发等.     

Polymer dynamics from synthetic polymers to proteins

Starting from the standard model of polymer motion — the Rouse model — we briefly present some key experimental results on the mesoscopic dynamics of polymer systems. We touch the role of topological confinement as expressed in the reptation model and discuss in some more detail processes limiting the confinement. In the second part we relate to some new developments concerning the measurement of large-scale internal dynamics of proteins by neutron spin echo.      

Reference database of Raman spectra of biological molecules

Raman spectra of biological materials are very complex, because they consist of signals from all molecules present in cells. In order to obtain chemical information from these spectra, it is necessary to know the Raman patterns of the possible components of a cell. In this paper, we present a collection of Raman spectra of biomolecules that can serve as references for the interpretation of Raman spectra of biological materials. We included the most important components present in a cell: (1) DNA and RNA bases (adenine, cytosine, guanine, thymine and uracil), (2) amino acids (glycine, L ‐alanine, L ‐valine, L ‐serine, L ‐glutamic acid, L ‐arginine, L ‐phenylalanine, L ‐tyrosine, L ‐tryptophan, L ‐histidine, L ‐proline), (3) fatty acids and fats (lauric acid, myristic acid, palmitic acid, stearic acid, 12‐methyltetradecanoic acid, 13‐methylmyristic acid, 14‐methylpentadecanoic acid, 14‐methylhexadecanoic acid, 15‐methylpalmitic acid, oleic acid, vaccenic acid, glycerol, triolein, trilinolein, trilinolenin), (4) saccharides (β‐D ‐glucose, lactose, cellulose, D ‐(+)‐dextrose, D ‐(+)‐trehalose, amylose, amylopectine, D ‐(+)‐mannose, D ‐(+)‐fucose, D ‐(−)‐arabinose, D ‐(+)‐xylose, D ‐(−)‐fructose, D ‐(+)‐galactosamine, N‐acetyl‐D ‐glucosamine, chitin), (5) primary metabolites (citric acid, succinic acid, fumarate, malic acid, pyruvate, phosphoenolpyruvate, coenzyme A, acetyl coenzyme A, acetoacetate, D ‐fructose‐6‐phosphate) and (6) others (β‐carotene, ascorbic acid, riboflavin, glutathione). Examples of Raman spectra of bacteria and fungal spores are shown, together with band assignments to the reference products. Copyright © 2007 John Wiley & Sons, Ltd.     

Optical behaviour of mammarian neoplastic liquids

Summary Experimental research plays an important role to point out non-invasive diagnostic techniques to show eventual pathologies of the breast. The aim of the present investigation is to study the specific response of complex liquids as solutions originating from normal and neoplastic mammary tissue in the interaction with e.m. waves, in order to discover all the eventual frequencies at which e.m. radiation can be selectively absorbed by neoplastic mammary tissue, chromophores to eventually use these elements in diagnosis of these neoplastic diseases. Characteristic chromophores absorption has been enhanced in spectra of samples drawn from neoplastic tissues. We did this by carrying out a spectrophotometric examination in the IR, VIS and UV range of solutions of the various fractions of healthy and neoplastic mammary tissue, obtained after preparation including differentiated ultracentrifugation of the nuclear, mitochondrial and lysosomial fractions. Paper presented at the I International Conference on Scaling Concepts and Complex Fluids, Copanello, Italy, July 4–8, 1994.     

Relation between delayed luminescence and functional state in soya seeds

Summary The possibility of using the parameters connected to delayed luminescence to detect thermal stress conditions in soya seeds is discussed here and the results of the measurement of photoinduced emission conducted on soya seeds characterized by a different vegetative vigour are presented. A phenomenological relationship between the total re-emission and the growth velocity was found. The distributions of the decay times relative to the different conditions of stress on the seeds have given indications towards the existence of different dynamics. On the basis of the results it seems that a correlation exists between the functional state of the seeds and delayed luminescence. The authors of this paper have agreed to not receive the proofs for correction.     

Temperature dependence of the ultraweak spontaneous photon emission from soya seeds

Summary The ultraweak radiation emitted from soya seeds during germination has been measured for different values of the temperature (20–35°C). The parameters relative to the photon emission time-counting series have been compared with the ones relative to germination and imbibition; it has been found that the activation energy relative to the process of the photon emission from live seeds is equal to that of the germination process (51 KJ/mole), demonstrating that the two processes are correlated. A function of the experimental parameters which eliminates the explicit dependence of the above biological processes on temperature has been proposed. The authors of this paper have agreed to not receive the proofs for correction.     

