Flocculation in brewing yeasts: a computer simulation study

A new simulator, INDISIM-FLOC, based on the individual-based simulator INDISIM, is used to examine the predictions of two different models of yeast flocculation. The first, proposed by Calleja is known as the "addition" model. The second, proposed by Stratford is known as the "cascade" model. The simulations show that the latter exhibits a better qualitative agreement with available experimental data.     

Proton relaxation in aqueous DNA solutions

By use of D₂O we found that the shortening of the longitudinal proton relaxation time which occurs in the investigated aqueous yeast DNA solutions (≦ 2.4% with 2% protein) was not based on a hydration effect, but was caused by magnetic impurities only. An estimate shows that the mobility of the hydrated water molecules is reduced by less than two orders of magnitude in comparison with the free water molecules.     

Carbon doped boron phosphide nanotubes: A computational study

A computational study based on density functional theory (DFT) calculations has been performed to investigate the properties of the electronic structure of carbon doped boron phosphide nanotube (C-doped BPNT). Pristine and the C-doped structures of two representative (6,0) zigzag and (4,4) armchair BPNTs have been investigated. At first, the geometries of the structures have been allowed to relax by optimization. Subsequently, NMR parameters have been calculated in the optimized structures. The results indicated that the influence of C-doping was more significant on the geometries of the zigzag model than the armchair one. The difference of band gap energies between the pristine and C-doped armchair BPNT was larger than the zigzag model. Significant differences of NMR parameters of those nuclei directly contributed to the C-doping atoms have been observed.     

Dielectric relaxation of DNA in aqueous solutions.

Using a four-electrode cell and a new electronic system for direct detection of the frequency differences specturm of solution impedance, the complex dielectric constant of calf thymus DNA (M_r = 4 × 10⁶) in aqueous NaCl at 10°C is measured at frequencies ranging from 0.2 Hz to 30 kHz. The DNA concentrations are C_p = 0.01% and 0.05%, and the NaCl concentrations are varied from C_s = 10^?4 M to 10^?3 M. A single relaxation regions is found in this frequency range, the relaxation frequency being 10 Hz at C_p = 0.01% and C_s = 10^?3 M. At C_p = 0.05% it is evidenced that the DNA chains have appreciable intermolecular interactions. The dielectric relaxaton time τ_d at C_p = 0.01% agrees well with the rotational relaxation time estimated from the reduced visocisty on the assumption that the DNA is not representable as a rigid rod but a coiled chain. It is concluded that the dielectric relaxiatioinis ascribed to the rotation of the molecule. Observed values of dielectric increment and other experimental findings are reasonably explained by assuming that the dipole moment of DNA results from the slow counterion fluctuation which has a longer relaxation time than τ_d.     

Conformations of bombolitins I and III in aqueous solutions: circular dichroism, 1H NMR, and computer simulation studies

The heptadecapeptides bombolitin I and bombolitin III are two of a series of peptides postulated to be biologically active within a membrane environment. In the preceding paper [Bairaktari, E., Mierke, D.F., Mammi, S., & Peggion, E. (1990) Biochemistry (preceding paper in this issue)] the conformational preferences of these peptides in the presence of SDS surfactant micelles, a mimetic for biological membranes, were examined. During these studies the conformations of these peptides were investigated in aqueous solutions by circular dichroism and nuclear magnetic resonance. A large difference was observed for the two peptides. Bombolitin I lacks any observable secondary structure in aqueous solution, independent of temperature, pH, and concentration. In striking contrast, bombolitin III adopts a well-defined alpha-helix at concentrations greater than 1.3 mM. This is indeed surprising given the great similarity of the two peptides. The alpha-helix of bombolitin III is pH dependent, with a great decrease in the observed secondary structure at pH values below 3.5. This observation could only be due to the protonation of the Asp residue at the fifth position. These findings suggest that the secondary structure arises from molecular aggregation of bombolitin III through the formation of a salt bridge involving the Asp side chain. The alpha-helix observed at "high" concentration (greater than 2.5 mM) has been characterized by CD and by the NOE's measured throughout a majority of the peptide. The experimentally determined structure has been energy refined with restrained molecular dynamics. The conformational results from this study are then compared with the conformations found in the presence of surfactant micelles.     