Good vibrations: probing biomolecular structure and interactions through spectroscopy in the gas phase

Spectroscopic investigations of biomolecular structure and interactions in the gas phase, free from environmental ‘disturbance’, have become a growth industry over the last decade. The great majority however, have taken their ‘bio-pedigrees’ as a given rather than an issue to be addressed. This review attempts to move towards aspects of their biological, or perhaps more accurately, biochemical relevance, by reviewing some recent and current investigations of peptide and carbohydrate systems in the gas phase, chosen not just because they are ‘do-able’ but because of the biochemical questions they address. Hopefully, this will help to foster better communication between the molecular physics, biochemistry and molecular biology communities.     

Chemistry and morphology of dried‐up pollen suspension residues

Pollen grains are covered with lots of different biochemical compounds, like proteins, saccharides and lipids, which are only loosely attached to the pollen. Therefore, they can be separated from the pollen by suspending them in water. Since these compounds play a key role in many atmospheric processes (e.g. cloud condensation nucleation, ice nucleation, aerial allergen exposure), their separation and analyzing are of interest. The chemical composition of whole pollen grains is compared by both Raman and infrared spectroscopy with material that could be extracted from pollen with water. The dominant signals in the pollen grain Raman spectra are those from sporopollenin and carotenoids. These bands decrease in the washing water spectra, since sporopollenin is high molecular and thus is not extractable. The released material shows in turn a chemical composition that differs significantly between species, what is quite expected, since they differ even in the optical properties of their aqueous suspensions. The FTIR spectra show some additional bands to appear in comparison to the Raman spectra. Furthermore, we investigated the pollen rupturing and material release in the aqueous suspensions by drying them up and picturing the residues with a scanning electron microscope. We saw that corn pollen ejected loads of micrometer‐sized organelles, which are most likely starch granules. The more the pollen disrupted, the more the measured samples were covered with an amorphous film, which consists of the extracted pollen material, like lipids, sugars, and proteins – the same substances we detected by spectroscopy. Copyright © 2013 John Wiley & Sons, Ltd.     

Comparison among human-blood liquid solutions

Summary In this paper the authors intend to illustrate the results of optical properties of human blood as suspension of cells in aqueous solutions of electrolytes and non-electrolytes, which are highly complex liquid systems susceptible to important phase transitions. They carried out normal and derivative spectrophotometric measurements of non-pathologic diluted blood and serum samples to show optical absorption peak positions of haematological chromophores including haemoglobin and fibrinogen. The authors think that optical behaviour of the chromophores may be influenced by interaction with different environmental situations relative to coagulated and uncoagulated samples. They continue these studies with particular reference to the nature of the solute-induced modifications. Paper presented at the I International Conference on Scaling Concepts and Complex Fluids, Copanello, Italy, July 4–8, 1994.     

High hydrostatic pressure equipment for neutron scattering studies of samples in solutions

The design of new high pressure equipment for structural and dynamical studies on samples in solution is described. We present two sample cells for applying pressures up to 150 and 700 MPa (i.e. 1.5 and 7 kbar), respectively. These cells are mounted on special sticks and inserted into the calorimeter of a cryostat to regulate the temperature. Different parts of the equipment – the pressure controller, the sticks and the cells – are described. In addition, radiography tests which were performed with neutrons in situ at the Institut Laue Langevin to verify the tightness of the cells and the hydrostatic transmission of the pressure to the sample are presented. First results on model lipids are in agreement with former results by R. Winter et al. [Towards an understanding of the temperature/pressure configurational and free-energy landscape of biomolecules, J. Non-Equilib. Thermodyn. 32 (2007), pp. 41–97].     

生物大分子多尺度理论和计算方法

分子模拟是研究生物大分子的重要手段. 过去二十年来, 人们将分子模拟与实验研究相结合, 揭示出生物大分子结构和动力学方面的诸多重要性质. 传统分子模拟主要采用全原子分子模型或各种粗粒化的分子模型. 在实际应用中, 传统分子模拟方法通常存在精度或效率瓶颈, 一定程度上限制了其应用范围. 近年来, 多尺度分子模型越来越受到人们的关注. 多尺度分子模型基于统计力学原理, 将全原子模型和粗粒化模型相耦合, 有望克服传统分子模拟方法中的精度/效率瓶颈, 进而拓展分子模拟在生物大分子研究中的应用范围. 根据模型之间的耦合方式, 近年来发展起来的多尺度分子模拟方法可归纳为如下四种类型: 混合分辨多尺度模型、并行耦合多尺度模型、单向耦合多尺度模型、以及自学习多尺度模型. 本文将对上述四类多尺度模型做简要介绍, 并讨论其主要优缺点、应用范围以及进一步发展方向.     