The structure of percolated polymer systems: a computer simulation study

We studied the percolation process in a system consisting of long flexible polymer chains and solvent molecules. The polymer chains were approximated by linear sequences of beads on a two-dimensional triangular lattice. The system was athermal and the excluded volume was the only potential. The properties of the model system across the entire range of polymer concentrations were determined by Monte Carlo simulations employing a cooperative motion algorithm (CMA). The scaling behavior and the structure of the percolation clusters are presented and discussed.     

DNA conformation and thermostability in urea aqueous solutions

It is suggested from the character of the change of circular dichroism spectra that in the presence of urea winding of DNA double helix takes place within the bounds of B-family of forms. It is shown that the realized conformation of DNA differs from the experimentally known forms of DNA belonging to B-family. Urea destabilizes the DNA molecules without connection with helical and melt pairs of DNA nitrous bases. Urea affects the conformational state of DNA by water destruction around DNA, which is accompanied by dehydration of DNA and basic metal ions.     

Oxygen doped SiC nanocrystals: first principles study of the optical properties

We have studied a typical spherical SiC nanocrystal with a diameter of 1.2 nm (Si₄₃C₄₄H₇₆) using linear combination of atomic orbitals in combination with pesudopotential density functional calculation. The role of fluorine and oxygen impurities was investigated on the electronic and optical properties of the Si₄₃C₄₄H₇₆ nanocrystal. Total energy calculations show that the fluorine doped Si₄₃C₄₄H₇₆ nanocrystals are unstable. Oxygen doped Si₄₃C₄₄H₇₆ have different binding energies in various substitutional and interstitial defects. The maximum binding energy of the oxygen at carbon substitutional defect is about ?0.5 eV and at interstitial defect is ?0.18 eV. The HOMO-LUMO gap of the pure Si₄₃C₄₄H₇₆ is about 6.71 eV and after doping with oxygen changes on the order of 0.1 eV. Our studies show that the refractive index of the doped Si₄₃C₄₄H₇₆ nanocrystal significantly dispersed in comparison with pure SiC nanocrystal especially at the range of 6 to 8 eV.     

Calorimetric and molecular simulation study on unfrozen water characteristics in aqueous sugar solutions: implications for biopreservation

Intensive studies have been conducted to determine the protective mechanisms of sugars that have proven beneficial to the biopreservation application. However, little has been known about the unfrozen water content that aqueous sugar solutions can possess when frozen at cryogenic temperatures. This study conducted calorimetric measurements to determine the unfrozen water content in frozen aqueous solutions of glucose, fructose, sucrose and trehalose of multiple concentrations. The hydrogen-bonding network in these solutions was characterised by molecular simulations. The experimental results showed that more water could be prevented from ice crystallisation in a more concentrated solution. Disaccharides, especially trehalose, are more effective than other protectants (e.g., glucose, glycerol and dimethyl sulfoxide) for detaining water in the unfrozen state. Moreover, it was found that, at molecular levels, there were more hydrogen bonds between sugar and water molecules in a more concentrated solution. From both macro- and microscopic perspectives, trehalose was demonstrated to be a much more effective cryoprotectant than others. This comparative study proved that the unfrozen water should be mainly attributed to hydrogen bonds between sugar and water in the mixture. Our findings will provide valuable information for determining the physical state of cryopreserved biomatrix and guiding the preparation of protective formulations.     

Atomic force microscopy of DNA in aqueous solutions.

DNA on mica can be imaged in the atomic force microscope (AFM) in water or in some buffers if the sample has first been dehydrated thoroughly with propanol or by baking in vacuum and if the sample is imaged with a tip that has been deposited in the scanning electron microscope (SEM). Without adequate dehydration or with an unmodified tip, the DNA is scraped off the substrate by AFM-imaging in aqueous solutions. The measured heights and widths of DNA are larger in aqueous solutions than in propanol. The measured lengths of DNA molecules are the same in propanol and in aqueous solutions and correspond to the base spacing for B-DNA, the hydrated form of DNA; when the DNA is again imaged in propanol after buffer, however, it shortens to the length expected for dehydrated A-DNA. Other results include the imaging of E. coli RNA polymerase bound to DNA in a propanol-water mixture and the observation that washing samples in the AFM is an effective way of disaggregating salt-DNA complexes. The ability to image DNA in aqueous solutions has potential applications for observing processes involving DNA in the AFM.     

Transcription regulation by steroid hormones: a computer simulation study.

Three-dimensional structures of complexes of 66 amino acid-DNA binding domains of human progesterone (hPR), estrogen (hER) and glucocorticoid (hGR) receptors (proteins), with ten base pair DNA duplexes: d(AGGTCATGCT).d(AGCATGACCT) and d(AGAACATGCT).d(AGCATGTTCT) were obtained using computer modeling and molecular mechanics techniques. Cartesian coordinates for the proteins were obtained from: 1) structural data of hER and hGR by NMR spectroscopy; 2) steric constraints imposed by tetrahedral coordination of the zinc ion to Cys residues, and 3) energy minimization in torsional and cartesian space. The proteins were made to interact with DNA (in B-form) in major groove through alpha-helical linker between the two zinc fingers. The geometry of the complexes was obtained by allowing them to slide, glide, penetrate in to and out of the groove, and to rotate about the helical axis. The complexes were energy minimized. Also maximized was the number of H-bonds between proteins and DNA. The complex structures were refined by molecular mechanics using AMBER 3.0. Structural parameters of DNA were analyzed in each complex and compared with those of native DNA optimized separately. The stereochemical differences of the complexes are discussed.     

Combining particle tracking microrheology and viscometry for the study of DNA aqueous solutions

We use video particle tracking microrheology (VPTMR) in order to investigate the viscoelasticity of salmon DNA and correlate it to its steady-flow shear-thinning viscosity. Aqueous solutions of DNA are tested in a wide concentration range from the dilute to the semidilute unentangled concentration regime. The observed mean squared displacement shows power-law scaling with lag-time which is equivalent to power-law behavior of the complex modulus as a function of frequency that is, |G^*(ω)| = S ∙ ω ^α . The relaxation exponent α changes abruptly with concentration in the semidilute regime from about 1 to about 0.5 which is the exponent predicted by the Rouse model. The quasi-property S follows the scaling of viscosity for uncharged polymers near θ-conditions in the semidilute regime that is, with ν_eff = 0.50 − 0.51 . The shear-thinning exponent observed by viscometry increases gradually towards the value of 0.5 which has been predicted for Rouse chains under flow. Our findings are in agreement with recent studies of DNA solutions where DNA is treated as a model polymer and addresses the low-molar mass regime of DNA viscoelasticity. This work demonstrates that the combination of passive particle tracking with viscometry can provide a complete picture on the viscoelasticity of DNA-based biopolymer materials.     

The effect of a low-frequency electromagnetic field on DNA molecules in aqueous solutions

A chemiluminescence study showed that hepatitis B virus (HBV) and hepatitis C virus (HCV) DNA amplicons are capable of induced radiation when exposed to electromagnetic fields (EMFs) that range from 7.5 to 30 Hz in frequency and from 24 to 40 A/m in field strength. An EMF with a frequency of 9 Hz was shown to exert the greatest effect on aqueous solutions of the hepatitis virus DNA amplicons. The hydration shell of the DNA amplicons was observed to change. The change in the DNA hydration shell on exposure to a low-frequency EMF was presumed to restore hydrogen bonds, to induce crosslinks, and to facilitate DNA repair.     

Differential growth and plant tropisms: a study assisted by computer simulation

Tropisms and other movements of a plant organ result from alterations in local rates of cell elongation and a consequent development of a growth differential between its opposite sides. Relative elemental rates of elongation (RELELs) are useful to characterize the pattern of growth along and round an organ. We assume that the value of the RELEL at a given point is dependent on distance from the tip and that the distribution of values along the organ surface can be characterized in terms of the spread and the position of the maximum value. A computer model is described which accommodates these parameters and simulates tropic curvatures due to differential growth. Additional regulatory functions help to return the simulated organ to its original orientation. Particular attention is given to the simulation of root gravitropism because here not only do each of the various growth and regulatory parameters have a known biological counterpart, but some can also be given an actual quantitative value. The growth characteristics relate to the biophysical properties of cells in the elongation zone of the root, while the regulatory functions relate to aspects of the graviperception and transmission systems. We believe that, given a suitably flexible model, computer simulation is a powerful means of characterizing, in a quantitative way, the contribution of each parameter to the elongation of plant organs in general and their tropisms in particular.     