Acridones and Quinacridones: Novel Fluorophores for Fluorescence Lifetime Studies

Two new families of fluorescent probe, acridones and quinacridones, whose fluorescence lifetime can be altered to produce a range of lifetimes from 3 ns to 25 ns are described. Both families of fluorophore have fluorescence lifetimes which are unaffected by pH in the range of 5 to 9 and show a marked resistance to photobleaching. The probes have been modified to allow them to be attached to biomolecules and the labelling of a neuropeptide (substance P) is described. The labelled peptides have the same fluorescence lifetime as the free fluorophore. Quinacridone, with an emission around 550 nm offers a long fluorescence lifetime, photostable alternative to fluorescein.     

纳米尺度物质的生物效应和安全性

纳米尺度的物质包括碳纳米管、纳米二氧化碳、纳米三氧化铁和四氧化三铁等，它们与包括氨基酸在内的生物分子和细胞以及动物整体的相互作用受到广泛关注和研究．结果表明这些纳米材料都能和这些生物成分和生物体相互作用，具有明显的生物效应，能够影响生物分子的结构或构象、细胞的生长，且它们的毒性都较小．但从我们获得的资料看，有些纳米物质对生物的整体特性和人的健康有较重的影响．这是我们应该引起严重注意的．     

Charge self-trapping in two strand biomolecules: Adiabatic polaron approach

We investigate the properties of the excess charge (electron, hole) introduced into a two-strand biomolecule. We consider the possibility that the stable soliton excitation can be formed due to interaction of excess charge with the phonon subsystem. The influence of overlap of the molecular orbitals between adjacent structure elements of the macromolecular chain on the soliton properties is discussed. Special attention is paid to the influence of the overlapping of the molecular orbitals between structure elements placed on the different chains. Using the literature values of the basic energy parameters of the two-chain biomolecular structures, possible types of soliton solutions are discussed.     

Vectorial photoinduced electron transfer in phospholipid vesicles and LB bilayers

Summary Photoinduced electron transfer (PET) was studied in phospholipid vesicles and in Langmuir-Blodgett bilayers in the attempt to produce a model for electron transfer processes in biological media. Spatial organization of the reaction centers in lipid membranes needs to be controlled in order to provide high efficiency of light-to-chemical energy conversion. We designed a phospholipid system where the donor is localized in the inner bilayer whereas the acceptor is at the polar groups-water interface. We used dipalmitoylphosphatidic acid vesicles containing low molar fractions of dipalmitoylphosphatidylcholine with pyrene (donor) bound to one of the alkyl chains. Methylviologen (acceptor) was added to the external aqueous phase; upon photoexcitation of the donor we observed the electron transfer to take place in a unidirectional manner from the inside of the bilayer to the interface. Information about the location of the donor was obtained studying the photophysical properties of the pyrene chromophore in vesicles and in LB layers. The photoinduced electron transfer reaction was evidenced by quenching of pyrene fluorescence in the presence of increasing concentrations of acceptor, the process was studied both with steady-state and time-resolved fluorescence emission. Fluorescence intensity was found to decrease with increasing concentration of methylviologen, similar results were obtained for vesicles and LB layers of analog composition immersed in a methylviologen solution. Lifetimes of the excited species were found to be of the same order of magnitude in vesicle and LB-layer systems. Paper presented at the I International Conference on Scaling Concepts and Complex Fluids, Copanello, Italy, July 4–8, 1994.     

Widely Frequency-Tunable Terahertz Wave Generation and Spectroscopic Application

The THz-wave generator based on the resonance of phonon-polaritons in GaP enabled THz spectral measurements of organic molecules like DNA/RNA-related molecules in wide frequency range (0.6–5.8 THz). High spectral purity of the generated THz-wave enables even the detection of defect structures of organic compounds, and will give a new tool for molecular sciences. We demonstrated THz imaging of a liver cancer. The THz-wave generator can be made small-size, light-weight system.