Molecular simulation of self-assembly of hydrophilic functionalized aromatics in aqueous solutions

This study identifies mechanisms of self-assembly of hydrophilic functionalized aromatic molecules—a distinct class of lyotropic materials. Results from molecular dynamics studies used to understand the moieties of the lyotropic molecule that affect the structure are consistent with experimental observations of these self-assembled structures. Coulombic forces, dominated by π–π interactions drives the self-assembly of this class of materials. Intra-molecular configurations of the aromatic rings—the extent of torsion or bending between the rings—as well as the structure of functional groups connected to the rings affect the self-assembled structures. In addition, the chemistry of the functional groups also affects how the molecules are oriented as they self assemble. Molecular modeling provides insight into design of these molecules.     

The DNA melting transition in aqueous magnesium salt solutions.

The melting transition of the magnesium salt of DNA has been systematically examined in the presence of various types of anions. The addition of ClO4- to a concentration of 3.0 N results in the biphasic optical transition, with the first phase exhibiting rapid reversibility and independence of the DNA concentration. This subtransition, which is interpreted as an intramolecular condensation to a collapsed form of DNA, is followed by a DNA concentration-dependent aggregation reaction. The aggregation can be reversed by increasing the ClO4- concentration to 6.0 N while elevating the temperature to post-transition levels. Alternatively, both the collapse and the aggregation can be prevented by melting in the presence of trichloroacetate, the most strongly chaotropic solvent for DNA which has been reported (K. Hamaguchi and E. P. Geiduschek (1962), J. Am. Chem. Soc. 84, 1329). The forces responsible for mediating both the collapse and the aggregation are superficially similar to those involved in maintaining duplex stability. The collapsed form, in particular, possibly possesses features in common with the condensed structures which can be produced in aqueous solution of certain polymers, such as polyethylene glycol (Lerman, L.S. (1971), Proc. Natl. Acad. Sci. U.S.A. 68, 1886).     

On the competition between water,sodium ions,and spermine in binding to DNA: a molecular dynamics computer simulation study

The interaction of DNA with the polyamine spermine(4+) (Spm(4+)), sodium ions, and water molecules has been studied using molecular dynamics computer simulations in a system modeling a DNA crystal. The simulation model consisted of three B-DNA decamers in a periodic hexagonal cell, containing 1200 water molecules, 8 Spm(4+), 32 Na(+), and 4 Cl(-) ions. The present paper gives a more detailed account of a recently published report of this system and compares results on this mixed Spm(4+)/Na(+)-cation system with an molecular dynamics simulation carried out for the same DNA decamer under similar conditions with only sodium counterions (Korolev et al., J. Mol. Biol. 308:907). The presence of Spm(4+) makes significant influence on the DNA hydration and on the interaction of the sodium ions with DNA. Spermine pushes water molecules out of the minor groove, whereas Na(+) attracts and organizes water around DNA. The major binding site of the Spm(4+) amino groups and the Na(+) ions is the phosphate group of DNA. The flexible polyamine spermine displays a high presence in the minor groove but does not form long-lived and structurally defined complexes. Sodium ions compete with Spm(4+) for binding to the DNA bases in the minor groove. Sodium ions also have several strong binding sites in the major groove. The ability of water molecules, Spm(4+), and Na(+) to modulate the local structure of the DNA double helix is discussed.     

Estimating the power of a proposed linkage study: a practical computer simulation approach.

I describe a simulation method to estimate the power to detect linkage given a set of pedigrees of known structure and for which family history data may be available. This method can be applied to autosomal and X-linked dominant diseases; depending on the pedigrees under consideration, it will often be applicable for autosomal and X-linked recessive diseases. This power calculation can most usefully be undertaken after family history data are gathered, but prior to examination and testing of pedigree members to obtain marker information. Of key importance, the power calculation is straightforward to carry out and not too time-consuming; it is practical even on a microcomputer. The result of the power calculation is an objective answer to the question: Will my families be sufficient to demonstrate linkage?     

An experimental study of potentiated aqueous solutions

A systematic study was undertaken of luminescent aqueous solutions of homeopathic preparation of sodium chloride at a dilution from D1 to D30, produced by "Weleda" company (Moscow) was carried out. It was shown that intensity of luminescence versus the degree of dilution is a non-monotonous function with several maxima, the main maximum corresponds to 13-14 decimal dilution. The dynamics of spectra was registered for several weeks. A systematic study of water samples (D1-D30) exposed to a similar procedure of potentization but without salt addition was also performed. The difference in the luminescence spectra of water of different stages of potentization was shown. The motility of infusoria Spirostoma ambiquum in solutions being examined was studied. A significant negative correlation between the infusoria motility and luminescence intensity was registered.